Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
$
A
- a - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
- a - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- a - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- a - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- a - Variable in class org.jmol.dssx.Bridge
- a - Variable in class org.jmol.g3d.PrecisionRenderer
- a - Variable in class org.jmol.jvxl.readers.MapFileReader
- a - Variable in class org.jmol.minimize.forcefield.Calculation
- a - Variable in class org.jmol.render.SticksRenderer
- a - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- a - Variable in class org.jmol.util.SimpleUnitCell
- a_ - Variable in class org.jmol.util.SimpleUnitCell
- A_WINS - Static variable in class org.jmol.symmetry.CIPChirality
- a0 - Variable in class org.jmol.modelkit.ModelKit
- A0 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
- a1 - Variable in class org.jmol.g3d.HermiteRenderer
- a1 - Variable in class org.jmol.util.Modulation
- a2 - Variable in class org.jmol.g3d.HermiteRenderer
- a2 - Variable in class org.jmol.util.Modulation
- a3 - Variable in class org.jmol.modelkit.ModelKit
- a4 - Variable in class org.jmol.render.SticksRenderer
- A4_BNDK - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- A4_CHRG - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- A4_SB - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- A4_SBDEF - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- A4_VDW - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- aa - Variable in class org.jmol.g3d.TriangleRenderer
- aa - Variable in class org.jmol.renderbio.BioMeshRenderer
- aabb - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- aaLen - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- aaPlus - Static variable in class org.jmol.modelsetbio.BioExt
- aaRet - Variable in class org.jmol.modelset.AtomCollection
- aaSp2 - Static variable in class org.jmol.modelsetbio.BioExt
- aaSp21 - Static variable in class org.jmol.modelsetbio.BioExt
- aaStep - Variable in class org.jmol.thread.MoveToThread
- aaStepCenter - Variable in class org.jmol.navigate.Navigator
- aaStepCenter - Variable in class org.jmol.thread.MoveToThread
- aaStepNavCenter - Variable in class org.jmol.thread.MoveToThread
- aaT - Variable in class org.jmol.render.MeasuresRenderer
- aaTest1 - Variable in class org.jmol.viewer.TransformManager
- aatoken - Variable in class org.jmol.script.ScriptContext
- aatoken - Variable in class org.jmol.script.ScriptEval
- aatoken - Variable in class org.jmol.script.ScriptFunction
- aatokenCompiled - Variable in class org.jmol.script.ScriptCompiler
- aaTotal - Variable in class org.jmol.thread.MoveToThread
- ab - Variable in class org.jmol.awt.AwtSwingComponent
- abc - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- ABI_IJ - Static variable in class org.jmol.minimize.forcefield.ForceField
- ABI_JK - Static variable in class org.jmol.minimize.forcefield.ForceField
- abinitContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- AbinitReader - Class in org.jmol.adapter.readers.xtal
- AbinitReader() - Constructor for class org.jmol.adapter.readers.xtal.AbinitReader
- abNo - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- aboutAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- AboutAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
- AboutDialog - Class in org.openscience.jmol.app.jmolpanel
- AboutDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog
- abs - Static variable in class org.jmol.script.T
- absolute - Static variable in class org.jmol.script.T
- ABSOLUTE - Enum constant in enum org.jmol.atomdata.RadiusData.EnumType
- ABSOLUTE_MIN_MESH_SIZE - Static variable in class org.jmol.renderbio.BioMeshRenderer
- absoluteButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- AbstractButton - Class in org.jmol.awtjs.swing
- AbstractButton(String) - Constructor for class org.jmol.awtjs.swing.AbstractButton
- AbstractTableModel - Interface in org.jmol.awtjs.swing
- abYes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- ac - Variable in class org.jmol.adapter.readers.cif.CifReader
- ac - Variable in class org.jmol.adapter.readers.cif.MSRdr
- ac - Variable in class org.jmol.adapter.readers.more.MdTopReader
- ac - Variable in class org.jmol.adapter.readers.more.Mol2Reader
- ac - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- ac - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- ac - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- ac - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
- ac - Variable in class org.jmol.adapter.readers.simple.AmpacReader
- ac - Variable in class org.jmol.adapter.readers.simple.CubeReader
- ac - Variable in class org.jmol.adapter.readers.simple.InputReader
- ac - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- ac - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- ac - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- ac - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- ac - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- ac - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- ac - Variable in class org.jmol.adapter.smarter.AtomIterator
- ac - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- ac - Variable in class org.jmol.atomdata.AtomData
- ac - Variable in class org.jmol.geodesic.EnvelopeCalculation
- ac - Variable in class org.jmol.jvxl.readers.AtomDataReader
- ac - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- ac - Variable in class org.jmol.minimize.forcefield.Calculations
- ac - Variable in class org.jmol.minimize.Minimizer
- ac - Variable in class org.jmol.modelset.AtomCollection
- ac - Variable in class org.jmol.popup.JmolPopup
- ac - Variable in class org.jmol.shapesurface.Contact
- ac - Variable in class org.jmol.smiles.SmilesGenerator
- ac - Variable in class org.jmol.util.JmolMolecule
- ac0 - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- ac0 - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- ac0 - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- accept(File) - Method in class org.jmol.dialog.Dialog.TypeFilter
- accept(File) - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
- accept(File, String) - Method in class org.jmol.console.JmolConsole.FileChecker
- ACCEPTOR - Enum constant in enum org.jmol.c.HB
- access - Variable in class org.jmol.viewer.Viewer
- ACCESS() - Constructor for enum org.jmol.viewer.Viewer.ACCESS
- acdAssignments - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- acdMolFile - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- ACF_ANG - Static variable in class org.jmol.adapter.readers.xtal.SiestaReader
- ACF_BOHR - Static variable in class org.jmol.adapter.readers.xtal.SiestaReader
- ACF_M - Static variable in class org.jmol.adapter.readers.xtal.SiestaReader
- ACF_NM - Static variable in class org.jmol.adapter.readers.xtal.SiestaReader
- acfFactor - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- acfUnits - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- acm - Variable in class org.jmol.viewer.Viewer
- acos - Static variable in class org.jmol.script.T
- acr - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- act - Variable in class org.jmol.modelset.Model
-
atom count; includes deleted atoms only if not being nulled (Jmol 14.31 or below)
- action - Variable in class org.jmol.viewer.Gesture
- action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
- action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
- action(String) - Method in interface org.jmol.api.JmolAudioPlayer
- action(String) - Method in class org.jmol.util.JmolAudio
-
Execute an action from load audio "xxxxx.wav" filter "id=a1 action=xxx"
- ACTION_assignNew - Static variable in class org.jmol.viewer.ActionManager
- ACTION_center - Static variable in class org.jmol.viewer.ActionManager
- ACTION_clickFrank - Static variable in class org.jmol.viewer.ActionManager
- ACTION_connectAtoms - Static variable in class org.jmol.viewer.ActionManager
- ACTION_count - Static variable in class org.jmol.viewer.ActionManager
- ACTION_deleteAtom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_deleteBond - Static variable in class org.jmol.viewer.ActionManager
- ACTION_depth - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragAtom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragDrawObject - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragDrawPoint - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragLabel - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragMinimize - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragMinimizeMolecule - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragSelected - Static variable in class org.jmol.viewer.ActionManager
- ACTION_dragZ - Static variable in class org.jmol.viewer.ActionManager
- ACTION_multiTouchSimulation - Static variable in class org.jmol.viewer.ActionManager
- ACTION_navTranslate - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickAtom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickIsosurface - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickLabel - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickMeasure - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickNavigate - Static variable in class org.jmol.viewer.ActionManager
- ACTION_pickPoint - Static variable in class org.jmol.viewer.ActionManager
- ACTION_popupMenu - Static variable in class org.jmol.viewer.ActionManager
- ACTION_reset - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotate - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotateBranch - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotateSelected - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotateZ - Static variable in class org.jmol.viewer.ActionManager
- ACTION_rotateZorZoom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_select - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectAndDrag - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectAndNot - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectNone - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectOr - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectToggle - Static variable in class org.jmol.viewer.ActionManager
- ACTION_selectToggleExtended - Static variable in class org.jmol.viewer.ActionManager
- ACTION_setMeasure - Static variable in class org.jmol.viewer.ActionManager
- ACTION_slab - Static variable in class org.jmol.viewer.ActionManager
- ACTION_slabAndDepth - Static variable in class org.jmol.viewer.ActionManager
- ACTION_slideZoom - Static variable in class org.jmol.viewer.ActionManager
- ACTION_spinDrawObjectCCW - Static variable in class org.jmol.viewer.ActionManager
- ACTION_spinDrawObjectCW - Static variable in class org.jmol.viewer.ActionManager
- ACTION_stopMotion - Static variable in class org.jmol.viewer.ActionManager
- ACTION_swipe - Static variable in class org.jmol.viewer.ActionManager
- ACTION_translate - Static variable in class org.jmol.viewer.ActionManager
- ACTION_wheelZoom - Static variable in class org.jmol.viewer.ActionManager
- ActionChangedListener(AbstractButton) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
- actionCommand - Variable in class org.jmol.awtjs.swing.JComponent
- actionInfo - Static variable in class org.jmol.viewer.ActionManager
- actionListener - Variable in class org.jmol.awtjs.swing.JComponent
- actionManager - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- actionManager - Variable in class org.jmol.thread.HoverWatcherThread
- ActionManager - Class in org.jmol.viewer
- ActionManager() - Constructor for class org.jmol.viewer.ActionManager
- ActionManagerMT - Class in org.jmol.multitouch
- ActionManagerMT() - Constructor for class org.jmol.multitouch.ActionManagerMT
- actionNames - Static variable in class org.jmol.viewer.ActionManager
- actionPerformed(ActionEvent) - Method in class org.jmol.awt.AwtPopupHelper
- actionPerformed(ActionEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- actionPerformed(ActionEvent) - Method in class org.jmol.console.AppletConsole
- actionPerformed(ActionEvent) - Method in class org.jmol.console.ImageDialog
- actionPerformed(ActionEvent) - Method in class org.jmol.console.JmolConsole
- actionPerformed(ActionEvent) - Method in class org.jmol.console.ScriptEditor
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.DeselectallAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.FrameDeltaDisplayAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.PickAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.PopulationDisplayAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.RotateAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.SelectallAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.AtomSetChooserAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.SaveNmrAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Test
- actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
- actionRotateBond(int, int, int, int, boolean) - Method in class org.jmol.modelkit.ModelKit
-
Actually rotate the bond.
- actions - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- actionStates - Variable in class org.jmol.viewer.StateCreator
- actionStatesRedo - Variable in class org.jmol.viewer.StateCreator
- activate() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- activate() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- activate() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- active - Variable in class org.jmol.dialog.FilePreview
- active_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- activeMenu - Variable in class org.jmol.modelkit.ModelKitPopup
- actualID - Variable in class org.jmol.shapesurface.Isosurface
- adapter - Variable in class org.jmol.multitouch.ActionManagerMT
- adapterModelCount - Variable in class org.jmol.modelset.ModelLoader
- adapterTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
- add - Static variable in class org.jmol.script.T
- add(int, int, int, long) - Method in class org.jmol.viewer.Gesture
- add(Container, JmolAbstractButton) - Method in class org.jmol.console.AppletConsole
- add(String) - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- add(Map<String, Object>, NucleicMonomer, NucleicMonomer) - Static method in class org.jmol.modelsetbio.BasePair
- add(SC) - Method in interface org.jmol.api.SC
- add(SC) - Method in class org.jmol.awt.AwtSwingComponent
- add(SC) - Method in class org.jmol.awtjs.swing.AbstractButton
- add(SC) - Method in class org.jmol.awtjs.swing.ButtonGroup
- add(Component) - Method in class org.jmol.awtjs.swing.Container
- add(JComponent, Object) - Method in class org.jmol.awtjs.swing.JPanel
- add(JComponent, GridBagConstraints) - Method in class org.jmol.awtjs.swing.Grid
- ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JC
- addActionListener(Object) - Method in interface org.jmol.api.SC
- addActionListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
- addActionListener(Object) - Method in class org.jmol.awtjs.swing.JComponent
-
Note that it will be the job of the JavaScript on the page to do with actionListener what is desired.
- addActions(List<Action>) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- addActions(List<Action>) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- addActions(List<Action>) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- addAllCheckboxItems(SC, String[]) - Method in class org.jmol.modelkit.ModelKitPopup
- addAlleneLonePair(SmilesAtom, Node[], int) - Method in class org.jmol.smiles.SmilesStereo
-
for allenes, we must check for missing atoms
- addAllLists(Lst<SV>, Lst<SV>) - Method in class org.jmol.scriptext.MathExt
- addAllTriangles() - Method in class org.jmol.jvxl.calc.MarchingSquares
- addAssembly(String[]) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addAtom() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
- addAtom() - Method in class org.jmol.smiles.SmilesSearch
- addAtom(boolean, BS, int, int, String, int, float, Lst<Object>, float, float, P3, boolean, int, int, String, V3, char, float, float) - Method in class org.jmol.modelset.ModelLoader
- addAtom(double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
-
add a proton to the atom list
- addAtom(float[], String, String) - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
- addAtom(int, Group, int, String, String, int, int, int, P3, float, V3, int, float, float, float, Lst<Object>, boolean, byte, BS, float) - Method in class org.jmol.modelset.ModelSet
- addAtom(int, SimpleNode, boolean, boolean, boolean) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Add a new atom or return null
- addAtom(Lst<Object>, int, byte[], int[], String[], int, Lst<Object>, float[], Lst<Object>, float[], BS, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- addAtom(TopoCifParser.TAtom) - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- addAtom(TopoCifParser.TAtom) - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- addAtom(Atom) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addAtomChooser - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addAtomComment - Variable in class org.jmol.smiles.SmilesGenerator
- addAtomModulation(String, char, char, double[], String, double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Create a list of modulations for each atom type (atom name).
- addAtomProp(int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
- addAtoms(int) - Method in class org.jmol.modelset.Group
- addAtoms(BS) - Method in interface org.jmol.api.AtomIndexIterator
- addAtoms(BS) - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
turns this into a SPHERICAL iterator for "within Distance" measures
- addAtoms(BS) - Method in class org.jmol.symmetry.UnitCellIterator
- addAtomstoMatrix() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
Generate noeMatrix and map fields for DistanceJMolecule.
- addAtomWithMappedName(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addAtomWithMappedSerialNumber(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addAtomXYZSymName(String[], int, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addAttr() - Method in class org.jmol.export._MayaExporter
- addAttrib(Lst<String[]>, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
- addAuxFile(Map<String, Object>, String, Map<String, Object>) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
- addAxis(int, V3) - Method in class org.jmol.symmetry.PointGroup
- addAzacyclicN(int) - Method in class org.jmol.symmetry.CIPData
- addBasePair(BasePair) - Method in class org.jmol.modelsetbio.NucleicMonomer
- addBasis(Map<String, Object>) - Method in class org.jmol.adapter.writers.QCJSONWriter
-
Add a basis to the associative array moBases keyed on its hashcode
- addBetaSet - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- addBinding(String, Object) - Method in class org.jmol.viewer.binding.Binding
- addBioMoleculeOperation(M4, boolean) - Method in interface org.jmol.api.SymmetryInterface
- addBioMoleculeOperation(M4, boolean) - Method in class org.jmol.symmetry.Symmetry
- addBioPolymer(BioPolymer) - Method in class org.jmol.modelsetbio.BioModel
- addBond(Bond) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- addBond(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addBond(MinBond, int) - Method in class org.jmol.minimize.MinAtom
- addBond(SmilesBond) - Method in class org.jmol.smiles.SmilesAtom
-
Add a bond to the atom.
- addBondOr() - Method in class org.jmol.smiles.SmilesBond
- addBonds - Variable in class org.jmol.adapter.writers.CMLWriter
- addBonds(String, int) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- addBonds(Lst<Bond>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- addBondToAtom(Atom, Bond) - Method in class org.jmol.modelset.BondCollection
- addBoundBoxPoint(T3) - Method in class org.jmol.util.BoxInfo
- addBrace(T) - Method in class org.jmol.script.ScriptCompiler
- addBracketedBioName(SB, Node, String, boolean) - Method in class org.jmol.smiles.SmilesGenerator
- addBridge(Bridge, Map<int[][], Boolean>) - Method in class org.jmol.dssx.Bridge
- addBs(SB, String, BS) - Method in class org.jmol.viewer.StateCreator
- addBundle(Viewer, String, String) - Method in class org.jmol.i18n.GT
- addBundles(Viewer, String, String, String, String) - Method in class org.jmol.i18n.GT
- addButton(JPanel, String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- addButton(JmolAbstractButton, String) - Method in class org.jmol.console.GenericConsole
- addBZ(Lst<P4>, Lst<P3>, Lst<P4>, Lst<P3>, int) - Method in class org.jmol.util.BZone
- addCellType(String, String, boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
-
(magnetic CIF or LOAD ...
- addCGO(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- addChiralAtoms(Lst<CIPChirality.CIPAtom>, int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Create an ASCII string that allows the list of descriptors to be generated in order.
- addCifAtom(Atom, String, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
- addCoef(Map<String, Object>, float[], String, float, float, int) - Method in class org.jmol.adapter.readers.quantum.MOReader
- addColix(int) - Method in class org.jmol.shapecgo.CGOMesh
- addColix(short, boolean) - Method in class org.jmol.export._IdtfExporter
- addColor(Integer, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
- addColors(Lst<Object>, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Add new colors from the main "colors" map object.
- addColorToMap(Map<String, BS>, String, BS) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
-
adds a set of specifically-colored vertices to the map, ensuring that no vertex is in two maps.
- addCommand(int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- addCommand(String) - Method in class org.jmol.util.CommandHistory
-
Adds any number of lines to the command history
- addCommand(String) - Method in class org.jmol.viewer.Viewer
-
Adds one or more commands to the command history
- addCommandLine(String) - Method in class org.jmol.util.CommandHistory
-
Adds a single line to the bottom of the list, resets list position.
- addCompare(T, T) - Method in class org.jmol.script.ScriptTokenParser
- addComponent(Component) - Method in class org.jmol.awtjs.swing.Container
- addConnect() - Method in class org.jmol.export._MayaExporter
- addConnection(int[]) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- addConsoleListener(Object) - Method in interface org.jmol.api.JmolAbstractButton
- addConsoleListener(Object) - Method in class org.jmol.console.JmolButton
- addConsoleListener(Object) - Method in class org.jmol.console.JmolLabel
- addConsoleListener(Object) - Method in class org.jmol.console.JmolToggleButton
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBox
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBoxMenuItem
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenu
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenuItem
- addConsoleListener(Object) - Method in class org.jmol.console.KeyJRadioButtonMenuItem
- addConstraint(int, ModelKit.Constraint) - Method in class org.jmol.modelkit.ModelKit
- addConstraint(Object[]) - Method in class org.jmol.minimize.Minimizer
- addContextVariable(Map<String, SV>, String) - Static method in class org.jmol.script.ScriptCompiler
- addContourPoints(Lst<Object>, BS, int, SB, T3[], float[], int, int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
- addContourVertex(P3, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- addCount - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- addCouple(int, int, int, int, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- addCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- addData(float[][], float[]) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
Add Fortran zeta data
- addData(MOCalculation, boolean) - Method in interface org.jmol.quantum.mo.DataAdder
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder11H
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder13I
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder7F
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdder9G
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderF
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderG
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderH
- addData(MOCalculation, boolean) - Method in class org.jmol.quantum.mo.DataAdderI
- addData5D() - Method in class org.jmol.quantum.MOCalculation
- addData6D() - Method in class org.jmol.quantum.MOCalculation
- addDataP() - Method in class org.jmol.quantum.MOCalculation
- addDataS() - Method in class org.jmol.quantum.MOCalculation
- addDataSP() - Method in class org.jmol.quantum.MOCalculation
- addDirectory(String, String) - Static method in class org.jmol.viewer.FileManager
- addDisplayedBackbone(Atom, boolean) - Method in class org.jmol.shapebio.Backbone
- addDisplayedBond(int, boolean) - Method in class org.jmol.modelset.Atom
- addedData - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addedDataKey - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addEdge(int, int, int) - Method in class org.jmol.util.MeshCapper
-
Input method from MeshSlicer.
- addEdge(Lst<int[]>, Map<String, Object>, Integer, int[], int, P3[]) - Method in class org.jmol.shapespecial.Polyhedra
-
Check each edge to see that (a) it has not been used before (b) it does not have vertex points on both sides of it (c) if it runs opposite another edge, then both edge masks are set properly
- addEdgeData(float) - Method in class org.jmol.jvxl.calc.MarchingCubes
- addEdges(Hashtable<String, SmilesRingSet>) - Method in class org.jmol.smiles.SmilesRing
- addEquiv(double[], double[], double[]) - Method in class org.jmol.quantum.NMRNoeMatrix
- addExplicitLatticeVector(int, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addFace(IsoSolventReader.Face) - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- addFacet(int, int, int, P3, P3[], V3[], int[][], int, int, boolean, V3) - Method in class org.jmol.shapespecial.Polyhedra
-
Add one of the three "facets" that compose the planes of a "collapsed" polyhedron.
- addFile(String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
Adds this file to the history.
- addFilterAttribute(Map<String, Object>, String, String) - Method in class org.jmol.script.ScriptEval
- addFlags(int, String) - Static method in class org.jmol.smiles.SmilesSearch
- addForce(V3d, int, double) - Method in class org.jmol.minimize.forcefield.Calculations
- addForces(Calculation, int) - Method in class org.jmol.minimize.forcefield.Calculations
- addFunction(JmolScriptFunction) - Method in class org.jmol.viewer.Viewer
- addFunction(ScriptFunction) - Method in class org.jmol.script.ScriptExpr
- addFunctions(SB, Map<String, JmolScriptFunction>, String, boolean, boolean) - Method in class org.jmol.viewer.StateCreator
- addGroup(Lst<Object>, String, int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Create a hierarchical list of named groups as generally seen on the PyMOL app's right-hand object menu.
- addGroup(Chain, Group) - Method in class org.jmol.modelset.ModelLoader
- addGroup3Name(String) - Static method in class org.jmol.modelsetbio.BioResolver
-
These can overrun 3 characters; that is not significant.
- addGroupAtoms(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
- addH(Lst<SmilesAtom>, SmilesAtom, int) - Method in class org.jmol.inchi.InChIJNI
- addHbond(Monomer, Monomer, int, int, Map<String, Boolean>) - Method in class org.jmol.dssx.DSSP
- addHBond(Atom, Atom, int, float) - Method in class org.jmol.modelset.BondCollection
- addHeader() - Method in class org.jmol.adapter.readers.cif.CifReader
- addHeader() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- addHelpItems(JMenu, String, String) - Method in class org.jmol.console.AppletConsole
- addHelpMenuBar(JMenuBar) - Method in class org.jmol.console.AppletConsole
- addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addHetero(String, String, boolean, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addHighL(int) - Method in class org.jmol.quantum.MOCalculation
-
modular loading of high-L data adders
- addHistoryWindowDimInfo(String, Component, Dimension) - Method in interface org.jmol.api.JmolAppAPI
- addHistoryWindowDimInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.JmolApp
- addHistoryWindowInfo(String, Component, Point) - Method in interface org.jmol.api.JmolAppAPI
- addHistoryWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.JmolApp
- addHydrogenBond(Lst<Bond>, Atom, Atom) - Static method in class org.jmol.modelsetbio.NucleicPolymer
- addhydrogens - Static variable in class org.jmol.script.T
- addHydrogens - Variable in class org.jmol.jvxl.readers.Parameters
- addHydrogens() - Method in class org.jmol.modelsetbio.BioResolver
- addHydrogens(BS, int) - Method in class org.jmol.viewer.Viewer
- addHydrogens(Lst<Atom>, P3[]) - Method in class org.jmol.modelset.ModelSet
-
these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEW
- addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in interface org.jmol.api.JmolScriptManager
- addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in class org.jmol.script.ScriptManager
-
Add hydrogens to a model
- addHydrogensInline(BS, Lst<Atom>, P3[], Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- addImagePixel(byte, int, int, int, int, int) - Method in class org.jmol.g3d.Pixelator
- addImplicitHydrogenAtoms(JmolAdapter, int, int) - Method in class org.jmol.modelsetbio.BioResolver
-
Get bonding info for double bonds and add implicit hydrogen atoms, if needed.
- addIncompleteFaces(BS) - Method in class org.jmol.geodesic.EnvelopeCalculation
- addIndex - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- addInfo(Map<String, Object>, String, Object) - Method in class org.jmol.modelkit.ModelKit
- addInfo(SB, String[], String, String) - Method in class org.jmol.viewer.binding.Binding
- addInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
- addIntersectionVertex(T3, float, int, int, Map<String, Integer>, int, int) - Method in class org.jmol.util.MeshSlicer
- addIsosurface(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- addItemListener(Object) - Method in interface org.jmol.api.SC
- addItemListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
- addItemListener(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
- addItems(int, T[], int, Lst<Object>, Viewer) - Static method in class org.jmol.shapecgo.CGOMesh
- addItems(String[][]) - Method in class org.jmol.popup.PopupResource
- addItemText(SB, char, int, String, String, String, String) - Static method in class org.jmol.popup.GenericPopup
- addJmolCouple(int, int, int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- addJmolDataProperties(Model, Map<String, float[]>) - Method in class org.jmol.modelset.ModelLoader
- addJmolDistance(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
Add using Jmol atom index
- addJmolObject(int, BS, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- addJmolProperties(Properties) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addJmolWindowInfo(String, Component, Point) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Deprecated.
- addJmolWindowInnerInfo(String, Component, Dimension) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addKey(Lst<Object>, String) - Static method in class org.jmol.shapecgo.CGOMesh
- addKeyBuffer(char) - Method in class org.jmol.awt.Mouse
- addKeyBuffer(char) - Method in class org.jmol.awtjs2d.Mouse
- addLabel(int, int, int, float[], String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- addLadder(Map<int[][], Boolean>) - Method in class org.jmol.dssx.Bridge
- addLatticeVector(Lst<float[]>, String) - Method in class org.jmol.adapter.readers.cif.MSRdr
- addLatticeVector(Lst<float[]>, String) - Method in interface org.jmol.adapter.smarter.MSInterface
- addLatticeVectors() - Method in class org.jmol.adapter.readers.cif.CifReader
- addLatticeVectors(Lst<float[]>) - Method in interface org.jmol.api.SymmetryInterface
- addLatticeVectors(Lst<float[]>) - Method in class org.jmol.symmetry.SpaceGroup
- addLatticeVectors(Lst<float[]>) - Method in class org.jmol.symmetry.Symmetry
- addLine - Variable in class org.jmol.script.ScriptFlowContext
- addList(PyMOLGroup) - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
- addListener(JmolSelectionListener) - Method in class org.jmol.viewer.SelectionManager
- addListSelectionListener(Object) - Method in class org.jmol.awtjs.swing.JTable
-
It will be the function of the JavaScript on the page to do with selectionListener what is desired.
- addListSelectionListener(Object) - Method in interface org.jmol.awtjs.swing.ListSelectionModel
- addLoadData(SB, String, Map<String, Object>, int) - Method in class org.jmol.script.ScriptEval
- addLockedAtoms(BS) - Method in class org.jmol.modelkit.ModelKit
- addMacrosMenu - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addMacrosMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addMatrix(String, M4, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addMeasurements(MeasurementData[], int, Lst<Object>, BS, int, Lst<Object>, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtJmolPopup
- addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.awt.AwtModelKitPopup
- addMenu(String, String, SC, String, PopupResource) - Method in class org.jmol.popup.GenericPopup
- addMenuItem(SC, String) - Method in class org.jmol.popup.GenericPopup
- addMenuItems(String, String, SC, PopupResource) - Method in class org.jmol.popup.GenericPopup
- addMesh(int, Lst<Object>, String, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- addMesh(String, MeshSurface, M4, M4, short, int[], BS) - Method in class org.jmol.export._ObjExporter
-
Adds a new mesh using the given data (faces, vertices, and normals) and colix after transforming it via the given affine transform matrix.
- addMeshData(String, int, int, int, int, SB, SB, SB, SB, SB, SB) - Method in class org.jmol.export._IdtfExporter
- addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Contact
- addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Isosurface
- addMethyl(double, double, double, double, double, double, double, double, double) - Method in class org.jmol.quantum.NMRNoeMatrix
-
Add a methyl group to the atom list
- addMMTFBonds(int[], int[], int, boolean, boolean) - Method in class org.jmol.adapter.readers.cif.MMTFReader
- addMo(String, int, float, float) - Method in class org.jmol.adapter.readers.quantum.AdfReader
- addMod(String, String, String, double[]) - Method in class org.jmol.adapter.readers.cif.MSCifParser
- addMOData(int, Lst<String>[], Map<String, Object>[]) - Method in class org.jmol.adapter.readers.quantum.MOReader
- addMODataOR(int, Lst<String>, Lst<String>[], Map<String, Object>[]) - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- addModel() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- addModelTitle(String) - Method in class org.jmol.adapter.readers.cif.CifReader
- addModulation(Map<String, double[]>, String, double[], int) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Types include O (occupation) D (displacement) U (anisotropy) M (magnetic moment) _coefs_ indicates this is a wave description
- addModulation(Map<String, double[]>, String, double[], int) - Method in interface org.jmol.adapter.smarter.MSInterface
- addMol() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- addMol() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- addMolAtom(int, int, String, int, float, float, float) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- addMolBond(String, String, int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- addMolecule(JmolMolecule[], int, Node[], int, BS, int, int, BS) - Static method in class org.jmol.util.JmolMolecule
- addMolFile(int, SB, BS, BS, boolean, boolean, boolean, Quat) - Method in class org.jmol.adapter.writers.MOLWriter
- addMolSS(String, STR) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Secondary structure definition.
- addMolStructures() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- addMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
-
Note that this method does not check to see that there are no overlapping protein structures.
- addMore() - Method in class org.jmol.adapter.readers.cif.CifReader
- addMouseListener(Object) - Method in interface org.jmol.api.SC
- addMouseListener(Object) - Method in class org.jmol.awt.AwtSwingComponent
- addMouseListener(Object) - Method in class org.jmol.awtjs.swing.Component
- addName(String) - Method in class org.jmol.script.ContextToken
- addNeighboringVertexes(short[], short, short) - Static method in class org.jmol.util.Geodesic
- addNested(String) - Method in class org.jmol.smiles.SmilesSearch
- addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNewBond(int, int, int) - Method in class org.jmol.adapter.readers.cif.CifReader
-
add the bond and mark it for molecular processing
- addNewBond(String, String, int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- addNewBondFromNames(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNewBondWithOrder(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNewBondWithOrderA(Atom, Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addNextToken() - Method in class org.jmol.script.ScriptTokenParser
- addNextTokenIf(int) - Method in class org.jmol.script.ScriptTokenParser
- addNode() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- addNOE(int, int, String, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- addNormal(V3, V3, float) - Static method in class org.jmol.smiles.SmilesAromatic
-
adds a normal if similarity is within limits
- addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addNormix(int) - Method in class org.jmol.shapecgo.CGOMesh
- addNumber(int, int, Object) - Method in class org.jmol.script.ScriptCompiler
- addObject(JmolObject) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- addOp(T) - Method in class org.jmol.script.ScriptMathProcessor
-
addOp The primary driver of the Reverse Polish Notation evaluation engine.
- addOp(SymmetryOperation, String, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- addOpAllowMath(T, boolean, int) - Method in class org.jmol.script.ScriptMathProcessor
- addOperation(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- addPeakData(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- addPeakData(String) - Method in interface org.jmol.api.JmolJDXMOLReader
- addPixel(int, int, int) - Method in class org.jmol.g3d.Pixelator
- addPixel(int, int, int) - Method in class org.jmol.g3d.PixelatorScreened
- addPixel(int, int, int) - Method in class org.jmol.g3d.PixelatorShaded
- addPixel(int, int, int) - Method in class org.jmol.g3d.PixelatorT
- addPluginMenu(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addPngFileBytes(String, byte[], int, Hashtable<Object, String>, boolean, String, int, Lst<Object>) - Method in class org.jmol.viewer.OutputManager
- addPoint(int) - Method in class org.jmol.smiles.SmilesMeasure
- addPoint(int, int) - Method in class org.jmol.util.MeshCapper
-
The MeshSlicer class manages all introduction of vertices; we must pass on to it the subset of vertices from the original Jmol isosurface being capped.
- addPoint(int, Point3fi, boolean) - Method in class org.jmol.modelset.MeasurementPending
- addPoint(T3, int) - Method in class org.jmol.shapespecial.Draw
- addPoint(T3, T3, T3, float) - Static method in class org.jmol.util.BoxInfo
- addPoints(int, Object) - Method in class org.jmol.shapespecial.Draw
- addPointXYZ(float, float, float, P3, P3, float) - Static method in class org.jmol.util.BoxInfo
- addPolygon(int[], BS) - Method in class org.jmol.util.MeshSurface
- addPolygonC(int[], int, BS, boolean) - Method in class org.jmol.util.MeshSurface
- addPolygonV3(int, int, int, int, int, int, BS) - Method in class org.jmol.util.MeshSurface
- addPolyhedron(Polyhedron) - Method in class org.jmol.shapespecial.Polyhedra
- addPopulation(double[]) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- addPreferencesDialog - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- addPrimitive() - Method in class org.jmol.smiles.SmilesBond
- addProcess(String, ScriptContext) - Method in interface org.jmol.api.JmolParallelProcessor
- addProcess(String, ScriptContext) - Method in class org.jmol.script.ScriptParallelProcessor
- addProcess(Lst<T[]>, int, int) - Method in class org.jmol.script.ScriptEval
- addProperties(Properties) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the given properties to the history.
- addProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the given property to the history.
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
- addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
- addRenderer(int) - Method in interface org.jmol.api.JmolRendererInterface
- addRenderer(int) - Method in class org.jmol.export.Export3D
- addRenderer(int) - Method in class org.jmol.g3d.Graphics3D
-
allows core JavaScript loading to not involve these classes
- addRenderer(int) - Method in class org.jmol.util.GData
- addRequiredFile(String) - Method in interface org.jmol.jvxl.api.MeshDataServer
- addRequiredFile(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- addRequiredFile(String) - Method in class org.jmol.shapesurface.Isosurface
- addResidueHydrogenBond(Atom, Atom, int, int, float, Lst<Bond>) - Method in class org.jmol.modelsetbio.AminoPolymer
- addReturnPath(CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Add the path back to the root for an auxiliary center.
- addRing(SmilesRing) - Method in class org.jmol.smiles.SmilesRingSet
- addRotatedTensor(Atom, Tensor, int, boolean, SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- addScr(String, String, String, boolean) - Method in class org.jmol.script.ScriptManager
- addScript(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
- addScript(String, boolean) - Method in class org.jmol.script.ScriptManager
- addSecondaryStructure(STR, String, int, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
- addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
- addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
- addSet(SmilesRingSet, Hashtable<String, SmilesRingSet>) - Method in class org.jmol.smiles.SmilesRingSet
- addSetting(int, int, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- addShader(String, short) - Method in class org.jmol.export._IdtfExporter
- addShapeProperty(Lst<Object[]>, String, Object) - Method in class org.jmol.scriptext.IsoExt
- addSinCos(int, String, String, boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
Add x, y, and z modulations as [ csin, ccos, 0 ] or, possibly Legendre [ coef, order, 0 ]
- addSites(Map<String, Map<String, Object>>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addSiteScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addSlabInfo(Object[]) - Method in class org.jmol.jvxl.readers.Parameters
- addSlater(int, int, int, int, int, double, float) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
- addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
- addSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MOReader
-
See MopacSlaterReader
- addSpaceGroupOperation(String, boolean) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- addSpaceGroupOperation(String, int) - Method in interface org.jmol.api.SymmetryInterface
- addSpaceGroupOperation(String, int) - Method in class org.jmol.symmetry.Symmetry
- addStateScript(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- addStateScript(String, BS, BS, BS, String, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
- addStereoCheck(int, int, SimpleNode, String, BS) - Method in class org.jmol.smiles.SmilesGenerator
-
checks a group and either adds a new group to the growing check string or returns null
- addString(Atom, int, String, String) - Method in class org.jmol.shape.Labels
- addStructure(Structure) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addStructure(STR, String, int, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.AlphaPolymer
- addStructureByBS(int, int, STR, BS) - Method in class org.jmol.modelsetbio.BioModel
- addStructureProtected(STR, String, int, int, int, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
- addStructuresFromTags(STR[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
- addStructureSymmetry() - Method in class org.jmol.adapter.readers.cif.MMTFReader
-
We must add groups to the proper bsStructure element
- addSubAtom(SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesAtom
- addSubstituteTokenIf(int, T) - Method in class org.jmol.script.ScriptTokenParser
- addSubsystem(String, Matrix) - Method in class org.jmol.adapter.readers.cif.MSRdr
- addSubsystem(String, Matrix) - Method in interface org.jmol.adapter.smarter.MSInterface
- addSubSystemOp(String, Matrix, Matrix, Matrix) - Method in interface org.jmol.api.SymmetryInterface
- addSubSystemOp(String, Matrix, Matrix, Matrix) - Method in class org.jmol.symmetry.Symmetry
- addSymmetry(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- addSymmetrySM(String, M4) - Method in class org.jmol.symmetry.SpaceGroup
- addTensor(int, String[]) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- addTensor(Tensor, String) - Method in class org.jmol.modelset.AtomCollection
- addTensor(Tensor, String, boolean) - Method in class org.jmol.adapter.smarter.Atom
- addTexture(short, String) - Method in class org.jmol.export._ObjExporter
-
Adds a texture to the .mtl file if it is a new texture.
- addTickInfo(SB, TickInfo, boolean) - Static method in class org.jmol.viewer.StateCreator
- addTo(T3, float) - Method in interface org.jmol.api.JmolModulationSet
- addTo(T3, float) - Method in class org.jmol.util.ModulationSet
- addToBonds(Bond, Bond[]) - Method in class org.jmol.modelset.BondCollection
- addToken(String, T) - Static method in class org.jmol.script.T
- addTokenToPostfix(int, Object) - Method in class org.jmol.script.ScriptTokenParser
- addTokenToPostfixInt(int, int, Object) - Method in class org.jmol.script.ScriptTokenParser
- addTokenToPostfixToken(T) - Method in class org.jmol.script.ScriptTokenParser
- addTokenToPrefix(T) - Method in class org.jmol.script.ScriptCompiler
- addToMeasurement(int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
- addTracePt(int, Point3fi) - Method in class org.jmol.util.Vibration
- addTriangle(int, int, int) - Method in class org.jmol.util.MeshSlicer
-
from MeshCapper
- addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
- addTriangle(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- addTriangle(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- addTriangle(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
- addTriangle(MeshCapper.CapVertex, MeshCapper.CapVertex, MeshCapper.CapVertex, String) - Method in class org.jmol.util.MeshCapper
-
Add the triangle and remove v1 from the chain.
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.shapesurface.Isosurface
- addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
- addTuple(int, P3) - Method in class org.jmol.bspt.Bspf
- addTuple(int, T3) - Method in class org.jmol.bspt.Element
- addTuple(int, T3) - Method in class org.jmol.bspt.Leaf
- addTuple(int, T3) - Method in class org.jmol.bspt.Node
- addTuple(T3) - Method in class org.jmol.bspt.Bspt
-
Iterate through all of your data points, calling addTuple
- addType(int, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
-
sets an auxiliaryInfo string to "HNMR 13CNMR" or "IR" or "MS"
- addTypeStr(String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- addUnit(int, String, BS, Map<String, BS>) - Method in class org.jmol.modelsetbio.BioModelSet
-
Repetitively AND unit components to get the final set of atoms
- addUnitCellOffset(P3) - Method in class org.jmol.viewer.Viewer
- addUStr(Atom, String, float) - Method in class org.jmol.adapter.readers.cif.MSRdr
- addUTens(String, float) - Method in class org.jmol.util.ModulationSet
- addV(T3, boolean) - Method in class org.jmol.util.MeshSurface
- addValuesSquared(float) - Method in class org.jmol.quantum.MOCalculation
- addVariable(String, boolean) - Method in class org.jmol.script.ScriptFunction
- addVC(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- addVCVal(T3, float, boolean) - Method in class org.jmol.util.MeshSurface
- addVectors(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- addVertex(int, int, int, int, float) - Method in class org.jmol.jvxl.calc.MarchingCubes
- addVertexCopy(T3, float, int, boolean) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
- addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.data.MeshData
- addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.shapesurface.Isosurface
- addVertexCopy(T3, float, int, boolean, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- addVibrations - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- addVibrationVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addVibrationVectorWithSymmetry(int, float, float, float, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- addWidget(int) - Method in class org.openscience.jmol.app.webexport.JmolInstance
- addWindowBorder(String, Point) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the window border to the history.
- addWindowDim(String, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
- addWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the window informations to the history.
- addWindowInfo(String, Component, Point, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
- addWindowInnerInfo(String, Component, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
- addWindowListener() - Method in class org.jmol.console.JmolConsole
- addWindowPosition(String, Point) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the window position to the history.
- addWindowSize(String, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the window size to the history.
- addWindowVisibility(String, boolean) - Method in class org.openscience.jmol.app.HistoryFile
-
Adds the window visibility to the history.
- addX(SV) - Method in class org.jmol.script.ScriptMathProcessor
- addXAD(double[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAF(float[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAFF(float[][]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAI(int[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAII(int[][]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAS(String[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXAV(SV[]) - Method in class org.jmol.script.ScriptMathProcessor
- addXBool(boolean) - Method in class org.jmol.script.ScriptMathProcessor
- addXBs(BS) - Method in class org.jmol.script.ScriptMathProcessor
- addXCopy(SV) - Method in class org.jmol.script.ScriptMathProcessor
- addXFloat(float) - Method in class org.jmol.script.ScriptMathProcessor
- addXInt(int) - Method in class org.jmol.script.ScriptMathProcessor
- addXList(Lst<?>) - Method in class org.jmol.script.ScriptMathProcessor
- addXM3(M3) - Method in class org.jmol.script.ScriptMathProcessor
- addXM4(M4) - Method in class org.jmol.script.ScriptMathProcessor
- addXMap(Map<String, ?>) - Method in class org.jmol.script.ScriptMathProcessor
- addXNum(T) - Method in class org.jmol.script.ScriptMathProcessor
- addXObj(Object) - Method in class org.jmol.script.ScriptMathProcessor
- addXPt(P3) - Method in class org.jmol.script.ScriptMathProcessor
- addXPt4(P4) - Method in class org.jmol.script.ScriptMathProcessor
- addXStr(String) - Method in class org.jmol.script.ScriptMathProcessor
- addXtalHydrogens - Variable in class org.jmol.modelkit.ModelKit
-
when TRUE, add H atoms to C when added to the modelSet.
- addZoomTranslationNavigationText(SB) - Method in class org.jmol.viewer.TransformManager
- adfContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- AdfReader - Class in org.jmol.adapter.readers.quantum
-
TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.
- AdfReader() - Constructor for class org.jmol.adapter.readers.quantum.AdfReader
- AdfReader.SymmetryData - Class in org.jmol.adapter.readers.quantum
- adjust - Static variable in class org.jmol.script.T
- adjustAtomArrays(int[], int, int) - Method in class org.jmol.modelset.ModelSet
- adjustCartoonSeamNormals(int, int) - Method in class org.jmol.renderbio.BioMeshRenderer
-
Matches normals for adjacent mesh sections to create a seamless overall mesh.
- adjustForWindow - Variable in class org.jmol.modelset.Text
- adjustM40Occupancies() - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
M40 occupancies are divided by the site multiplicity; here we factor that back in.
- adjustRangeMinMax(T3[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- aDOMNode - Variable in class org.jmol.io.DOMReader
- ADP_FACTOR - Static variable in class org.jmol.util.Tensor
- ADP_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- adpmax - Static variable in class org.jmol.script.T
- ADPMAX - Enum constant in enum org.jmol.c.VDW
- adpmin - Static variable in class org.jmol.script.T
- ADPMIN - Enum constant in enum org.jmol.c.VDW
- adpMode - Variable in class org.jmol.atomdata.AtomData
- aflowContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- AFLOWReader - Class in org.jmol.adapter.readers.more
-
A reader for various AFLOW file types.
- AFLOWReader() - Constructor for class org.jmol.adapter.readers.more.AFLOWReader
- afterMath - Variable in class org.jmol.script.ScriptCompiler
- afterWhite - Variable in class org.jmol.script.ScriptCompiler
- AimsReader - Class in org.jmol.adapter.readers.xtal
-
FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).
- AimsReader() - Constructor for class org.jmol.adapter.readers.xtal.AimsReader
- AlchemyReader - Class in org.jmol.adapter.readers.simple
-
TRIPOS simple Alchemy reader.
- AlchemyReader() - Constructor for class org.jmol.adapter.readers.simple.AlchemyReader
- alert(String) - Method in class org.jmol.viewer.Viewer
- alertedNoEdit - Variable in class org.jmol.modelkit.ModelKit
- align - Variable in class org.jmol.modelset.Text
- align - Static variable in class org.jmol.script.T
- align1 - Variable in class org.jmol.smiles.PolyhedronStereoSorter
- align2 - Variable in class org.jmol.smiles.PolyhedronStereoSorter
- alignLeft - Variable in class org.jmol.modelset.LabelToken
- alignment_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- alignUnitCells() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- alignZX(P3, P3, P3) - Method in class org.jmol.navigate.Navigator
-
brings pt0-pt1 vector to [0 0 -1], then rotates about [0 0 1] until ptVectorWing is in xz plane
- alkeneChild - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
last atom of an alkene or cumulene atom
- alkeneParent - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
first atom of an alkene or cumulene atom
- all - Static variable in class org.jmol.script.T
- ALL - Enum constant in enum org.jmol.viewer.Viewer.ACCESS
- ALL_BONDS - Static variable in class org.jmol.smiles.SmilesBond
- ALL_BUTTONS - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- all_states - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- allCarbohydrates - Static variable in class org.jmol.modelsetbio.BioResolver
-
this form is used for counting groups in ModelSet GLX added for 13.1.16
- allconnected - Static variable in class org.jmol.script.T
- allEmptyString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- ALLENE - Static variable in class org.jmol.smiles.SmilesStereo
- alleneStereo - Variable in class org.jmol.smiles.SmilesGenerator
- allfloat - Static variable in class org.jmol.script.T
- allFractionalRelative - Variable in class org.jmol.symmetry.UnitCell
-
this flag TRUE causes an update of matrixCtoFNoOffset each time an offset is changed so that it is updated and the two stay the same; set true only for isosurfaceMesh
- allFramesCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- allInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
- allNaN() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- allNull() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- allocateArray(JmolMolecule[], int) - Static method in class org.jmol.util.JmolMolecule
- allocateBioPolymer(Group[], int, boolean, int) - Static method in class org.jmol.modelsetbio.BioResolver
- allocateBuffers(int, int, boolean, boolean) - Method in class org.jmol.g3d.Platform3D
- allocateColix(int, boolean) - Static method in class org.jmol.util.C
- allocateCubeIterator() - Method in class org.jmol.bspt.Bspt
- allocateExpCouples(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- allocateExpNoes(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- allocateLabelArray(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- allocateOffscreenImage(int, int) - Method in class org.jmol.g3d.Platform3D
- allocateRgbImage(int, int, int[], int, boolean) - Static method in class org.jmol.awt.Image
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in interface org.jmol.api.GenericPlatform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awt.Platform
- allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awtjs2d.Platform
-
Create an "image" that is either a canvas with width/height/buf32 (from g3d.Platform32) or just an associative array with those (image writing
- allocateRgbImage(int, int, int[], int, boolean, Object) - Static method in class org.jmol.awtjs2d.Image
- allocateTBuffers(boolean) - Method in class org.jmol.g3d.Platform3D
- allocateViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
-
a simpler option
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.api.JmolViewer
-
legacy only
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.api.JmolViewer
-
This is the older main access point for creating an application or applet vwr.
- allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.viewer.Viewer
-
old way...
- allocDipole(String, String) - Method in class org.jmol.shapespecial.Dipoles
- allocDotsConvexMaps(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
- allocMesh(String, Mesh) - Method in class org.jmol.shape.MeshCollection
- allocMesh(String, Mesh) - Method in class org.jmol.shapecgo.CGO
- allocMesh(String, Mesh) - Method in class org.jmol.shapespecial.Draw
- allocMesh(String, Mesh) - Method in class org.jmol.shapesurface.Isosurface
- allocRaster(boolean, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
- allocTempEnum(int) - Method in class org.jmol.util.TempArray
- allocTempEnum(int) - Method in class org.jmol.viewer.Viewer
- allocTempPoints(int) - Method in class org.jmol.util.TempArray
- allocTempPoints(int) - Method in class org.jmol.viewer.Viewer
- allocTempScreens(int) - Method in class org.jmol.util.TempArray
- allocTempScreens(int) - Method in class org.jmol.viewer.Viewer
- allocVertexColixes() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- allOperators - Variable in class org.jmol.modelkit.ModelKit
- allow_a_len_1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- allow2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- allowAromaticBond(Bond) - Method in class org.jmol.modelset.BondCollection
- allowArrayDotNotation - Variable in class org.jmol.viewer.Viewer
- allowAtomName(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- allowaudio - Static variable in class org.jmol.script.T
- allowAudio - Variable in class org.jmol.viewer.GlobalSettings
- allowCapture() - Method in class org.jmol.viewer.Viewer
- allowDashed - Variable in class org.jmol.render.MeshRenderer
- allowDebug - Static variable in class org.jmol.i18n.GT
- allowedQuaternionFrames - Static variable in class org.jmol.viewer.JC
- allowedTypes - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- allowembeddedscripts - Static variable in class org.jmol.script.T
- allowEmbeddedScripts - Variable in class org.jmol.viewer.GlobalSettings
- allowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
- allowGaussian - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- allowgestures - Static variable in class org.jmol.script.T
- allowGestures - Variable in class org.jmol.viewer.GlobalSettings
- allowHighPrecision - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
- allowJavaConsole - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- allowJSThreads - Variable in class org.jmol.script.ScriptContext
- allowJSThreads - Variable in class org.jmol.script.ScriptEval
- allowkeystrokes - Static variable in class org.jmol.script.T
- allowKeyStrokes - Variable in class org.jmol.viewer.GlobalSettings
- allowMapData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
- allowMesh - Variable in class org.jmol.shapesurface.Isosurface
- allowMissingEnd - Variable in class org.jmol.script.ScriptCompiler
- allowmodelkit - Static variable in class org.jmol.script.T
- allowModelkit - Variable in class org.jmol.viewer.GlobalSettings
- allowMopacDCoef - Variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- allowmoveatoms - Static variable in class org.jmol.script.T
- allowMoveAtoms - Variable in class org.jmol.viewer.GlobalSettings
- allowMultiple - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- allowmultitouch - Static variable in class org.jmol.script.T
- allowMultiTouch - Variable in class org.jmol.viewer.GlobalSettings
- allowNegative - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- allowNoOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
- allowPDBFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- allowPopup - Variable in class org.jmol.modelkit.ModelKitPopup
- allowPreferences - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- allowRecentFiles - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- allowrotateselected - Static variable in class org.jmol.script.T
- allowRotateSelected - Variable in class org.jmol.viewer.GlobalSettings
- allowRotations - Variable in class org.jmol.adapter.readers.cif.CifReader
- allowScripting - Variable in class org.jmol.viewer.Viewer
- allowSelf - Variable in class org.jmol.modelset.MeasurementData
- allowSigma - Variable in class org.jmol.jvxl.readers.SurfaceReader
- allowSignedFeatures - Variable in class org.jmol.popup.GenericPopup
- allowSmilesUnbracketed(String) - Static method in class org.jmol.smiles.SmilesAtom
- allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
- allowSurface - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- allowUnderflow - Variable in class org.jmol.script.ScriptMathProcessor
- allowVolumeRender - Variable in class org.jmol.jvxl.data.JvxlData
- allowVolumeRender - Variable in class org.jmol.jvxl.readers.Parameters
- allPositive - Variable in class org.jmol.symmetry.HallRotationTerm
- allSame() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- allSelectedWidgets() - Method in class org.openscience.jmol.app.webexport.WebPanel
- allStates - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- allTrajectories - Variable in class org.jmol.adapter.writers.CMLWriter
- allTrajectories - Variable in class org.jmol.adapter.writers.PDBWriter
- allTypes - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- allZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- almost180 - Static variable in class org.jmol.modelset.AtomCollection
- alpha - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- alpha - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- alpha - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- alpha - Variable in class org.jmol.jvxl.readers.MapFileReader
- alpha - Variable in class org.jmol.util.SimpleUnitCell
- ALPHA - Static variable in class org.jmol.shapecgo.CGOMesh
- ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.viewer.JC
- ALPHA_SHIFT - Static variable in class org.jmol.util.C
- ALPHA_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
- alphaBeta - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- AlphaMonomer - Class in org.jmol.modelsetbio
- AlphaMonomer() - Constructor for class org.jmol.modelsetbio.AlphaMonomer
- alphaOffsets - Static variable in class org.jmol.modelsetbio.AlphaMonomer
- alphaOffsets - Static variable in class org.jmol.modelsetbio.CarbohydrateMonomer
- alphaOnly - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- AlphaPolymer - Class in org.jmol.modelsetbio
- AlphaPolymer(Monomer[], int) - Constructor for class org.jmol.modelsetbio.AlphaPolymer
- AlphaPolymer.Code - Enum in org.jmol.modelsetbio
- alphas - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- alphaTypes - Static variable in class org.jmol.modelsetbio.BioExt
- ALT - Static variable in class org.jmol.util.ColorEncoder
- ALT - Static variable in class org.jmol.viewer.binding.Binding
- ALT_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ALT_MASK - Static variable in class org.jmol.awtjs.Event
- altArgbsCpk - Variable in class org.jmol.viewer.ColorManager
- altArgbsCpk - Static variable in class org.jmol.viewer.JC
- altElementCounts - Variable in class org.jmol.util.JmolMolecule
- altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
- altElementMax - Static variable in class org.jmol.util.Elements
-
length of the altElementSymbols, altElementNames, altElementNumbers arrays
- altElementMax - Variable in class org.jmol.util.JmolMolecule
- altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
- altElementNames - Static variable in class org.jmol.util.Elements
- altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
- altElementNumbers - Static variable in class org.jmol.util.Elements
- altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
- altElementSymbols - Static variable in class org.jmol.util.Elements
- altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
- altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
- altloc - Variable in class org.jmol.modelset.Atom
- altloc - Static variable in class org.jmol.script.T
- altLoc - Variable in class org.jmol.adapter.smarter.Atom
- ALTLOC - Enum constant in enum org.jmol.c.PAL
- ALTLOC - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- altLocCount - Variable in class org.jmol.modelset.Model
- altlocs - Variable in class org.jmol.popup.JmolPopup
- altNames - Variable in class org.jmol.adapter.readers.pdb.P2nReader
- altType - Variable in class org.jmol.util.Tensor
- altVertices - Variable in class org.jmol.util.MeshSurface
- am - Variable in class org.jmol.modelset.ModelSet
- am - Variable in class org.jmol.thread.AnimationThread
- am - Variable in class org.jmol.viewer.Viewer
- ambient - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ambient_occlusion_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ambient_occlusion_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ambient_occlusion_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ambientFraction - Variable in class org.jmol.util.Shader
- ambientocclusion - Static variable in class org.jmol.script.T
- ambientOcclusion - Variable in class org.jmol.util.GData
- ambientpercent - Static variable in class org.jmol.script.T
- ambientPercent - Variable in class org.jmol.util.Shader
- ambiguityType - Variable in class org.jmol.symmetry.SpaceGroup
- ambiguousNames - Static variable in class org.jmol.symmetry.SpaceGroup
- amino - Static variable in class org.jmol.script.T
- AMINO - Enum constant in enum org.jmol.c.PAL
- AMINO - Static variable in class org.jmol.util.ColorEncoder
- AminoMonomer - Class in org.jmol.modelsetbio
- AminoMonomer() - Constructor for class org.jmol.modelsetbio.AminoMonomer
- AminoPolymer - Class in org.jmol.modelsetbio
- AminoPolymer(Monomer[], int) - Constructor for class org.jmol.modelsetbio.AminoPolymer
- ampacContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- AmpacReader - Class in org.jmol.adapter.readers.simple
-
A reader for AMPAC output.
- AmpacReader() - Constructor for class org.jmol.adapter.readers.simple.AmpacReader
- AMPLITUDE_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Maximum value for vibration scale.
- AMPLITUDE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Precision of the vibration scale slider
- AMPLITUDE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Initial value of vibration scale.
- amplitudeSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- anaglyph_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- anaglyphChannelBytes - Variable in class org.jmol.g3d.Graphics3D
- anaglyphLength - Variable in class org.jmol.g3d.Graphics3D
- anchor - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- andBitSet(BS) - Method in class org.jmol.shapespecial.Polyhedra
- andequals - Static variable in class org.jmol.script.T
- andNot(BS, BS) - Static method in class org.jmol.util.BSUtil
- angle - Static variable in class org.jmol.script.T
- angle - Variable in class org.jmol.thread.SpinThread
- angle_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- angle_label_position - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- angle_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- angleCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- angleCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
- angleCount - Variable in class org.jmol.minimize.forcefield.Calculations
- anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.Slice
- anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- angleUnits - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- angleUnitsPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- angleXY - Variable in class org.openscience.jmol.app.surfacetool.Slice
- angleXY - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- angleXYSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- angleZSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- angMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- angstroms - Static variable in class org.jmol.script.T
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.Parameters
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.SurfaceReader
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JC
- angstromsToPixels(float) - Method in class org.jmol.viewer.TransformManager
- angularPart(double, double, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- animation - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- animation - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
- animation - Static variable in class org.jmol.script.T
- animation(boolean) - Method in class org.jmol.viewer.AnimationManager
- animation_duration - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- animationDirection - Variable in class org.jmol.viewer.AnimationManager
- animationfps - Static variable in class org.jmol.script.T
- animationFps - Variable in class org.jmol.viewer.AnimationManager
- animationFps - Variable in class org.jmol.viewer.GlobalSettings
- animationFrames - Variable in class org.jmol.viewer.AnimationManager
- AnimationManager - Class in org.jmol.viewer
- AnimationManager(Viewer) - Constructor for class org.jmol.viewer.AnimationManager
- animationmode - Static variable in class org.jmol.script.T
- animationOn - Variable in class org.jmol.viewer.AnimationManager
- animationPaused - Variable in class org.jmol.viewer.AnimationManager
- animationReplayMode - Variable in class org.jmol.viewer.AnimationManager
- animationStep - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
- animationThread - Variable in class org.jmol.viewer.AnimationManager
- AnimationThread - Class in org.jmol.thread
- AnimationThread() - Constructor for class org.jmol.thread.AnimationThread
- AnimationWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
- AnimButton(ImageIcon, String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- ANIMFRAME - Enum constant in enum org.jmol.c.CBK
- animThread - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- anionLookupTable - Static variable in class org.jmol.util.Elements
- aniosU - Variable in class org.jmol.jvxl.readers.Parameters
- ANISO_B11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_B12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_B13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_B22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_B23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_B33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_BETA_11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_BETA_12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_BETA_13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_BETA_22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_BETA_23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_BETA_33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_LABEL - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_MMCIF_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_MMCIF_U11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_MMCIF_U12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_MMCIF_U13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_MMCIF_U22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_MMCIF_U23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_MMCIF_U33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_U11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_U12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_U13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_U22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_U23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ANISO_U33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- anisoB - Variable in class org.jmol.jvxl.readers.Parameters
- anisoBorU - Variable in class org.jmol.adapter.smarter.Atom
- anisotropy - Variable in class org.jmol.jvxl.readers.Parameters
- anisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
- anisotropy - Static variable in class org.jmol.script.T
- anisotropy() - Method in class org.jmol.util.Tensor
-
anisotropy = directed distance from (center of two closest) to (the furthest)
- anisou() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- ANISOU - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- Annotation - Class in org.jmol.modelsetbio
- Annotation() - Constructor for class org.jmol.modelsetbio.Annotation
- ANNOTATION - Enum constant in enum org.jmol.c.STR
- annotationParser - Variable in class org.jmol.viewer.Viewer
- AnnotationParser - Class in org.jmol.dssx
-
A parser for output from 3DNA web service.
- AnnotationParser() - Constructor for class org.jmol.dssx.AnnotationParser
- antialias - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- antialias - Variable in class org.jmol.render.MeshRenderer
- antialias - Variable in class org.jmol.viewer.TransformManager
- antialias2 - Variable in class org.jmol.g3d.Graphics3D
- antiAliasCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- antialiasdisplay - Static variable in class org.jmol.script.T
- antialiasDisplay - Variable in class org.jmol.viewer.GlobalSettings
- antialiasDisplay - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- antialiased - Variable in class org.jmol.viewer.Viewer
- antialiasEnabled - Variable in class org.jmol.util.GData
- antialiasimages - Static variable in class org.jmol.script.T
- antialiasImages - Variable in class org.jmol.viewer.GlobalSettings
- antialiasThisFrame - Variable in class org.jmol.util.GData
- antialiastranslucent - Static variable in class org.jmol.script.T
- antialiasTranslucent - Variable in class org.jmol.viewer.GlobalSettings
- ANUM - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- AO_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- aobuf - Variable in class org.jmol.g3d.Graphics3D
- aoMax - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- aoMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- aPar - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
- ApbsReader - Class in org.jmol.jvxl.readers
- ApbsReader() - Constructor for class org.jmol.jvxl.readers.ApbsReader
- aperatureAngle - Variable in class org.jmol.viewer.TransformManager
- apertureAngle - Variable in class org.jmol.export.___Exporter
- apiPlatform - Variable in class org.jmol.api.JmolViewer
- apiPlatform - Variable in class org.jmol.g3d.Platform3D
- apiPlatform - Variable in class org.jmol.util.GData
- apivot - Static variable in class org.jmol.script.T
- apm - Variable in class org.jmol.viewer.ActionManager
-
picking modes set picking....
- apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
- app(SB, String) - Method in class org.jmol.viewer.GlobalSettings
- app(SB, String) - Method in class org.jmol.viewer.StateCreator
- appCheckItem(String, SC) - Method in class org.jmol.popup.GenericPopup
-
Opportunity to do something special with an item.
- appCheckItem(String, SC) - Method in class org.jmol.popup.JmolPopup
- appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.GenericPopup
-
Opportunity to do something special with a given submenu is created
- appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.JmolPopup
- AppCloser() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
- appConsole - Variable in class org.jmol.viewer.Viewer
- AppConsole - Class in org.openscience.jmol.app.jmolpanel.console
- AppConsole() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
- AppConsole(JmolViewer, Container, String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
-
general entry point
- AppConsole.ConsoleDocument - Class in org.openscience.jmol.app.jmolpanel.console
- AppConsole.ConsoleTextPane - Class in org.openscience.jmol.app.jmolpanel.console
- AppConsole.ExecuteCommandThread - Class in org.openscience.jmol.app.jmolpanel.console
- append - Variable in class org.jmol.dialog.FilePreview
- append - Static variable in class org.jmol.script.T
- append(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
- append(String) - Method in class org.jmol.console.AppletConsole.GenericTextPane
- append(String) - Method in interface org.jmol.console.GenericTextArea
- append(String) - Method in class org.jmol.util.JSONWriter
- APPEND - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- appendAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesSearch
- appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Appends an AtomSetCollection
- appendAtomSetCollectionList(Lst<?>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- appendAtomTokenValue(Viewer, Atom, LabelToken, SB, int[], P3) - Static method in class org.jmol.modelset.LabelToken
- appendBuffer(String, boolean) - Method in class org.jmol.script.ScriptEval
- appendCmd(SB, String) - Static method in class org.jmol.shape.Shape
- appendContourTriangleIntersection(int, float, float, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
appends an integer (3, 5, or 6) representing two sides of a triangle ABC -- AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges for the intersection point base-90-encoded.
- appendedData - Variable in class org.jmol.adapter.readers.cif.CifReader
- appendEncodedBitSetTag(SB, String, BS, int, Object[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
- appendFontCmd(SB) - Method in class org.jmol.modelset.Text
- appendKey(SB, String) - Method in class org.jmol.adapter.writers.CIFWriter
- appendLoadNote(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- appendLoadStates(SB) - Method in class org.jmol.viewer.StateCreator
- appendLogData(String) - Method in class org.jmol.minimize.forcefield.Calculations
- appendnew - Static variable in class org.jmol.script.T
- appendNew - Variable in class org.jmol.modelset.ModelLoader
- appendNew - Variable in class org.jmol.viewer.GlobalSettings
- appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- APPENDS - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- appendState(Lst<String>) - Method in class org.jmol.viewer.StateManager
- appendTag(SB, String, String[]) - Static method in class org.jmol.adapter.writers.CMLWriter
- appendTickInfo(String, SB, TickInfo) - Method in class org.jmol.viewer.StateCreator
- appendToModelIndex - Variable in class org.jmol.modelset.ModelLoader
- appendUunitCellInfo(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- appendXmlColorData(SB, String, boolean, boolean, float, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
- appendXmlEdgeData(SB, JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
- appendXmlTriangleData(SB, int[][], int, BS, int[], boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
encode triangle data -- [ia ib ic] [ia ib ic] [ia ib ic] ...
- appendXmlVertexData(SB, JvxlData, int[], T3[], float[], int, String, int, BS, int[], boolean, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
encode the vertex data.
- appendXmlVertexOnlyData(SB, JvxlData, MeshData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
- appFixLabel(String) - Method in class org.jmol.popup.GenericPopup
- appFixLabel(String) - Method in class org.jmol.popup.JmolGenericPopup
- appGetBooleanProperty(String) - Method in class org.jmol.modelkit.ModelKitPopup
- appGetBooleanProperty(String) - Method in class org.jmol.popup.GenericPopup
- appGetBooleanProperty(String) - Method in class org.jmol.popup.JmolGenericPopup
- appGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
- appGetMenuAsString(String) - Method in class org.jmol.popup.JmolPopup
- applet - Variable in class org.jmol.awtjs.swing.AbstractButton
- appletCodeBase - Static variable in class org.jmol.viewer.Viewer
- AppletConsole - Class in org.jmol.console
- AppletConsole - Class in org.jmol.consolejs
-
An interface to Jmol.Console.
- AppletConsole() - Constructor for class org.jmol.console.AppletConsole
- AppletConsole() - Constructor for class org.jmol.consolejs.AppletConsole
- AppletConsole.ControlEnterTextArea - Class in org.jmol.console
- AppletConsole.GenericTextPane - Class in org.jmol.console
- appletContext - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- appletDocumentBase - Static variable in class org.jmol.viewer.Viewer
- appletDocumentBaseURL - Variable in class org.jmol.viewer.FileManager
- appletIdiomaBase - Static variable in class org.jmol.viewer.Viewer
- appletInfoDivs - Variable in class org.openscience.jmol.app.webexport.WebPanel
- appletName - Variable in class org.jmol.viewer.Viewer
- appletObject - Variable in class org.jmol.util.GenericApplet
- appletParamPanel() - Method in class org.openscience.jmol.app.webexport.PopInJmol
- appletParamPanel() - Method in class org.openscience.jmol.app.webexport.ScriptButtons
- appletParamPanel() - Method in class org.openscience.jmol.app.webexport.WebPanel
- appletPath - Variable in class org.openscience.jmol.app.webexport.Test
- appletproxy - Static variable in class org.jmol.script.T
- appletProxy - Variable in class org.jmol.viewer.FileManager
- appletProxy - Variable in class org.jmol.viewer.GlobalSettings
- APPLETREADY - Enum constant in enum org.jmol.c.CBK
- appletSizeSpinnerH - Variable in class org.openscience.jmol.app.webexport.WebPanel
- appletSizeSpinnerP - Variable in class org.openscience.jmol.app.webexport.WebPanel
- appletSizeSpinnerW - Variable in class org.openscience.jmol.app.webexport.WebPanel
- apply() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- apply(ModulationSet, double[][]) - Method in class org.jmol.util.Modulation
- applyAllSymmetry(MSInterface, BS) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- applyAnaglygh(STER, int[]) - Method in class org.jmol.g3d.Graphics3D
- applyAnaglygh(STER, int[]) - Method in class org.jmol.util.GData
- applyButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- applyColorScale() - Method in class org.jmol.jvxl.readers.SurfaceReader
- applyEmpiricalRules(MinObject, double[], int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- applyLeftMouse(int) - Static method in class org.jmol.awt.Mouse
- applyLeftMouse(int) - Static method in class org.jmol.awtjs2d.Mouse
- applyPerspective(T3, T3) - Method in class org.jmol.viewer.TransformManager
-
adjusts the temporary point for perspective and offsets
- applyRotation(M3, boolean, BS, V3, boolean, M4) - Method in class org.jmol.viewer.TransformManager
- applyStereochemistry() - Method in class org.jmol.modelset.ModelLoader
- applySymmetry - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- applySymmetry() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- applySymmetry(Atom, M4[], int, T3) - Static method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Apply the symmetry and translation
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.CifReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- applySymmetryBio(Map<String, Object>, boolean, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- applySymmetryFromReader(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- applySymmetryLattice() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- applysymmetrytobonds - Static variable in class org.jmol.script.T
- applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- applySymmetryToBonds - Variable in class org.jmol.viewer.GlobalSettings
- applySymTrajASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- appRestorePopupMenu() - Method in class org.jmol.popup.GenericPopup
- appRestorePopupMenu() - Method in class org.jmol.popup.JmolGenericPopup
- appRestorePopupMenu() - Method in class org.jmol.popup.JmolPopup
- approx(T3) - Static method in class org.jmol.symmetry.SymmetryDesc
- approx0(float) - Method in class org.jmol.symmetry.PointGroup.Operation
- approx0(float) - Method in class org.jmol.symmetry.SpaceGroupFinder
- approx0(T3) - Static method in class org.jmol.symmetry.SymmetryDesc
- approx000(float) - Method in class org.jmol.symmetry.SpaceGroupFinder
- approx0014(float) - Method in class org.jmol.symmetry.SpaceGroupFinder
- approx0f(float) - Static method in class org.jmol.symmetry.SymmetryDesc
- approxF(float) - Static method in class org.jmol.symmetry.SymmetryOperation
- approxInt(float) - Method in class org.jmol.adapter.readers.cif.MSRdr
- approxInt(float) - Method in class org.jmol.symmetry.SpaceGroupFinder
- approxZero(double) - Static method in class org.jmol.adapter.readers.cif.Subsystem
- appRunScript(String) - Method in class org.jmol.modelkit.ModelKit
- appRunScript(String) - Method in class org.jmol.popup.GenericPopup
- appRunScript(String) - Method in class org.jmol.popup.JmolGenericPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
- appRunSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.JmolGenericPopup
- appUpdateForShow() - Method in class org.jmol.modelkit.ModelKitPopup
- appUpdateForShow() - Method in class org.jmol.popup.GenericPopup
- appUpdateForShow() - Method in class org.jmol.popup.JmolPopup
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
-
Set the active menu based on updating a value -- usually by the user, but also during setup (ignored).
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.GenericPopup
- appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.JmolPopup
-
(1) setOption --> set setOption true or set setOption false
- arc - Static variable in class org.jmol.script.T
- ARC - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- area - Static variable in class org.jmol.script.T
- areas - Variable in class org.jmol.util.BZone
- areAxesTainted() - Method in class org.jmol.viewer.Viewer
- areEqual(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
- areEqual(String, String) - Method in class org.jmol.smiles.SmilesMatcher
- areEqual(BS, BS) - Static method in class org.jmol.util.BSUtil
- areEqual(SV, SV) - Static method in class org.jmol.script.SV
-
For legacy reasons, "x" == "X" but see isLike()
- areEqualTest(String, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
-
for JUnit test, mainly
- argb - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- argb - Variable in class org.jmol.awtjs.swing.Color
- argb - Variable in class org.jmol.g3d.TextString
- argbCurrent - Variable in class org.jmol.util.GData
- argbEndcap - Variable in class org.jmol.g3d.CylinderRenderer
- argbNoisyDn - Variable in class org.jmol.util.GData
- argbNoisyUp - Variable in class org.jmol.util.GData
- argbs - Static variable in class org.jmol.util.C
- argbsAmino - Static variable in class org.jmol.modelsetbio.BioResolver
- argbsAmino - Variable in class org.jmol.util.ColorEncoder
- argbsChainAtom - Static variable in class org.jmol.modelsetbio.BioResolver
-
some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
- argbsChainAtom - Static variable in class org.jmol.util.ColorEncoder
- argbsChainHetero - Static variable in class org.jmol.modelsetbio.BioResolver
- argbsChainHetero - Static variable in class org.jmol.util.ColorEncoder
- argbsCpk - Static variable in enum org.jmol.c.PAL
-
Default table of CPK atom colors.
- argbsCpk - Variable in class org.jmol.util.ColorEncoder
- argbsCpk - Variable in class org.jmol.viewer.ColorManager
- argbsCpkRasmol - Static variable in enum org.jmol.c.PAL
- argbsFormalCharge - Static variable in class org.jmol.viewer.JC
- argbsGreyscale - Static variable in class org.jmol.util.C
- argbsHbondType - Static variable in class org.jmol.util.Edge
- argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JC
- argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JC
- argbsNucleic - Static variable in class org.jmol.modelsetbio.BioResolver
- argbsNucleic - Variable in class org.jmol.util.ColorEncoder
- argbsRoygb - Variable in class org.jmol.util.ColorEncoder
- argbsRoygbScale - Static variable in class org.jmol.viewer.JC
- argbsRwb - Variable in class org.jmol.util.ColorEncoder
- argbsRwbScale - Static variable in class org.jmol.viewer.JC
- argbsShapely - Static variable in class org.jmol.modelsetbio.BioResolver
- argbsShapely - Variable in class org.jmol.util.ColorEncoder
- arom - Variable in class org.jmol.minimize.forcefield.AtomType
-
MMFF aromatic types 37, 38, 39, 44, 58, 59, 63, 64, 65, 66, 69, 78, 79, 81, 82
- aromatic - Static variable in class org.jmol.script.T
- AROMATIC - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- AROMATIC_DOUBLE - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- AROMATIC_SINGLE - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- aromaticAmbiguous - Variable in class org.jmol.smiles.SmilesAtom
- aromaticDefined - Variable in class org.jmol.smiles.SmilesSearch
- aromaticDouble - Variable in class org.jmol.smiles.SmilesGenerator
- aromaticDouble - Variable in class org.jmol.smiles.SmilesSearch
- aromaticMMFF94 - Variable in class org.jmol.smiles.SmilesSearch
- aromaticOpen - Variable in class org.jmol.smiles.SmilesSearch
- aromaticPlanar - Variable in class org.jmol.smiles.SmilesSearch
- aromaticRings - Variable in class org.jmol.smiles.SmilesGenerator
- aromaticStrict - Variable in class org.jmol.smiles.SmilesSearch
- aromaticUnknown - Variable in class org.jmol.smiles.SmilesSearch
- array - Static variable in class org.jmol.script.T
- arrayAdd(Object) - Method in class org.jmol.util.JSONWriter
- arrayClose(boolean) - Method in class org.jmol.util.JSONWriter
- arrayListHandler - Variable in class org.openscience.jmol.app.webexport.Test
- ArrayListTransferable(Lst<String>) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
- ArrayListTransferHandler - Class in org.openscience.jmol.app.webexport
- ArrayListTransferHandler(WebPanel) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- ArrayListTransferHandler.ArrayListTransferable - Class in org.openscience.jmol.app.webexport
- arrayOpen(boolean) - Method in class org.jmol.util.JSONWriter
- arrayPt - Variable in class org.jmol.script.SV.Sort
- arrow - Static variable in class org.jmol.script.T
- Arrow(boolean, int, int) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter.Arrow
- ARROW - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- arrowHeadBase - Static variable in class org.jmol.renderspecial.DipolesRenderer
- arrowHeadFaces - Static variable in class org.jmol.renderbio.RocketRenderer
- arrowHeadOffset - Static variable in class org.jmol.renderspecial.DipolesRenderer
- arrowHeadOffset - Static variable in class org.jmol.renderspecial.VectorsRenderer
- arrowHeadTip - Static variable in class org.jmol.renderspecial.DipolesRenderer
- arrowHeadWidthFactor - Static variable in class org.jmol.renderspecial.DipolesRenderer
- as - Static variable in class org.jmol.script.T
- asBitSet - Variable in class org.jmol.script.ScriptMathProcessor
- asBoolean() - Method in class org.jmol.script.SV
- asc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- asc - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- ASCENDER - Static variable in class org.jmol.util.MeshCapper
- ASCENDING - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- ascent - Variable in class org.jmol.g3d.TextRenderer
- ascent - Variable in class org.jmol.modelset.Text
- ascent - Variable in class org.jmol.render.LabelsRenderer
- ascent - Variable in class org.jmol.util.Font
- asFloat() - Method in class org.jmol.script.SV
- ashades - Variable in class org.jmol.util.Shader
- ashadesGreyscale - Variable in class org.jmol.util.Shader
- asHTML(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- ASimpleJvxlWriter - Class in org.openscience.jvxl.simplewriter
- ASimpleJvxlWriter() - Constructor for class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
- asInt() - Method in class org.jmol.script.SV
- asLineOnly - Variable in class org.jmol.render.FontLineShapeRenderer
- aspectRatio - Variable in class org.jmol.renderbio.BioShapeRenderer
- asQuads - Variable in class org.jmol.jvxl.readers.Ras3DReader
- asResidues - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
- ASSEM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- ASSEM_LIST - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- ASSEM_OPERS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- assemblyFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- assemblyIdAtoms - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- assign - Static variable in class org.jmol.script.T
- assign() - Method in class org.jmol.scriptext.CmdExt
-
Though a command, not documented.
- assignAromaticBondsBs(boolean, BS) - Method in class org.jmol.modelset.BondCollection
-
algorithm discussed above.
- assignAromaticDouble(Bond) - Method in class org.jmol.modelset.BondCollection
-
try to assign AROMATICDOUBLE to this bond.
- assignAromaticDoubleForAtom(Atom) - Method in class org.jmol.modelset.BondCollection
-
N atoms with 3 bonds cannot also have a double bond; other atoms need one and only one double bond; the rest must be single bonds.
- assignAromaticMustBeSingle(Atom) - Method in class org.jmol.modelset.BondCollection
- assignAromaticNandO(BS) - Method in class org.jmol.modelset.BondCollection
- assignAromaticSingle(Bond) - Method in class org.jmol.modelset.BondCollection
-
try to assign AROMATICSINGLE to this bond.
- assignAromaticSingleForAtom(Atom, int) - Method in class org.jmol.modelset.BondCollection
-
N atoms with 3 bonds cannot also have a double bond; other atoms needs all single bonds, because the bond leading up to it is double.
- assignAtom(int, String, boolean, boolean, boolean, BS) - Method in class org.jmol.modelkit.ModelKit
-
Original ModelKitPopup functionality -- assign an atom.
- assignAtomClick(int, String, P3) - Method in class org.jmol.modelkit.ModelKit
- assignAtoms(P3, boolean, int, String, String, boolean, BS, int, int, SymmetryInterface, Lst<P3>, String) - Method in class org.jmol.modelkit.ModelKit
-
Change element, charge, and deleting an atom by clicking on it or via the MODELKIT ASSIGN ATOM command.
- assignBond(int, char, BS) - Method in class org.jmol.modelkit.ModelKit
-
Original ModelKit functionality -- assign a bond.
- assignLeft - Variable in class org.jmol.script.ScriptMathProcessor
- assignMoveAtom(int, P3, BS) - Method in class org.jmol.modelkit.ModelKit
- assignNew() - Method in class org.jmol.viewer.ActionManager
- assignPDBH(String, String) - Method in class org.jmol.dssx.AnnotationParser
- assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MepCalculation
- assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MlpCalculation
- assignSpaceGroup(BS, String, int) - Method in class org.jmol.viewer.Viewer
- assignValueFromGapColorForKin(String) - Method in class org.jmol.jvxl.readers.KinemageReader
-
C++ code gives these as " value > x.x ? "xxxxx", etc.
- assocCutoff - Variable in class org.jmol.jvxl.readers.Parameters
- assocCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
- assocGridPointMap - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- assocGridPointNormals - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- associatedAtoms - Variable in class org.jmol.modelset.BondSet
- associateNormals - Variable in class org.jmol.shapesurface.Isosurface
- ASSOCIATION - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- asString() - Method in class org.jmol.script.SV
- asString() - Method in class org.jmol.symmetry.SpaceGroup
- assumeAtomRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- astrType - Static variable in class org.jmol.script.T
- asVector - Variable in class org.jmol.script.ScriptMathProcessor
- asVector - Variable in class org.jmol.smiles.SmilesSearch
- asymMatrix - Variable in class org.jmol.util.Tensor
- asymmetry() - Method in class org.jmol.util.Tensor
-
asymmetry = deviation from a symmetric tensor
- async - Static variable in class org.jmol.script.T
- async - Variable in class org.jmol.viewer.Viewer
- async_builds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- at - Variable in class org.jmol.modelset.AtomCollection
- atemp - Variable in class org.jmol.smiles.SmilesGenerator
- aTemp - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- aTemp - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- ati_bugs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- atModel - Variable in class org.jmol.adapter.readers.cif.MSRdr
- atNos - Variable in class org.jmol.util.JmolMolecule
- atokenInfix - Variable in class org.jmol.script.ScriptTokenParser
- atom - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- atom - Variable in class org.jmol.adapter.readers.xml.XmlReader
- atom - Variable in class org.jmol.adapter.smarter.AtomIterator
- atom - Variable in class org.jmol.minimize.MinAtom
- atom - Variable in class org.jmol.quantum.QMAtom
- atom - Variable in class org.jmol.render.LabelsRenderer
- atom - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
the associated Jmol (or otherwise) atom; use of the SimpleNode interface allows us to implement this in SMILES or Jmol as well as providing an interface other programs could use if implementing this code
- atom() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- atom() - Method in class org.jmol.adapter.readers.xtal.CgdReader
- Atom - Class in org.jmol.adapter.smarter
- Atom - Class in org.jmol.modelset
- Atom() - Constructor for class org.jmol.adapter.smarter.Atom
- Atom() - Constructor for class org.jmol.modelset.Atom
- ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- ATOM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ATOM_INFRAME - Static variable in class org.jmol.modelset.Atom
- ATOM_INFRAME_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
- ATOM_MODE - Static variable in class org.jmol.modelkit.ModelKit
- atom_name_wildcard - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ATOM_NOFLAGS - Static variable in class org.jmol.modelset.Atom
- ATOM_NOTHIDDEN - Static variable in class org.jmol.modelset.Atom
- ATOM_SHAPE_VIS_MASK - Static variable in class org.jmol.modelset.Atom
- atom_type_format - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ATOM_TYPE_OXIDATION_NUMBER - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ATOM_TYPE_RADIUS_BOND - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ATOM_TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cif.CifReader
- ATOM_VISIBLE - Static variable in class org.jmol.modelset.Atom
- ATOM_VISSET - Static variable in class org.jmol.modelset.Atom
- atom1 - Variable in class org.jmol.modelset.Bond
- atom1 - Variable in class org.jmol.smiles.SmilesBond
- atom2 - Variable in class org.jmol.modelset.Bond
- atom2 - Variable in class org.jmol.smiles.SmilesBond
- atomArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- atomBool(byte[], int, int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- atomCapacity - Variable in class org.jmol.modelset.AtomCollection
- atomCenterOrCoordinateParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
- atomCharges - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- atomClass - Variable in class org.jmol.smiles.SmilesAtom
- AtomCollection - Class in org.jmol.modelset
- AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
- AtomCollection.AtomSorter - Class in org.jmol.modelset
- atomColorList - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- atomConstraints - Variable in class org.jmol.modelkit.ModelKit
- atomCoordAngstroms - Variable in class org.jmol.quantum.MepCalculation
- atomCount - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- atomCount - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- atomCount - Variable in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- atomCount - Variable in class org.jmol.adapter.readers.quantum.OrcaReader
- atomCount - Variable in class org.jmol.adapter.readers.simple.OrcaReader
- atomCount - Variable in class org.jmol.smiles.SmilesStereo
- atomCounter - Variable in class org.jmol.quantum.NMRNoeMatrix
- atomData - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- atomData - Variable in class org.jmol.geodesic.EnvelopeCalculation
- atomData - Variable in class org.jmol.jvxl.readers.AtomDataReader
- AtomData - Class in org.jmol.atomdata
- AtomData() - Constructor for class org.jmol.atomdata.AtomData
- AtomDataReader - Class in org.jmol.jvxl.readers
- AtomDataReader() - Constructor for class org.jmol.jvxl.readers.AtomDataReader
- atomDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- AtomDataServer - Interface in org.jmol.atomdata
- atomEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
- atomExpression - Static variable in class org.jmol.viewer.PropertyManager
- atomExpression(T[], int, int, boolean, boolean, Object[], boolean) - Method in class org.jmol.script.ScriptExpr
- atomExpressionAt(int) - Method in class org.jmol.script.ScriptExpr
- atomExpressionAt(int) - Method in class org.jmol.scriptext.ScriptExt
- atomExpressionCommand - Static variable in class org.jmol.script.T
- atomFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- atomFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
- atomFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- atomFloat(byte[], int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- atomFormats - Variable in class org.jmol.shape.Hover
- atomFrag - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- atomGroup - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- atomHighlighted - Variable in class org.jmol.viewer.Viewer
- atomHoverLabel - Variable in class org.jmol.modelkit.ModelKit
- ATOMIC_ORBITAL_ZERO_CUT_OFF - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
- atomicAndIsotopeNumber - Variable in class org.jmol.modelset.Atom
- atomicMass - Variable in class org.jmol.smiles.SmilesAtom
- atomicMass - Static variable in class org.jmol.util.Elements
- atomicNumber - Variable in class org.jmol.atomdata.AtomData
- atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- atomicorbital - Static variable in class org.jmol.script.T
- atomid - Static variable in class org.jmol.script.T
- atomID - Variable in class org.jmol.modelset.Atom
- ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JC
- ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JC
- ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C2 - Static variable in class org.jmol.viewer.JC
- ATOMID_C2_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C4 - Static variable in class org.jmol.viewer.JC
- ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C5 - Static variable in class org.jmol.viewer.JC
- ATOMID_C5_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_C5M - Static variable in class org.jmol.viewer.JC
- ATOMID_C6 - Static variable in class org.jmol.viewer.JC
- ATOMID_C7 - Static variable in class org.jmol.viewer.JC
- ATOMID_C8 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JC
- ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JC
- ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JC
- ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JC
- ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JC
- ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_MAX - Static variable in class org.jmol.modelsetbio.BioResolver
- ATOMID_N1 - Static variable in class org.jmol.viewer.JC
- ATOMID_N2 - Static variable in class org.jmol.viewer.JC
- ATOMID_N3 - Static variable in class org.jmol.viewer.JC
- ATOMID_N4 - Static variable in class org.jmol.viewer.JC
- ATOMID_N6 - Static variable in class org.jmol.viewer.JC
- ATOMID_N7 - Static variable in class org.jmol.viewer.JC
- ATOMID_N9 - Static variable in class org.jmol.viewer.JC
- ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JC
- ATOMID_O1 - Static variable in class org.jmol.viewer.JC
- ATOMID_O1P - Static variable in class org.jmol.viewer.JC
- ATOMID_O2 - Static variable in class org.jmol.viewer.JC
- ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O2P - Static variable in class org.jmol.viewer.JC
- ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O4 - Static variable in class org.jmol.viewer.JC
- ATOMID_O4_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JC
- ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JC
- ATOMID_O6 - Static variable in class org.jmol.viewer.JC
- ATOMID_OP1 - Static variable in class org.jmol.viewer.JC
- ATOMID_OP2 - Static variable in class org.jmol.viewer.JC
- ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JC
- ATOMID_S4 - Static variable in class org.jmol.viewer.JC
- ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JC
- atomIdNames - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- atomindex - Static variable in class org.jmol.script.T
- atomIndex - Variable in class org.jmol.adapter.readers.simple.HyperChemReader
- atomIndex - Variable in class org.jmol.atomdata.AtomData
- atomIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
- atomIndex - Variable in class org.jmol.jvxl.readers.Parameters
- atomIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
- atomIndex - Variable in class org.jmol.shape.Hover
- atomIndex - Variable in class org.jmol.shape.Mesh
- atomIndex - Variable in class org.jmol.shapesurface.Isosurface
- atomIndex - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
the application-assigned unique atom index for this atom; used in updating lstSmallRings
- atomIndex0 - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- atomIndex1 - Variable in class org.jmol.adapter.smarter.Bond
- atomIndex1 - Variable in class org.jmol.shapespecial.Dipoles
- atomIndex1 - Variable in class org.jmol.util.Tensor
- atomIndex1 - Variable in class org.jmol.viewer.Connection
- atomIndex2 - Variable in class org.jmol.adapter.smarter.Bond
- atomIndex2 - Variable in class org.jmol.shapespecial.Dipoles
- atomIndex2 - Variable in class org.jmol.util.Tensor
- atomIndex2 - Variable in class org.jmol.viewer.Connection
- AtomIndexIterator - Interface in org.jmol.api
-
note: YOU MUST RELEASE THE ITERATOR
- atomIndexLast - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- atomIndexSphere - Variable in class org.jmol.modelkit.ModelKit
- atomInt(byte[], int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- AtomIterator - Class in org.jmol.adapter.smarter
- AtomIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.AtomIterator
- AtomIteratorWithinModel - Class in org.jmol.modelset
- AtomIteratorWithinModel() - Constructor for class org.jmol.modelset.AtomIteratorWithinModel
- AtomIteratorWithinModelSet - Class in org.jmol.modelset
- AtomIteratorWithinModelSet(BS) - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
- atomLabel - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- atomLabel - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- atomLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- atomLabels - Variable in class org.jmol.shape.Labels
- atomList - Variable in class org.jmol.util.JmolMolecule
- atomMap - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
- atomMap - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- atomMap - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- atomMap - Variable in class org.jmol.adapter.readers.simple.InputReader
- atomMap - Variable in class org.jmol.minimize.Minimizer
- atomMap - Variable in class org.jmol.quantum.NMRNoeMatrix
- atomMap - Variable in class org.jmol.symmetry.PointGroup
- atomMapAnyCase - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomMolecule - Variable in class org.jmol.atomdata.AtomData
- ATOMMOVED - Enum constant in enum org.jmol.c.CBK
- atomname - Static variable in class org.jmol.script.T
- atomName - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- atomName - Variable in class org.jmol.adapter.smarter.Atom
- atomName1 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- atomName2 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- atomNames - Variable in class org.jmol.adapter.readers.pdb.JmolDataReader
- atomNames - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- atomNames - Variable in class org.jmol.adapter.readers.quantum.PsiReader
- atomNames - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- atomNames - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- atomNames - Variable in class org.jmol.modelset.AtomCollection
- atomno - Static variable in class org.jmol.script.T
- atomNo - Variable in class org.jmol.jvxl.readers.AtomDataReader
- atomNo - Variable in class org.jmol.quantum.SlaterData
- atomNumber - Variable in class org.jmol.smiles.SmilesAtom
- atomOrPointPicked(int, Point3fi) - Method in class org.jmol.viewer.ActionManager
- atomPicked(int) - Method in interface org.jmol.api.JmolJSpecView
- atomPicked(int) - Method in class org.jmol.jsv.JSpecView
- atompicking - Static variable in class org.jmol.script.T
- atomPicking - Variable in class org.jmol.viewer.GlobalSettings
- atomPositions - Variable in class org.jmol.adapter.readers.simple.AmpacReader
- atomProp - Variable in class org.jmol.jvxl.readers.AtomDataReader
- atomproperty - Static variable in class org.jmol.script.T
- atomPropertyFloat(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
-
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
- atomPropertyInt(int) - Method in class org.jmol.modelset.Atom
-
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
- AtomPropertyMapper - Class in org.jmol.jvxl.readers
-
maps property data
- AtomPropertyMapper() - Constructor for class org.jmol.jvxl.readers.AtomPropertyMapper
- atomPropertyString(Viewer, int) - Method in class org.jmol.modelset.Atom
- atomPropertyTuple(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
- atomPt - Variable in class org.jmol.render.LabelsRenderer
- atomPts - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- atomRadius - Variable in class org.jmol.adapter.readers.cif.CifReader
- atomRadius - Variable in class org.jmol.atomdata.AtomData
- atomRadius - Variable in class org.jmol.jvxl.readers.AtomDataReader
- atomRadiusData - Variable in class org.jmol.jvxl.readers.Parameters
- atomResnos - Variable in class org.jmol.modelset.AtomCollection
- atoms - Variable in class org.jmol.adapter.readers.cif.CifReader
- atoms - Variable in class org.jmol.adapter.readers.cif.MSRdr
- atoms - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
list of TOPOL_ATOM loop data
- atoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- atoms - Variable in class org.jmol.adapter.smarter.AtomIterator
- atoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atoms - Variable in class org.jmol.atomdata.AtomData
- atoms - Variable in class org.jmol.minimize.Minimizer
- atoms - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- atoms - Variable in class org.jmol.modelset.MeasurementData
- atoms - Variable in class org.jmol.quantum.NMRNoeMatrix
- atoms - Static variable in class org.jmol.script.T
- atoms - Variable in class org.jmol.shapebio.BioShapeCollection
- atoms - Variable in class org.jmol.shapespecial.Dipole
- atoms - Variable in class org.jmol.shapesurface.Contact
- atoms - Variable in class org.jmol.smiles.SmilesGenerator
- atoms - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
the substituents -- up to four supported here at this time
- atoms - Variable in class org.jmol.symmetry.CIPData
-
all application atoms referenced by bit sets
- atoms - Variable in class org.jmol.symmetry.SpaceGroupFinder
- atoms - Variable in class org.jmol.symmetry.UnitCellIterator
- atomSeqIDs - Variable in class org.jmol.modelset.AtomCollection
- atomSerial - Variable in class org.jmol.adapter.smarter.Atom
- atomSerials - Variable in class org.jmol.modelset.AtomCollection
- AtomSet(int, String) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
- atomSetAtomCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomSetAtomIndexes - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomSetAuxiliaryInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomSetBondCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomSetChooser - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- AtomSetChooser - Class in org.openscience.jmol.app.jmolpanel
-
A JFrame that allows for choosing an Atomset to view.
- AtomSetChooser(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- AtomSetChooser.AtomSet - Class in org.openscience.jmol.app.jmolpanel
-
Objects in the AtomSetChooser tree
- atomsetchooserAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- AtomSetChooserAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.AtomSetChooserAction
- AtomSetChooserAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
- atomSetCollection - Variable in class org.jmol.io.DOMReader
- atomSetCollection - Variable in class org.jmol.io.FileReader
- atomSetCollection - Variable in class org.jmol.io.FilesReader
- AtomSetCollection - Class in org.jmol.adapter.smarter
- AtomSetCollection(String, AtomSetCollectionReader, AtomSetCollection[], Lst<?>) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
- AtomSetCollectionReader - Class in org.jmol.adapter.smarter
- AtomSetCollectionReader() - Constructor for class org.jmol.adapter.smarter.AtomSetCollectionReader
- atomSetCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomSetIndex - Variable in class org.jmol.adapter.smarter.Atom
- atomSetIndex - Variable in class org.jmol.adapter.smarter.AtomSetObject
- atomSetIndex - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
-
The index of that AtomSet
- atomSetInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomSetName - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
-
The name of the AtomSet
- atomSetNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- AtomSetObject - Class in org.jmol.adapter.smarter
- AtomSetObject() - Constructor for class org.jmol.adapter.smarter.AtomSetObject
- AtomShape - Class in org.jmol.shape
- AtomShape() - Constructor for class org.jmol.shape.AtomShape
- atomSite - Variable in class org.jmol.adapter.smarter.Atom
- atomSite - Variable in class org.jmol.modelset.Atom
- atomSite - Variable in class org.jmol.smiles.SmilesAtom
- atomsLabeledInline - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- atomsMax - Variable in class org.jmol.adapter.writers.CMLWriter
- AtomSorter() - Constructor for class org.jmol.modelset.AtomCollection.AtomSorter
- atomStartEnd - Variable in class org.jmol.adapter.smarter.Structure
- atomStr(byte[], int, int, String[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- atomSym - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- atomSymbolicMap - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- atomSymmetry - Variable in class org.jmol.modelset.Atom
- atomSyms - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- atomTensorList - Variable in class org.jmol.modelset.AtomCollection
- atomTensors - Variable in class org.jmol.modelset.AtomCollection
- atomTest - Static variable in class org.jmol.symmetry.SymmetryOperation
- atomtype - Static variable in class org.jmol.script.T
- atomType - Variable in class org.jmol.smiles.SmilesAtom
- AtomType - Class in org.jmol.minimize.forcefield
- AtomType(int, int, int, float, int, String, String) - Constructor for class org.jmol.minimize.forcefield.AtomType
- atomTypeFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
- atomTypeLen - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- atomTypePt0 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- atomtypes - Static variable in class org.jmol.script.T
- atomTypes - Variable in class org.jmol.adapter.readers.more.ForceFieldReader
- atomTypes - Variable in class org.jmol.adapter.readers.more.MdTopReader
- atomTypes - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
- atomTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- atomTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- atomTypes - Variable in class org.jmol.modelset.AtomCollection
- atomTypes - Variable in class org.jmol.viewer.GlobalSettings
- atomx - Static variable in class org.jmol.script.T
- atomX - Variable in class org.jmol.modelset.Text
- atomXyzTruncated - Variable in class org.jmol.jvxl.readers.AtomDataReader
- atomy - Static variable in class org.jmol.script.T
- atomY - Variable in class org.jmol.modelset.Text
- atomz - Static variable in class org.jmol.script.T
- atomZ - Variable in class org.jmol.modelset.Text
- ATROPIC_SWITCH - Static variable in class org.jmol.smiles.SmilesSearch
- ATROPISOMER - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- ATROPISOMER_SHIFT - Static variable in class org.jmol.util.Edge
- atropKeys - Variable in class org.jmol.smiles.SmilesSearch
- atropType - Variable in class org.jmol.smiles.SmilesBond
- attEcho - Variable in class org.jmol.console.ScriptEditor
- attEcho - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- attError - Variable in class org.jmol.console.ScriptEditor
- attError - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- attHighlight - Variable in class org.jmol.console.ScriptEditor
- attPrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- attribs - Variable in class org.jmol.adapter.readers.xml.XmlReader
- atts - Variable in class org.jmol.adapter.readers.xml.XmlReader
- attStatus - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- attUserInput - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- audio - Static variable in class org.jmol.script.T
- AUDIO - Enum constant in enum org.jmol.c.CBK
- audios - Variable in class org.jmol.viewer.StatusManager
- auditBlockCode - Variable in class org.jmol.adapter.readers.cif.CifReader
- augmentGroup3List(SC, String, boolean) - Method in class org.jmol.popup.JmolPopup
- AUTH_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- AUTH_ATOM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- AUTH_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- AUTH_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- auto - Static variable in class org.jmol.script.T
- AUTO - Enum constant in enum org.jmol.c.VDW
- AUTO_BABEL - Enum constant in enum org.jmol.c.VDW
- auto_classify_atoms - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_color_next - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_copy_images - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_defer_atom_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_defer_builds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_dss - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_hide_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_indicate_flags - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- AUTO_JMOL - Enum constant in enum org.jmol.c.VDW
- auto_number_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- AUTO_RASMOL - Enum constant in enum org.jmol.c.VDW
- auto_remove_hydrogens - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_rename_duplicate_objects - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_sculpt - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_show_lines - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_show_nonbonded - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_show_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_show_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- auto_zoom - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- autoAddImplicitH - Variable in class org.jmol.smiles.SmilesSearch
- autoAnimationDelay - Variable in class org.openscience.jmol.app.JmolApp
- autobond - Static variable in class org.jmol.script.T
- autoBond - Variable in class org.jmol.modelkit.ModelKit
-
set to true for proximity-based autobonding (prior to 14.32.4/15.2.4 the default was TRUE
- autoBond - Variable in class org.jmol.viewer.GlobalSettings
- autoBond - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- autoBond_Pre_11_9_24(BS, BS, BS, BS, short) - Method in class org.jmol.modelset.ModelSet
- autoBondBs4(BS, BS, BS, BS, short, boolean, SB) - Method in class org.jmol.modelset.ModelSet
- autoBondCheck(Atom, Atom, int, short, BS) - Method in class org.jmol.modelset.ModelSet
- autoCalculate(int, String) - Method in class org.jmol.viewer.Viewer
- autoClose - Variable in class org.jmol.util.JmolAudio
- autoclose_dialogs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- autoExit - Variable in class org.jmol.viewer.Viewer
- autofps - Static variable in class org.jmol.script.T
- autoFps - Variable in class org.jmol.viewer.GlobalSettings
- autoHbond(BS, BS, boolean) - Method in class org.jmol.modelset.ModelSet
-
a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.
- autoHbond(BS, BS, boolean) - Method in class org.jmol.viewer.Viewer
- autoplaymovie - Static variable in class org.jmol.script.T
- autoplayMovie - Variable in class org.jmol.viewer.GlobalSettings
- autoScaleOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
- autoScrolls - Variable in class org.jmol.awtjs.swing.JComponent
- auxChirality - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
auxiliary chirality as determined in createAuxiliaryRule4Data; possibilities include R/S, r/s, M/P, m/p, C/T (but not c/t), or ~ (ASCII 126, no stereochemistry); for sorting purposes C=M=R < p=r=s < ~
- auxEZ - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
auxiliary chirality E/Z for this atom node
- auxiliaryInfo - Variable in class org.jmol.modelset.Model
- auxSort(int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Sort by a given rule, preserving currentRule, which could be 4 or 5
- average - Static variable in class org.jmol.script.T
- average(P3[]) - Method in class org.jmol.util.BZone
- AviCreator - Class in org.jmol.image
- AviCreator() - Constructor for class org.jmol.image.AviCreator
- AwtClipboard - Class in org.jmol.awt
-
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
- AwtClipboard(Object) - Constructor for class org.jmol.awt.AwtClipboard
- AwtColor - Class in org.jmol.awt
- AwtColor(int) - Constructor for class org.jmol.awt.AwtColor
- AwtColor(int, int, int) - Constructor for class org.jmol.awt.AwtColor
- AwtColor(int, int, int, int) - Constructor for class org.jmol.awt.AwtColor
- AwtFile - Class in org.jmol.awt
-
a subclass of File allowing extension to JavaScript private to org.jmol.awt
- AwtFile(String) - Constructor for class org.jmol.awt.AwtFile
- AwtFont - Class in org.jmol.awt
-
methods required by Jmol that access java.awt.Font private to org.jmol.awt
- AwtFont() - Constructor for class org.jmol.awt.AwtFont
- AwtG2D - Class in org.jmol.awt
-
generic 2D drawing methods -- AWT version
- AwtG2D() - Constructor for class org.jmol.awt.AwtG2D
- AwtJmolPopup - Class in org.jmol.awt
- AwtJmolPopup() - Constructor for class org.jmol.awt.AwtJmolPopup
- AwtModelKitPopup - Class in org.jmol.awt
- AwtModelKitPopup() - Constructor for class org.jmol.awt.AwtModelKitPopup
- AwtPopupHelper - Class in org.jmol.awt
-
all popup-related awt/swing class references are in this file.
- AwtPopupHelper(GenericPopup) - Constructor for class org.jmol.awt.AwtPopupHelper
- AwtSwingComponent - Class in org.jmol.awt
-
A javax.swing implementation of SwingComponent that mirrors org.jmol.awtjs.swing for compatibility with compilation with java2script.
- AwtSwingComponent() - Constructor for class org.jmol.awt.AwtSwingComponent
- ax - Variable in class org.jmol.g3d.TriangleRenderer
- axE - Variable in class org.jmol.g3d.TriangleRenderer
- axes - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- axes - Static variable in class org.jmol.script.T
- axes - Variable in class org.jmol.shapespecial.DrawMesh
- axes - Variable in class org.jmol.symmetry.PointGroup
- Axes - Class in org.jmol.shape
- Axes() - Constructor for class org.jmol.shape.Axes
- AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
- axes2 - Variable in class org.jmol.shape.Axes
- axesAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- axesAreTainted - Variable in class org.jmol.viewer.Viewer
- axescolor - Static variable in class org.jmol.script.T
- axesLengths - Variable in class org.jmol.util.ModulationSet
-
unit cell axes -- used in Modulation for calculating magnetic modulations
- axesMaxN - Static variable in class org.jmol.symmetry.PointGroup
- axesmode - Static variable in class org.jmol.script.T
- axesMode - Variable in class org.jmol.viewer.GlobalSettings
- axesmolecular - Static variable in class org.jmol.script.T
- axesoffset - Static variable in class org.jmol.script.T
- axesOffset - Variable in class org.jmol.viewer.GlobalSettings
- axesorientationrasmol - Static variable in class org.jmol.script.T
- axesOrientationRasmol - Variable in class org.jmol.viewer.GlobalSettings
- axesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- AxesRenderer - Class in org.jmol.render
- AxesRenderer() - Constructor for class org.jmol.render.AxesRenderer
- axesscale - Static variable in class org.jmol.script.T
- axesScale - Variable in class org.jmol.viewer.GlobalSettings
- axesTypes - Static variable in class org.jmol.render.AxesRenderer
- axesunitcell - Static variable in class org.jmol.script.T
- axeswindow - Static variable in class org.jmol.script.T
- axis - Variable in class org.jmol.navigate.Navigator
- axis - Static variable in class org.jmol.script.T
- axis - Variable in class org.jmol.shapespecial.DrawMesh
- axis - Variable in class org.jmol.util.Modulation
- axis1color - Static variable in class org.jmol.script.T
- axis2color - Static variable in class org.jmol.script.T
- axis3color - Static variable in class org.jmol.script.T
- axisA - Variable in class org.jmol.modelsetbio.ProteinStructure
- axisangle - Static variable in class org.jmol.script.T
- axisangleT - Variable in class org.jmol.viewer.TransformManager
- axisB - Variable in class org.jmol.modelsetbio.ProteinStructure
- axisChoice - Variable in class org.jmol.symmetry.SpaceGroup
- axisLabels - Static variable in class org.jmol.render.AxesRenderer
- axisNX - Static variable in class org.jmol.viewer.JC
- axisNY - Static variable in class org.jmol.viewer.JC
- axisNZ - Static variable in class org.jmol.viewer.JC
- axisPoints - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- axisPoints - Variable in class org.jmol.shape.Axes
-
[x, y, z, -x, -y, -z] or [a, b, c, -a, -b, -c]
- axisType - Variable in class org.jmol.shape.Axes
- axisType - Variable in class org.jmol.symmetry.HallRotationTerm
- axisUnitVector - Variable in class org.jmol.modelsetbio.ProteinStructure
- axisX - Static variable in class org.jmol.viewer.JC
- axisXY - Variable in class org.jmol.shape.Axes
- axisY - Static variable in class org.jmol.viewer.JC
- axisZ - Static variable in class org.jmol.viewer.JC
- axW - Variable in class org.jmol.g3d.TriangleRenderer
- ay - Variable in class org.jmol.g3d.TriangleRenderer
- az - Variable in class org.jmol.g3d.TriangleRenderer
- azE - Variable in class org.jmol.g3d.TriangleRenderer
- azW - Variable in class org.jmol.g3d.TriangleRenderer
B
- b - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
- b - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- b - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- b - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- b - Variable in class org.jmol.dssx.Bridge
- b - Variable in class org.jmol.g3d.PrecisionRenderer
- b - Variable in class org.jmol.jvxl.readers.MapFileReader
- b - Variable in class org.jmol.minimize.forcefield.Calculation
- b - Variable in class org.jmol.render.SticksRenderer
- b - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- b - Variable in class org.jmol.util.Rgb16
- b - Variable in class org.jmol.util.SimpleUnitCell
- b - Variable in class org.jmol.viewer.ActionManager
- b_ - Variable in class org.jmol.util.SimpleUnitCell
- B_ISO - Static variable in class org.jmol.adapter.readers.cif.CifReader
- B_WINS - Static variable in class org.jmol.symmetry.CIPChirality
- b0 - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
base bond index to be added to any bond bitsets
- b1 - Variable in class org.jmol.g3d.HermiteRenderer
- b2 - Variable in class org.jmol.g3d.HermiteRenderer
- b8 - Static variable in class org.jmol.jvxl.readers.MrcBinaryReader
- babel - Static variable in class org.jmol.script.T
- BABEL - Enum constant in enum org.jmol.c.VDW
- babel21 - Static variable in class org.jmol.script.T
- BABEL21 - Enum constant in enum org.jmol.c.VDW
- back - Static variable in class org.jmol.script.T
- backbone - Static variable in class org.jmol.script.T
- Backbone - Class in org.jmol.shapebio
- Backbone() - Constructor for class org.jmol.shapebio.Backbone
- backboneBlockVis - Variable in class org.jmol.modelsetbio.Monomer
- backbonePt - Variable in class org.jmol.renderbio.NucleicRenderer
- BackboneRenderer - Class in org.jmol.renderbio
- BackboneRenderer() - Constructor for class org.jmol.renderbio.BackboneRenderer
- backboneScreen - Variable in class org.jmol.renderbio.NucleicRenderer
- backface_cull - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- background - Static variable in class org.jmol.script.T
- backgroundColix - Variable in class org.jmol.export.___Exporter
- backgroundColix - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- backgroundcolor - Static variable in class org.jmol.script.T
- BackgroundColorWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
- backgroundImage - Variable in class org.jmol.util.GData
- backgroundImageFileName - Variable in class org.jmol.viewer.GlobalSettings
- backgroundmodel - Static variable in class org.jmol.script.T
- backgroundModelIndex - Variable in class org.jmol.viewer.AnimationManager
- backgroundTransparent - Static variable in class org.jmol.g3d.Platform3D
- backlit - Static variable in class org.jmol.script.T
- backshell - Static variable in class org.jmol.script.T
- bad() - Method in class org.jmol.script.ScriptError
- balls - Static variable in class org.jmol.script.T
- Balls - Class in org.jmol.shape
- Balls() - Constructor for class org.jmol.shape.Balls
- BallsRenderer - Class in org.jmol.render
- BallsRenderer() - Constructor for class org.jmol.render.BallsRenderer
- bannerFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- BannerFrame - Class in org.openscience.jmol.app.jsonkiosk
-
A simple class that throws up a white rectangle that has a single centered label.
- BannerFrame(int, int) - Constructor for class org.openscience.jmol.app.jsonkiosk.BannerFrame
- bannerLabel - Variable in class org.openscience.jmol.app.jsonkiosk.BannerFrame
- barb - Static variable in class org.jmol.script.T
- barDistance - Variable in class org.jmol.modelset.Text
- barPixels - Variable in class org.jmol.modelset.Text
- barPixelsXYZ - Variable in class org.jmol.modelset.Text
- barray - Static variable in class org.jmol.script.T
- baseAtomIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- baseAtomIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
first atom index for this collection, current modelset.ac
- baseAtomIndex - Variable in class org.jmol.modelset.ModelLoader
- baseBondIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- baseBondIndex - Variable in class org.jmol.modelsetbio.BioResolver
- baseCenter - Variable in class org.jmol.modelsetbio.NucleicMonomer
- baseColor - Variable in class org.jmol.jvxl.data.JvxlData
- baseFont3d - Variable in class org.jmol.shape.Frank
- baseGroupIndex - Variable in class org.jmol.modelset.ModelLoader
- baseIndex - Variable in class org.jmol.quantum.NMRNoeMatrix
-
first index for this frame
- basemodel - Static variable in class org.jmol.script.T
- baseModel - Variable in class org.jmol.jsv.JDXMOLParser
- baseModelCount - Variable in class org.jmol.modelset.ModelLoader
- baseModelIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- baseModelIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- baseModelIndex - Variable in class org.jmol.modelset.ModelLoader
- basepair - Static variable in class org.jmol.script.T
- BasePair - Class in org.jmol.modelsetbio
- BasePair() - Constructor for class org.jmol.modelsetbio.BasePair
- basePt - Variable in class org.jmol.renderbio.NucleicRenderer
- baseScreen - Variable in class org.jmol.renderbio.NucleicRenderer
- baseStrandOffset - Variable in class org.jmol.renderbio.StrandsRenderer
- baseSymmetry - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- baseSymmetryAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- baseTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
- baseUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- BASIS_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- basisAtoms - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- basisBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- basisData - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- BasisFunctionReader - Class in org.jmol.adapter.readers.quantum
- BasisFunctionReader() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader
- BasisFunctionReader.MOEnergySorter - Class in org.jmol.adapter.readers.quantum
- basisFunctions - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
- basisId - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- basisID - Variable in class org.jmol.adapter.writers.QCJSONWriter
- basisIds - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- batch_prefix - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- BATOM1 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- BATOM2 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bb - Variable in class org.jmol.g3d.TriangleRenderer
- Bbcage - Class in org.jmol.shape
- Bbcage() - Constructor for class org.jmol.shape.Bbcage
- BbcageRenderer - Class in org.jmol.render
- BbcageRenderer() - Constructor for class org.jmol.render.BbcageRenderer
- bbcageTickEdges - Static variable in class org.jmol.util.BoxInfo
- bbCenter - Variable in class org.jmol.util.BoxInfo
- bbCorner0 - Variable in class org.jmol.util.BoxInfo
- bbCorner1 - Variable in class org.jmol.util.BoxInfo
- bboxAtoms - Variable in class org.jmol.modelset.ModelSet
- bboxModels - Variable in class org.jmol.modelset.ModelSet
- bButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- bbVector - Variable in class org.jmol.util.BoxInfo
- bbVertices - Variable in class org.jmol.util.BoxInfo
-
The ordering of these vertices is given below.
- bc0 - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- BCifDensityReader - Class in org.jmol.jvxl.readers
-
Binary CIF density reader.
- BCifDensityReader() - Constructor for class org.jmol.jvxl.readers.BCifDensityReader
- bdSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- beenSliced - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- BEG_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- BEG_INS_CODE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- BEG_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- BEGIN - Static variable in class org.jmol.shapecgo.CGOMesh
- beginRendering(boolean, boolean) - Method in class org.jmol.viewer.Viewer
- beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
- beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.util.GData
- best - Static variable in class org.jmol.script.T
- beta - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- beta - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- beta - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- beta - Variable in class org.jmol.jvxl.readers.MapFileReader
- beta - Static variable in class org.jmol.modelsetbio.AminoMonomer
- beta - Static variable in class org.jmol.script.T
- beta - Variable in class org.jmol.util.SimpleUnitCell
- BETA_SHEET - Enum constant in enum org.jmol.modelsetbio.AlphaPolymer.Code
- betaOnly - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- betas - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- bfactor - Variable in class org.jmol.adapter.smarter.Atom
- BFACTOR - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bfactor100Hi - Variable in class org.jmol.modelset.AtomCollection
- bfactor100Lo - Variable in class org.jmol.modelset.AtomCollection
- bfactor100s - Variable in class org.jmol.modelset.AtomCollection
- bfactorMax - Variable in class org.jmol.shapebio.BioShape
- bfactorMin - Variable in class org.jmol.shapebio.BioShape
- BFXN_ANGL - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- bg_gradient - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bg_image_filename - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bg_image_linear - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bg_image_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bg_image_tilesize - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bg_rgb - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bg_rgb_bottom - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bg_rgb_top - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bgargb - Variable in class org.jmol.g3d.TextString
- bgcolix - Variable in class org.jmol.modelset.Text
- bgcolix - Variable in class org.jmol.render.LabelsRenderer
- bgcolixes - Variable in class org.jmol.shape.Labels
- bgcolor - Variable in class org.jmol.awtjs.swing.Component
- bgcolor - Variable in class org.jmol.g3d.Pixelator
- bgcolor - Variable in class org.jmol.util.GData
- bgColor - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- bGlobals - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- bgRgb - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bgRGB - Variable in class org.jmol.g3d.PixelatorShaded
- BGYOR - Static variable in class org.jmol.util.ColorEncoder
- BHASSETTING - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- BID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bilbaoContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- BilbaoReader - Class in org.jmol.adapter.readers.xtal
-
Bilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML.
- BilbaoReader() - Constructor for class org.jmol.adapter.readers.xtal.BilbaoReader
- bin - Static variable in class org.jmol.script.T
- binary - Static variable in class org.jmol.script.T
- BinaryDcdReader - Class in org.jmol.adapter.readers.more
-
DCD binary trajectory file reader.
- BinaryDcdReader() - Constructor for class org.jmol.adapter.readers.more.BinaryDcdReader
- binarydoc - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
- binaryDoc - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- binaryDoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- binaryOp(T, SV, SV) - Method in class org.jmol.script.ScriptMathProcessor
- bind - Static variable in class org.jmol.script.T
- bind(String, String) - Method in class org.jmol.viewer.ActionManager
- bindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
- bindAction(String, String) - Method in class org.jmol.viewer.Viewer
- Binding - Class in org.jmol.viewer.binding
- Binding() - Constructor for class org.jmol.viewer.binding.Binding
- bindings - Variable in class org.jmol.viewer.binding.Binding
- bindName(int, String) - Method in class org.jmol.viewer.binding.Binding
- BINFLOAT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- BINGET - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- BININT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- BININT1 - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- BININT2 - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- BINPUT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- BINSTRING - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- BINUNICODE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- bioAtomName - Variable in class org.jmol.smiles.SmilesAtom
- BioExt - Class in org.jmol.modelsetbio
- BioExt() - Constructor for class org.jmol.modelsetbio.BioExt
- BioMeshRenderer - Class in org.jmol.renderbio
- BioMeshRenderer() - Constructor for class org.jmol.renderbio.BioMeshRenderer
- BioModel - Class in org.jmol.modelsetbio
- BioModel(ModelSet, int, int, String, Properties, Map<String, Object>) - Constructor for class org.jmol.modelsetbio.BioModel
- bioModelset - Variable in class org.jmol.modelset.AtomCollection
-
If any model in the collection is a BioModel, then it is also indicated here as a "bioModelset", meaning
- BioModelSet - Class in org.jmol.modelsetbio
- BioModelSet() - Constructor for class org.jmol.modelsetbio.BioModelSet
- biomtChainAtomCounts - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- bioPolymer - Variable in class org.jmol.modelsetbio.Monomer
- bioPolymer - Variable in class org.jmol.shapebio.BioShape
- BioPolymer - Class in org.jmol.modelsetbio
-
A "BioPolymer" is a constructed set of contiguous (probably connected) "Monomers", which may be one of Alpha (Calpha atoms), Amino (Calpha + backbone), Phosphorus (P atoms), Nucleic (DNA/RNA), or Carbohydrate.
- BioPolymer() - Constructor for class org.jmol.modelsetbio.BioPolymer
- bioPolymerCount - Variable in class org.jmol.dssx.DSSP
- bioPolymerCount - Variable in class org.jmol.modelsetbio.BioModel
- bioPolymerIndexInModel - Variable in class org.jmol.modelsetbio.BioPolymer
- bioPolymers - Variable in class org.jmol.dssx.DSSP
- bioPolymers - Variable in class org.jmol.modelsetbio.BioModel
- BioResolver - Class in org.jmol.modelsetbio
-
a class used by ModelLoader to handle all loading of operations specific to PDB/mmCIF files.
- BioResolver() - Constructor for class org.jmol.modelsetbio.BioResolver
- bioShape - Variable in class org.jmol.renderbio.BioShapeRenderer
- BioShape - Class in org.jmol.shapebio
- BioShape(BioShapeCollection, int, BioPolymer) - Constructor for class org.jmol.shapebio.BioShape
- BioShapeCollection - Class in org.jmol.shapebio
-
Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape for each BioPolymer in the model set.
- BioShapeCollection() - Constructor for class org.jmol.shapebio.BioShapeCollection
- BioShapeRenderer - Class in org.jmol.renderbio
- BioShapeRenderer() - Constructor for class org.jmol.renderbio.BioShapeRenderer
- bioShapes - Variable in class org.jmol.shapebio.BioShapeCollection
- biosymmetry - Variable in class org.jmol.modelset.Model
- biosymmetryCount - Variable in class org.jmol.modelset.Model
- bioType - Variable in class org.jmol.smiles.SmilesAtom
- bioType - Variable in class org.jmol.smiles.SmilesParser
- BIRTH - Static variable in class org.jmol.multitouch.ActionManagerMT
- bitset - Static variable in class org.jmol.script.T
- bitSetForModelFileNumber(int) - Method in class org.jmol.script.ScriptExpr
- BLACK - Static variable in class org.jmol.util.C
- BLOCK_ATOMS - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
- BLOCK_CALC - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
- BLOCK_MAGRES - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
- BLOCK_NEW - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
- BLOCK_NONE - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
- blockCubeData - Variable in class org.jmol.jvxl.readers.Parameters
- blockdata - Static variable in class org.jmol.script.T
- blockHeight - Variable in class org.jmol.renderbio.NucleicRenderer
- BLUE - Static variable in class org.jmol.util.C
- bnd(int, int...) - Method in class org.jmol.viewer.ActionManager
- bo - Variable in class org.jmol.modelset.BondCollection
- bohr_per_angstrom - Static variable in class org.jmol.quantum.QuantumCalculation
- bond - Variable in class org.jmol.adapter.readers.xml.XmlReader
- bond - Variable in class org.jmol.adapter.smarter.BondIterator
- bond - Variable in class org.jmol.render.SticksRenderer
- bond - Variable in class org.jmol.shapespecial.Dipole
- Bond - Class in org.jmol.adapter.smarter
- Bond - Class in org.jmol.modelset
- Bond() - Constructor for class org.jmol.adapter.smarter.Bond
- Bond(int, int, int) - Constructor for class org.jmol.adapter.smarter.Bond
- Bond(Atom, Atom, int, short, short) - Constructor for class org.jmol.modelset.Bond
- BOND - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- BOND_AROMATIC - Static variable in class org.jmol.util.Edge
- BOND_AROMATIC_DOUBLE - Static variable in class org.jmol.util.Edge
- BOND_AROMATIC_MASK - Static variable in class org.jmol.util.Edge
- BOND_AROMATIC_SINGLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_DOUBLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_MASK - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_QUADRUPLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_QUINTUPLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_sextuple - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_SINGLE - Static variable in class org.jmol.util.Edge
- BOND_COVALENT_TRIPLE - Static variable in class org.jmol.util.Edge
- BOND_GROWTH_INCREMENT - Static variable in class org.jmol.modelset.BondCollection
- BOND_H_CALC - Static variable in class org.jmol.util.Edge
- BOND_H_CALC_MASK - Static variable in class org.jmol.util.Edge
- BOND_H_MINUS_3 - Static variable in class org.jmol.util.Edge
- BOND_H_MINUS_4 - Static variable in class org.jmol.util.Edge
- BOND_H_NUCLEOTIDE - Static variable in class org.jmol.util.Edge
- BOND_H_PLUS_2 - Static variable in class org.jmol.util.Edge
- BOND_H_PLUS_3 - Static variable in class org.jmol.util.Edge
- BOND_H_PLUS_4 - Static variable in class org.jmol.util.Edge
- BOND_H_PLUS_5 - Static variable in class org.jmol.util.Edge
- BOND_H_REGULAR - Static variable in class org.jmol.util.Edge
- BOND_HBOND_SHIFT - Static variable in class org.jmol.util.Edge
- BOND_HYDROGEN_MASK - Static variable in class org.jmol.util.Edge
- BOND_MODE - Static variable in class org.jmol.modelkit.ModelKit
- BOND_NEW - Static variable in class org.jmol.util.Edge
- BOND_ORDER_ANY - Static variable in class org.jmol.util.Edge
- BOND_ORDER_NULL - Static variable in class org.jmol.util.Edge
- BOND_ORDER_UNSPECIFIED - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL_MASK - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL01 - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL12 - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL23 - Static variable in class org.jmol.util.Edge
- BOND_PARTIAL32 - Static variable in class org.jmol.util.Edge
- BOND_PYMOL_MULT - Static variable in class org.jmol.util.Edge
- BOND_PYMOL_NOMULT - Static variable in class org.jmol.util.Edge
- BOND_RENDER_SINGLE - Static variable in class org.jmol.util.Edge
-
Extended Bond Definition Types Originally these were short 16-bit values
- BOND_STEREO_FAR - Static variable in class org.jmol.util.Edge
- BOND_STEREO_MASK - Static variable in class org.jmol.util.Edge
- BOND_STEREO_NEAR - Static variable in class org.jmol.util.Edge
- BOND_STRUT - Static variable in class org.jmol.util.Edge
- BOND_SULFUR_MASK - Static variable in class org.jmol.util.Edge
- bondArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- bondAtomIndex1 - Variable in class org.jmol.modelkit.ModelKit
- bondAtomIndex2 - Variable in class org.jmol.modelkit.ModelKit
- bondAtoms(Object, Object, short) - Method in class org.jmol.modelset.ModelLoader
- bondAtoms(Atom, Atom, int, short, BS, float, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
- bondCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- bondCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
- BondCollection - Class in org.jmol.modelset
- BondCollection() - Constructor for class org.jmol.modelset.BondCollection
- bondcount - Static variable in class org.jmol.script.T
- bondCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- bondCount - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
- bondCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- bondCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- bondCount - Variable in class org.jmol.adapter.smarter.BondIterator
- bondCount - Variable in class org.jmol.minimize.forcefield.Calculations
- bondCount - Variable in class org.jmol.minimize.Minimizer
- bondCount - Variable in class org.jmol.modelset.BondCollection
- bondCount - Variable in class org.jmol.modelset.BondIteratorSelected
- bondCount - Variable in class org.jmol.modelset.Model
- bondCount - Variable in class org.jmol.smiles.SmilesAtom
- bondCount - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
true atom covalent bond count; cached for better performance
- bondCount - Variable in class org.jmol.viewer.Connections
- bondCount0 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- bondData - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- bondData - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
- bondDirectionPaired - Variable in class org.jmol.smiles.SmilesParser
- bonded - Static variable in class org.jmol.script.T
- BONDED - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bondedAtoms - Variable in class org.jmol.minimize.MinAtom
- bondedOnly - Variable in class org.jmol.shapespecial.Polyhedra
- bondFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- bondFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- bondHoverLabel - Variable in class org.jmol.modelkit.ModelKit
- bondIndex - Variable in class org.jmol.modelkit.ModelKit
- bondIndex0 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- BONDING - Enum constant in enum org.jmol.c.VDW
- bonding_vdw_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- bondingRadii - Variable in class org.jmol.modelset.AtomCollection
- bondingradius - Static variable in class org.jmol.script.T
- bondingRadius - Variable in class org.jmol.adapter.smarter.Atom
- bondingversion - Static variable in class org.jmol.script.T
- bondingVersion - Static variable in class org.jmol.util.Elements
- bondingVersion - Variable in class org.jmol.viewer.GlobalSettings
- bondingVersion - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- BondIterator - Class in org.jmol.adapter.smarter
- BondIterator - Interface in org.jmol.modelset
- BondIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.BondIterator
- BondIteratorSelected - Class in org.jmol.modelset
- BondIteratorSelected(Bond[], int, int, BS, boolean) - Constructor for class org.jmol.modelset.BondIteratorSelected
- bondmode - Static variable in class org.jmol.script.T
- bondmodeor - Static variable in class org.jmol.script.T
- bondModeOr - Variable in class org.jmol.viewer.GlobalSettings
- bondMutually(Atom, Atom, int, short, float) - Method in class org.jmol.modelset.BondCollection
- bondorder - Static variable in class org.jmol.script.T
- bondOrder - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- bondOrder - Variable in class org.jmol.render.SticksRenderer
- bondPicked(int) - Method in class org.jmol.viewer.ActionManager
- bondpicking - Static variable in class org.jmol.script.T
- bondPicking - Variable in class org.jmol.viewer.GlobalSettings
- bondPickingMode - Variable in class org.jmol.viewer.ActionManager
- bondradiusmilliangstroms - Static variable in class org.jmol.script.T
- bondRadiusMilliAngstroms - Variable in class org.jmol.viewer.GlobalSettings
- bondRotationCheckBox - Variable in class org.jmol.modelkit.ModelKitPopup
- bondRotationName - Variable in class org.jmol.modelkit.ModelKit
- bondRotationName - Variable in class org.jmol.modelkit.ModelKitPopup
- bonds - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- bonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- bonds - Variable in class org.jmol.adapter.smarter.BondIterator
- bonds - Variable in class org.jmol.minimize.MinAtom
- bonds - Variable in class org.jmol.minimize.Minimizer
- bonds - Variable in class org.jmol.modelset.Atom
-
MAY BE NULL
- bonds - Variable in class org.jmol.modelset.BondIteratorSelected
- bonds - Static variable in class org.jmol.script.T
- bonds - Variable in class org.jmol.smiles.SmilesAtom
- bondsBackbone - Variable in class org.jmol.render.SticksRenderer
- bondSelectionModeOr - Variable in class org.jmol.modelset.BondIteratorSelected
- bondset - Static variable in class org.jmol.script.T
- BondSet - Class in org.jmol.modelset
- BondSet() - Constructor for class org.jmol.modelset.BondSet
- bondsFound - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- bondsOr - Variable in class org.jmol.smiles.SmilesBond
- bondsPerp - Variable in class org.jmol.render.SticksRenderer
- bondtolerance - Static variable in class org.jmol.script.T
- bondTolerance - Variable in class org.jmol.viewer.GlobalSettings
- bondTolerance - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- bondType - Variable in class org.jmol.modelset.BondIteratorSelected
- bondTypes - Variable in class org.jmol.adapter.readers.cif.CifReader
- BONMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- BOOLEAN_OPTIONS - Static variable in class org.jmol.modelkit.ModelKit
- booleanparam - Static variable in class org.jmol.script.T
- booleanSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- bOptions - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- border - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- BORDER - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- BORDERCOLOR - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
- BorderLayout - Class in org.jmol.awtjs.swing
- BorderLayout() - Constructor for class org.jmol.awtjs.swing.BorderLayout
- BORDERSIZE - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
- bos - Variable in class org.jmol.export._StlExporter
- bottom - Variable in class org.jmol.awtjs.swing.Insets
- bottom - Static variable in class org.jmol.script.T
- bottomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- boundaryPlaneCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- boundbox - Static variable in class org.jmol.script.T
- boundboxAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- boundBoxCenter - Variable in class org.openscience.jmol.app.surfacetool.Slice
- boundboxcolor - Static variable in class org.jmol.script.T
- boundBoxNegCorner - Variable in class org.openscience.jmol.app.surfacetool.Slice
- boundBoxPosCorner - Variable in class org.openscience.jmol.app.surfacetool.Slice
- boundingBox - Variable in class org.jmol.jvxl.data.JvxlData
- boundingBox - Variable in class org.jmol.jvxl.readers.Parameters
- boundingBox - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- Box(String) - Static method in class org.jmol.popup.MainPopupResourceBundle
- boxFaces - Static variable in class org.jmol.renderbio.RocketRenderer
- boxHeight - Variable in class org.jmol.modelset.Text
- boxInfo - Variable in class org.jmol.modelset.ModelSet
- BoxInfo - Class in org.jmol.util
-
The BoxInfo class holds critical information about boundboxes.
- BoxInfo() - Constructor for class org.jmol.util.BoxInfo
- boxVec - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- boxWidth - Variable in class org.jmol.modelset.Text
- boxX - Variable in class org.jmol.modelset.Text
- boxXY - Variable in class org.jmol.modelset.Text
- boxXY - Variable in class org.jmol.render.LabelsRenderer
- boxY - Variable in class org.jmol.modelset.Text
- boxYoff2 - Variable in class org.jmol.modelset.Text
- bps - Variable in class org.jmol.modelsetbio.NucleicMonomer
- br - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
- br - Variable in class org.jmol.jvxl.readers.XmlReader
- braceCount - Variable in class org.jmol.script.ScriptCompiler
- braceCount - Variable in class org.jmol.script.ScriptMathProcessor
- braceCount - Variable in class org.jmol.smiles.SmilesParser
- bracketCount - Variable in class org.jmol.script.ScriptCompiler
- branch - Static variable in class org.jmol.script.T
- branchAtomIndex - Variable in class org.jmol.modelkit.ModelKit
- branchLevel - Variable in class org.jmol.smiles.SmilesParser
- breakAt(int) - Method in class org.jmol.script.ScriptEval
- breakcmd - Static variable in class org.jmol.script.T
- breakOutAtomTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- breakOutBondTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- breakOutTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- breakTie(CIPChirality.CIPAtom, int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Break a tie at any level in the iteration between to atoms that otherwise are the same by sorting their substituents.
- brickLayer - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
- brickLayerByteCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
- brickLayerVoxelCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
- brickRowByteCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
- Bridge - Class in org.jmol.dssx
-
A class for cataloging ladder bridges in a DSSP calculation
- Bridge(Atom, Atom, Map<int[][], Boolean>) - Constructor for class org.jmol.dssx.Bridge
- bridgesA - Variable in class org.jmol.dssx.DSSP
- bridgesP - Variable in class org.jmol.dssx.DSSP
- brillouin - Static variable in class org.jmol.script.T
- bs - Variable in class org.jmol.adapter.writers.PWMATWriter
- bs - Variable in class org.jmol.jvxl.data.MeshData.SSet
- bs - Variable in class org.jmol.smiles.SmilesRingSet
- bs14 - Variable in class org.jmol.minimize.MinAtom
- bsa - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- bsA() - Method in class org.jmol.viewer.Viewer
- bsAdded - Variable in class org.jmol.modelset.Group
- bsAddedHydrogens - Variable in class org.jmol.modelsetbio.BioResolver
- bsAddedMask - Variable in class org.jmol.modelsetbio.BioResolver
- bsAll - Variable in class org.jmol.adapter.smarter.Structure
- bsAll - Variable in class org.jmol.modelset.ModelSet
- bsAllModels - Variable in class org.jmol.shapespecial.Draw
- bsAnions - Static variable in class org.jmol.util.Elements
- bsAromatic - Variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- bsAromatic - Variable in class org.jmol.modelset.BondCollection
- bsAromatic - Variable in class org.jmol.smiles.SmilesGenerator
- bsAromatic - Variable in class org.jmol.smiles.SmilesSearch
- bsAromatic - Variable in class org.jmol.symmetry.CIPData
-
Jmol's definition of aromatic
- bsAromatic5 - Variable in class org.jmol.smiles.SmilesSearch
- bsAromatic6 - Variable in class org.jmol.smiles.SmilesSearch
- bsAromaticDouble - Variable in class org.jmol.modelset.BondCollection
- bsAromaticRings - Variable in class org.jmol.smiles.SmilesSearch
- bsAromaticSingle - Variable in class org.jmol.modelset.BondCollection
- bsAssigned - Variable in class org.jmol.modelsetbio.BioResolver
- bsAsymmetricUnit - Variable in class org.jmol.modelset.Model
-
tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.
- bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
- bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- bsAtomOK - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- bsAtoms - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- bsAtoms - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- bsAtoms - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- bsAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- bsAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsAtoms - Variable in class org.jmol.adapter.smarter.AtomIterator
- bsAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- bsAtoms - Variable in class org.jmol.adapter.smarter.BondIterator
- bsAtoms - Variable in class org.jmol.minimize.Minimizer
- bsAtoms - Variable in class org.jmol.modelset.Model
-
Note that this bitset may or may not include bsAtomsDeleted
- bsAtoms - Variable in class org.jmol.symmetry.CIPData
-
bit set of all atoms to process
- bsAtoms - Variable in class org.jmol.symmetry.PointGroup
- bsAtoms - Variable in class org.jmol.thread.SpinThread
- bsAtoms1 - Variable in class org.jmol.modelset.StateScript
- bsAtoms2 - Variable in class org.jmol.modelset.StateScript
- bsAtomsDeleted - Variable in class org.jmol.modelset.Model
- bsAtomsForHs - Variable in class org.jmol.modelsetbio.BioResolver
- bsAtropisomeric - Variable in class org.jmol.symmetry.CIPData
-
bit set of all biphenyl-like connections "[!H](.t1:-20,20)a{a(.t2:-20,20)-a}a[!H]"
- bsAzacyclic - Variable in class org.jmol.symmetry.CIPData
-
all N atoms that are sp3-hybridized and at small ring fusions
- bsb - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- bsBackbone - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
- bsBad - Variable in class org.jmol.dssx.DSSP
- bsBadIndex - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- bsBasis - Variable in class org.jmol.minimize.Minimizer
- bsBgColixSet - Variable in class org.jmol.shape.Labels
- bsBondDuplicates - Variable in class org.jmol.adapter.readers.cif.CifReader
- bsBonds - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- bsBonds - Variable in class org.jmol.modelset.StateScript
- bsBondsDn - Variable in class org.jmol.smiles.SmilesGenerator
- bsBondsUp - Variable in class org.jmol.smiles.SmilesGenerator
- bsBranches - Variable in class org.jmol.thread.SpinThread
- bsBytesExcluded - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- bsCartoon - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsCarve - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsCations - Static variable in class org.jmol.util.Elements
- bsCheck - Variable in class org.jmol.modelset.Model
- bsCheck - Variable in class org.jmol.smiles.SmilesSearch
- bsClickable - Variable in class org.jmol.modelset.AtomCollection
- bsColixSet - Variable in class org.jmol.shape.Shape
- bsConnected - Variable in class org.jmol.adapter.readers.cif.CifReader
- bsDeleted - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- bsDeleted - Variable in class org.jmol.viewer.SelectionManager
- bsDisplay - Variable in class org.jmol.shape.MeshCollection
- bsDisplay - Variable in class org.jmol.util.MeshSurface
- bsDisplay - Variable in class org.jmol.viewer.AnimationManager
- bsEdgesToCheck - Variable in class org.jmol.smiles.SmilesRing
- bsEnes - Variable in class org.jmol.symmetry.CIPData
-
all sp2-hybridized atoms that are not Kekule-ambiguous
- bsExclude - Variable in class org.jmol.adapter.readers.cif.CifReader
- bsExcluded - Variable in class org.jmol.jvxl.readers.Parameters
- bsExcluded - Variable in class org.jmol.quantum.QuantumCalculation
- bsExcludedPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- bsExcludedTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
- bsExcludedVertices - Variable in class org.jmol.jvxl.calc.MarchingCubes
- bsFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- bsFixed - Variable in class org.jmol.minimize.forcefield.ForceField
- bsFixed - Variable in class org.jmol.minimize.Minimizer
- bsFixed - Variable in class org.jmol.viewer.SelectionManager
- bsFixedDefault - Variable in class org.jmol.minimize.Minimizer
- bsFlat - Variable in class org.jmol.shapespecial.Polyhedron
- bsFontSet - Variable in class org.jmol.shape.Labels
- bsForPass2 - Variable in class org.jmol.render.SticksRenderer
- bsFound - Variable in class org.jmol.smiles.SmilesSearch
- bsFrameOffsets - Variable in class org.jmol.viewer.TransformManager
- bsFree - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
- bsGroupOps - Static variable in class org.jmol.symmetry.SpaceGroupFinder
- bsHandles - Variable in class org.jmol.renderspecial.DrawRenderer
- bsHelixM - Variable in class org.jmol.symmetry.CIPData
-
aromatic atoms at the end of a negative helical turn "A{a}(.t:-10,-40)a(.t:-10,-40)aaa"
- bsHelixP - Variable in class org.jmol.symmetry.CIPData
-
aromatic atoms at the end of a positive helical turn "A{a}(.t:10,40)a(.t:10,40)aaa"
- bsHidden - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsHidden - Variable in class org.jmol.modelset.AtomCollection
- bsHidden - Variable in class org.jmol.viewer.SelectionManager
- bsHighlight - Variable in class org.jmol.modelkit.ModelKit
- bsHighlight - Variable in class org.jmol.shape.Halos
- bsHydrogen - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsIgnore - Variable in class org.jmol.geodesic.EnvelopeCalculation
- bsIgnore - Variable in class org.jmol.jvxl.readers.Parameters
- bsIgnore - Variable in class org.jmol.shapespecial.Dots
- bsIgnored - Variable in class org.jmol.atomdata.AtomData
- bsIgnoreHydrogen - Variable in class org.jmol.smiles.SmilesGenerator
- bsIncludingH - Variable in class org.jmol.smiles.SmilesGenerator
- bsKekuleAmbiguous - Variable in class org.jmol.symmetry.CIPData
-
atoms that need specially-calculated element number in Rule 1a
- bsLabeled - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsLineBonds - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsLocale - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- bsMeshesVisible - Variable in class org.jmol.shapespecial.DrawMesh
- bsMinFixed - Variable in class org.jmol.minimize.Minimizer
- bsModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- bsModels - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
- bsModelsDefined - Variable in class org.jmol.adapter.smarter.StructureIterator
- bsModulated - Variable in class org.jmol.modelset.AtomCollection
- bsMol - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- bsMolecule - Variable in class org.jmol.adapter.readers.cif.CifReader
- bsMolecule - Variable in class org.jmol.shapespecial.Dipole
- bsMolecule - Variable in class org.jmol.symmetry.CIPData
-
atoms in all molecules containing the atoms of interest
- bsMolecules - Variable in class org.jmol.atomdata.AtomData
- bsMyIgnored - Variable in class org.jmol.jvxl.readers.AtomDataReader
- bsMySelected - Variable in class org.jmol.geodesic.EnvelopeCalculation
- bsMySelected - Variable in class org.jmol.jvxl.readers.AtomDataReader
- bsNearby - Variable in class org.jmol.jvxl.readers.AtomDataReader
- bsNeedRule - Variable in class org.jmol.symmetry.CIPChirality
-
set bits RULE_1a - RULE_6 to indicate a need for that rule based on what is in the model
- bsNegativeAromatic - Variable in class org.jmol.symmetry.CIPData
-
[a-]
- bsNonbonded - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsNoSurface - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsNucleic - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsOK - Variable in class org.jmol.quantum.NciCalculation
- bsOn - Variable in class org.jmol.shapespecial.Dots
- bsOpGroups - Static variable in class org.jmol.symmetry.SpaceGroupFinder
- bsOrderSet - Variable in class org.jmol.shape.Sticks
- bsPartialCharges - Variable in class org.jmol.modelset.AtomCollection
- bsPath - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
bitset of indices of the associated atoms in the path to this atom node from the root; used to keep track of the path to this atom in order to prevent infinite cycling; the last atom in the path when cyclic is a duplicate atom.
- bspf - Variable in class org.jmol.modelset.AtomCollection
-
Binary Space Partitioning Forest
- bspf - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- Bspf - Class in org.jmol.bspt
-
A Binary Space Partitioning Forest
- Bspf(int) - Constructor for class org.jmol.bspt.Bspf
- bsPolygons - Variable in class org.jmol.render.MeshRenderer
- bsPolygons - Variable in class org.jmol.shapesurface.PMeshWriter
- bsPolygons - Variable in class org.jmol.util.MeshSurface
- bsPolygonsToExport - Variable in class org.jmol.render.MeshRenderer
- bsPolys - Variable in class org.jmol.shapespecial.Polyhedra
- bspt - Variable in class org.jmol.bspt.CubeIterator
- bspt - Variable in class org.jmol.bspt.Element
- Bspt - Class in org.jmol.bspt
-
a Binary Space Partitioning Tree
- Bspt(int, int) - Constructor for class org.jmol.bspt.Bspt
-
Create a bspt with the specified number of dimensions.
- bspts - Variable in class org.jmol.bspt.Bspf
- bsptsValid - Variable in class org.jmol.bspt.Bspf
- bsr - Variable in class org.jmol.renderbio.BioMeshRenderer
- bsr - Variable in class org.jmol.renderbio.NucleicRenderer
- bsRenderableAtoms - Variable in class org.jmol.viewer.ShapeManager
- bsRenderMesh - Variable in class org.jmol.renderbio.BioMeshRenderer
- bsReturn - Variable in class org.jmol.smiles.SmilesSearch
- bsRingKeys - Variable in class org.jmol.smiles.SmilesGenerator
- bsRotateBranch - Variable in class org.jmol.modelkit.ModelKit
- bsRule6Subs - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
a list of only the undifferentiated ligands in Rule 6 -- root atom only
- bsSelected - Variable in class org.jmol.atomdata.AtomData
- bsSelected - Variable in class org.jmol.jvxl.readers.Parameters
- bsSelected - Variable in class org.jmol.minimize.Minimizer
- bsSelected - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- bsSelected - Variable in class org.jmol.modelset.BondIteratorSelected
- bsSelected - Variable in class org.jmol.quantum.MepCalculation
- bsSelected - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- bsSelected - Variable in class org.jmol.shape.Measures
- bsSelected - Variable in class org.jmol.shapebio.Backbone
- bsSelected - Variable in class org.jmol.shapespecial.Dots
- bsSelected - Variable in class org.jmol.smiles.SmilesGenerator
- bsSelected - Variable in class org.jmol.smiles.SmilesSearch
- bsSelectedAtoms - Variable in class org.jmol.viewer.TransformManager
- bsSelectedCells - Variable in class org.jmol.awtjs.swing.JTable
- bsSelectedMonomers - Variable in class org.jmol.modelsetbio.BioPolymer
- bsSelectedRows - Variable in class org.jmol.awtjs.swing.JTable
- bsSelection - Variable in class org.jmol.viewer.SelectionManager
- bsSelectRange(T, int) - Static method in class org.jmol.script.SV
- bsSelectToken(T) - Static method in class org.jmol.script.SV
- bsSets - Variable in class org.jmol.adapter.readers.cif.CifReader
- bsSizeDefault - Variable in class org.jmol.shape.AtomShape
- bsSizeSet - Variable in class org.jmol.shape.Shape
- bsSlabbedInternal - Variable in class org.jmol.viewer.ShapeManager
- bsSlabDisplay - Variable in class org.jmol.util.MeshSurface
- bsSlabGhost - Variable in class org.jmol.util.MeshSurface
- bsSolvent - Variable in class org.jmol.jvxl.readers.Parameters
- bsStickBonds - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsStructureDefined - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- bsStructuredModels - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- bsStructures - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- bsSubset - Variable in class org.jmol.viewer.SelectionManager
- bsSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
- bsSurface - Variable in class org.jmol.modelset.AtomCollection
- bsSurfaceDone - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- bsSurfacePoints - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- bsSurfaceVoxels - Variable in class org.jmol.jvxl.readers.AtomDataReader
- bsSymmetry - Variable in class org.jmol.adapter.smarter.Atom
- bsSymmetry - Variable in class org.jmol.modelset.ModelSet
- bsTaint - Variable in class org.jmol.minimize.Minimizer
- bsTemp - Variable in class org.jmol.geodesic.EnvelopeCalculation
- bsTemp - Variable in class org.jmol.renderbio.BioMeshRenderer
- bsTemp - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- bsTemp - Variable in class org.jmol.shape.Mesh
- bsTemp - Variable in class org.jmol.smiles.VTemp
- bsTemp - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
used to count the number of priorities
- bsTemp - Variable in class org.jmol.viewer.SelectionManager
- bsToArray(BS) - Method in class org.jmol.scriptext.ScriptExt
- bsToDo - Variable in class org.jmol.smiles.SmilesGenerator
- bsTranslucent - Variable in class org.jmol.render.RepaintManager
- bsUniqueBonds - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- bsUserVdws - Variable in class org.jmol.viewer.Viewer
- BSUtil - Class in org.jmol.util
- BSUtil() - Constructor for class org.jmol.util.BSUtil
- bsValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
- bsVdw - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- bsVdw - Variable in class org.jmol.minimize.MinAtom
- bsVdw - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- bsVertexCount - Variable in class org.jmol.shapespecial.Polyhedra
- bsVertices - Variable in class org.jmol.shapespecial.Polyhedra
- bsVisible - Variable in class org.jmol.modelset.AtomCollection
- bsVisible - Variable in class org.jmol.renderbio.BioShapeRenderer
- bsVisibleModels - Variable in class org.jmol.viewer.AnimationManager
- bsVoxelBitSet - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- bsVoxels - Variable in class org.jmol.jvxl.calc.MarchingCubes
- bsXAromatic - Variable in class org.jmol.symmetry.CIPData
-
excluded aromatics [r5d3n+0,r5d2o+0]
- bTest - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- btnType - Variable in class org.jmol.awtjs.swing.JMenuItem
- btSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- BTYPE - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- BUFF - Static variable in class org.jmol.minimize.forcefield.MMFFESCalc
- buffer - Variable in class org.openscience.jmol.app.InputScannerThread
- bufferedImage - Variable in class org.jmol.g3d.Platform3D
- bufferHeight - Variable in class org.jmol.g3d.Platform3D
- bufferSize - Variable in class org.jmol.g3d.Platform3D
- bufferSize - Variable in class org.jmol.util.GData
- bufferSizeT - Variable in class org.jmol.g3d.Platform3D
- bufferWidth - Variable in class org.jmol.g3d.Platform3D
- bufLen - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- build - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- BUILD - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- buildAdvancedPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- buildAtomsPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- buildBasicPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- buildBondPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- buildBox(P3, V3, V3, V3) - Method in class org.jmol.renderbio.RocketRenderer
- buildButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- buildDispPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- buildFilePanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- buildPolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
- buildScene(String, Lst<Object>, Map<String, Lst<Object>>, Map<String, Lst<Object>>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Build a scene at file reading time.
- buildSlaters() - Method in class org.jmol.adapter.readers.xml.XmlMOReader
- buildSpaceGroup(String) - Method in class org.jmol.symmetry.SpaceGroup
- buildStructure(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
- buildStructure(String) - Method in class org.jmol.popup.MainPopupResourceBundle
- buildStructure(String) - Method in class org.jmol.popup.PopupResource
- bundle - Static variable in class org.jmol.modelkit.ModelKitPopup
- BUNIQUEID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- button - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
- BUTTON_MASK - Static variable in class org.jmol.awtjs.Event
- BUTTON_MASK - Static variable in class org.jmol.viewer.binding.Binding
- button_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- button_mode_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- BUTTON_MODIFIER_MASK - Static variable in class org.jmol.viewer.binding.Binding
- buttonGroup - Variable in class org.jmol.awt.AwtPopupHelper
- buttonGroup - Variable in class org.jmol.awtjs2d.JSPopupHelper
- buttonGroup - Variable in class org.jmol.popup.GenericPopup
- ButtonGroup - Class in org.jmol.awtjs.swing
- ButtonGroup() - Constructor for class org.jmol.awtjs.swing.ButtonGroup
- buttonModelkit - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- buttonPanel - Variable in class org.jmol.console.ScriptEditor
- buttonPanel - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- buttonRotate - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- bValue(T) - Static method in class org.jmol.script.SV
- BW - Static variable in class org.jmol.util.ColorEncoder
- BWR - Static variable in class org.jmol.util.ColorEncoder
- bwSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- byChain - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- BYELEMENT_JMOL - Static variable in class org.jmol.util.ColorEncoder
- BYELEMENT_PREFIX - Static variable in class org.jmol.util.ColorEncoder
- BYELEMENT_RASMOL - Static variable in class org.jmol.util.ColorEncoder
- BYRESIDUE_AMINO - Static variable in class org.jmol.util.ColorEncoder
- BYRESIDUE_NUCLEIC - Static variable in class org.jmol.util.ColorEncoder
- BYRESIDUE_PREFIX - Static variable in class org.jmol.util.ColorEncoder
- BYRESIDUE_SHAPELY - Static variable in class org.jmol.util.ColorEncoder
- bySymop - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- byteArrayOS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
- byteFactor - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
- bytesOrStream - Variable in class org.jmol.io.FileReader
- bytesToString(Object) - Method in class org.jmol.adapter.readers.pymol.PickleReader
- bytesToString(Object) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- bzColor(int) - Method in class org.jmol.util.BZone
-
give each Brillouin zone a new color
- bzColors - Static variable in class org.jmol.util.BZone
- bzDrawPointsAndEdges - Variable in class org.jmol.util.BZone
- bzFaceCenters - Variable in class org.jmol.util.BZone
- bzGamma - Variable in class org.jmol.util.BZone
- bzLatticePts - Variable in class org.jmol.util.BZone
- bzLatticePtsAll - Variable in class org.jmol.util.BZone
- BZone - Class in org.jmol.util
-
class to represent and produce Brillouin zone polyhedra and Wigner-Seitz cells based on https://chemapps.stolaf.edu/jmol/jsmol/spt/ext/xtal/bz.spt
- BZone() - Constructor for class org.jmol.util.BZone
- bzones - Variable in class org.jmol.util.BZone
- bzPlanePts - Variable in class org.jmol.util.BZone
- bzSavePmeshes - Variable in class org.jmol.util.BZone
C
- c - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
- c - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- c - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- c - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- c - Variable in class org.jmol.awtjs.swing.Cell
- c - Variable in class org.jmol.jvxl.readers.MapFileReader
- c - Variable in class org.jmol.minimize.forcefield.Calculation
- c - Static variable in class org.jmol.quantum.NciCalculation
- c - Variable in class org.jmol.util.SimpleUnitCell
- C - Class in org.jmol.util
-
Note: Color table is now in javajs/util/CU.java
- C - Static variable in class org.jmol.modelsetbio.AminoMonomer
- C() - Constructor for class org.jmol.util.C
- c_ - Variable in class org.jmol.util.SimpleUnitCell
- c0_xxz_yyz - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c1 - Variable in class org.jmol.g3d.HermiteRenderer
- c1n_xxy - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c1n_yyy - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c1n_yzz - Static variable in class org.jmol.quantum.mo.DataAdder7F
- C1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- c1p_xxx - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c1p_xyy - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c1p_xzz - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c2 - Variable in class org.jmol.g3d.HermiteRenderer
- c2 - Static variable in class org.jmol.symmetry.PointGroup
- C2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- C2P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- c2p_xxz_yyz - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c3 - Static variable in class org.jmol.symmetry.PointGroup
- c3n_xxy - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c3n_yyy - Static variable in class org.jmol.quantum.mo.DataAdder7F
- C3P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- c3p_xxx - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c3p_xyy - Static variable in class org.jmol.quantum.mo.DataAdder7F
- c4 - Static variable in class org.jmol.symmetry.PointGroup
- C4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- C4P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- c5 - Static variable in class org.jmol.symmetry.PointGroup
- C5 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- C5P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- c6 - Static variable in class org.jmol.symmetry.PointGroup
- C6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- c8 - Static variable in class org.jmol.symmetry.PointGroup
- C8 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- CA - Static variable in class org.jmol.modelsetbio.AminoMonomer
- cA_ - Variable in class org.jmol.util.SimpleUnitCell
- cache - Static variable in class org.jmol.script.T
- cache - Variable in class org.jmol.viewer.FileManager
- cache() - Method in class org.jmol.scriptext.CmdExt
- cache_display - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cache_frames - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cache_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cache_memory - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cache_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cacheClear() - Method in class org.jmol.viewer.FileManager
- cacheClear() - Method in class org.jmol.viewer.Viewer
- cacheFileByName(String, boolean) - Method in class org.jmol.util.GenericApplet
- cacheFileByName(String, boolean) - Method in class org.jmol.viewer.Viewer
- cacheFileByNameAdd(String, boolean) - Method in class org.jmol.viewer.FileManager
- cacheGet(String, boolean) - Method in class org.jmol.viewer.FileManager
- cacheID - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- cacheList() - Method in class org.jmol.viewer.FileManager
- cacheName - Variable in class org.jmol.script.FileLoadThread
- cachePut(String, Object) - Method in class org.jmol.util.GenericApplet
- cachePut(String, Object) - Method in class org.jmol.viewer.FileManager
- cachePut(String, Object) - Method in class org.jmol.viewer.Viewer
-
JSInterface -- allows saving files in memory for later retrieval
- CACTUS_FILE_TYPES - Static variable in class org.jmol.viewer.JC
- caf - Variable in class org.jmol.viewer.AnimationManager
-
current animation frame
- CageRenderer - Class in org.jmol.render
- CageRenderer() - Constructor for class org.jmol.render.CageRenderer
- cai - Variable in class org.jmol.viewer.AnimationManager
- calc - Variable in class org.jmol.minimize.forcefield.ForceField
- calc(int, boolean, boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- CALC_ANGLE - Static variable in class org.jmol.minimize.forcefield.Calculations
- CALC_DISTANCE - Static variable in class org.jmol.minimize.forcefield.Calculations
- CALC_ES - Static variable in class org.jmol.minimize.forcefield.Calculations
- CALC_H_ALLOW_H - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_DOALL - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_HAVEH - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_IGNORE_H - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_JUSTC - Static variable in class org.jmol.modelset.AtomCollection
- CALC_H_QUICK - Static variable in class org.jmol.modelset.AtomCollection
- CALC_MAX - Static variable in class org.jmol.minimize.forcefield.Calculations
- CALC_OOP - Static variable in class org.jmol.minimize.forcefield.Calculations
- CALC_STRETCH_BEND - Static variable in class org.jmol.minimize.forcefield.Calculations
- CALC_TORSION - Static variable in class org.jmol.minimize.forcefield.Calculations
- CALC_VDW - Static variable in class org.jmol.minimize.forcefield.Calculations
- calc1Screen(P3, V3, short, float, P3) - Method in class org.jmol.renderbio.BioShapeRenderer
- calc2JHH(Atom, Atom, Atom) - Static method in class org.jmol.quantum.NMRCalculation
- calc2or3JorNOE(Viewer, Atom[], String, int) - Static method in class org.jmol.quantum.NMRCalculation
-
Calculate a 2-bond (geminal) or 3-bond (vicinal) coupling constant or an NOE;
- calc3JCH(String, double, boolean) - Static method in class org.jmol.quantum.NMRCalculation
- calc3JHHOnly(String[][], V3[][], V3, V3, V3, double, boolean) - Static method in class org.jmol.quantum.NMRCalculation
- calcAllRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
-
only for base models, not trajectories
- calcArgbEndcap(boolean, boolean) - Method in class org.jmol.g3d.CylinderRenderer
- calcArgbsGreyscale() - Static method in class org.jmol.util.C
- calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.api.JmolViewer
- calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.modelset.ModelSet
- calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.viewer.Viewer
- calcAxis() - Method in class org.jmol.modelsetbio.Helix
- calcAxis() - Method in class org.jmol.modelsetbio.ProteinStructure
- calcAxis() - Method in class org.jmol.modelsetbio.Sheet
- calcBarPixelsXYZ(TransformManager, Text, P3i, boolean) - Static method in class org.jmol.render.TextRenderer
- calcBfactorRange() - Method in class org.jmol.shapebio.BioShape
- calcBfactorRange(BS) - Method in class org.jmol.modelset.AtomCollection
- calcBoundBoxDimensions(BS, float) - Method in class org.jmol.modelset.ModelSet
- calcBoundBoxDimensions(BS, float) - Method in class org.jmol.viewer.Viewer
- calcCameraFactors() - Method in class org.jmol.viewer.TransformManager
-
sets all camera and scale factors needed by the specific perspective model instantiated
- calcContourPoint(float, float, float, P3) - Method in class org.jmol.jvxl.calc.MarchingSquares
- calcConvexBits() - Method in class org.jmol.geodesic.EnvelopeCalculation
- calcConvexMap(boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
- calcCosSin(float, float, float) - Method in class org.jmol.g3d.CylinderRenderer
- calcCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.BioPolymer
- calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.NucleicPolymer
- calcFactors(int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- calcFrameDelta() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- calcFrameDelta() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- calcHbondEnergy(P3, P3, AminoMonomer, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
-
based on RasMol 2.7.2.1.1 model checkDistances: When we are seriously looking for H bonds, we want to also check that distCN > distCH and that the OH distance is less than 3 Angstroms.
- calcJKarplus(double) - Static method in class org.jmol.quantum.NMRCalculation
- calcJmolCouple(int, int, int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- calcLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
- calcLegendre(int) - Method in class org.jmol.util.Modulation
- calcMeanPositionalDisplacement(int) - Method in class org.jmol.shapebio.BioShape
-
Calculates the mean positional displacement in milliAngstroms.
- calcMetrics() - Method in class org.jmol.shape.Frank
- calcNatomsPerModel() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- calcNatomsPerModel() - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
TODO This assumes we have the same structure in each model.
- calcNavCameraFactors(float) - Method in class org.jmol.viewer.TransformManager
- calcNavigationDepthPercent() - Method in class org.jmol.navigate.Navigator
- calcNavigationPoint() - Method in interface org.jmol.api.JmolNavigatorInterface
- calcNavigationPoint() - Method in class org.jmol.navigate.Navigator
- calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager
-
All the magic happens here.
- calcNavSlabAndDepthValues() - Method in class org.jmol.navigate.Navigator
- calcNOE(Viewer, Atom, Atom) - Static method in class org.jmol.quantum.NMRCalculation
- calcNOEImpl(Viewer, Atom, Atom) - Static method in class org.jmol.quantum.NMRCalculation
- calcNoeMatrix() - Method in class org.jmol.quantum.NMRNoeMatrix
- calcNOEs() - Method in class org.jmol.quantum.NMRNoeMatrix
-
calculate the NOESY spectrum at a particular mixing time.
- calcNOEs() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- calcOptions - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- calcParameters() - Method in class org.jmol.modelsetbio.BioPolymer
- calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.AminoPolymer
- calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.BioPolymer
- calcPhiPsiAngles2(AminoMonomer, AminoMonomer) - Method in class org.jmol.modelsetbio.AminoPolymer
- calcPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
-
For reduced density only; coloring is done point by point.
- calcPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
-
Fill this plane with data based on the current set of raw data planes.
- calcPoints(int, boolean) - Method in class org.jmol.g3d.CylinderRenderer
- calcProps - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- calcProps - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- calcRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
-
These are not actual hydrogen bonds.
- calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
- calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
- calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicPolymer
- calcRectRubberBand() - Method in class org.jmol.viewer.ActionManager
- calcRelaxMatrix() - Method in class org.jmol.quantum.NMRNoeMatrix
- calcRopeMidPoints() - Method in class org.jmol.renderbio.RocketsRenderer
- calcRotatedPoint(float, int, boolean, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
- calcRotationRadius(int, P3, boolean) - Method in class org.jmol.modelset.ModelSet
- calcRotationRadiusBs(BS) - Method in class org.jmol.modelset.ModelSet
- calcs - Variable in class org.jmol.minimize.forcefield.Calculation
- calcScreenControlPoints() - Method in class org.jmol.renderbio.BioShapeRenderer
- calcScreens(float, short[]) - Method in class org.jmol.renderbio.BioShapeRenderer
-
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
- calcSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
- calcSelectedGroupsCount() - Method in class org.jmol.modelset.ModelSet
- calcSelectedGroupsCount(BS) - Method in class org.jmol.modelset.Chain
-
prior to coloring by group, we need the chain count per chain that is selected
- calcSelectedGroupsCount(BS) - Method in class org.jmol.modelset.Model
- calcSelectedMoleculesCount() - Method in class org.jmol.modelset.ModelSet
- calcSelectedMonomersCount() - Method in class org.jmol.modelset.ModelSet
- calcSelectedMonomersCount() - Method in class org.jmol.modelsetbio.BioModelSet
- calcSelectedMonomersCount(BS) - Method in class org.jmol.modelsetbio.BioPolymer
- calcSheetUnitVectors() - Method in class org.jmol.modelsetbio.Sheet
- calcSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager
-
sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane.
- calcSP(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
- calcSphereShading() - Method in class org.jmol.util.Shader
- calcSurfaceDistances() - Method in class org.jmol.modelset.AtomCollection
- calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager
- calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager4D
- calcType - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- calcType - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
- calculate - Static variable in class org.jmol.script.T
- calculate() - Method in class org.jmol.scriptext.CmdExt
- calculate(T3, boolean) - Method in class org.jmol.util.ModulationSet
-
Calculate r_I internal d-space coordinate of an atom.
- calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolEnvCalc
- calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
- calculate(VolumeData, BS, P3[], Atom[], float[], int) - Method in class org.jmol.quantum.MepCalculation
- calculateAllPolymers(Group[], int, int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- calculateAllStructuresExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
- calculateAllstruts(Viewer, ModelSet, BS, BS) - Method in class org.jmol.modelsetbio.BioExt
- calculateAllStuctures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
- calculateAnglesInDegrees() - Method in class org.jmol.modelsetbio.AlphaPolymer
- calculateChirality(BS) - Method in class org.jmol.viewer.Viewer
- calculateChiralityForAtoms(BS, boolean) - Method in class org.jmol.modelset.ModelSet
- calculateChiralityForSmiles(String) - Method in class org.jmol.viewer.Viewer
- calculateCIPChiralityForAtoms(Viewer, BS) - Method in interface org.jmol.api.SymmetryInterface
- calculateCIPChiralityForAtoms(Viewer, BS) - Method in class org.jmol.symmetry.Symmetry
- calculateCIPChiralityForSmiles(Viewer, String) - Method in interface org.jmol.api.SymmetryInterface
- calculateCIPChiralityForSmiles(Viewer, String) - Method in class org.jmol.symmetry.Symmetry
- calculateCodes(float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
- calculateCutoff() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
- calculatedArea - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- calculatedArea - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- calculatedDipole - Variable in class org.jmol.shapespecial.Dipoles
- calculateDistance(P3, P3) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- calculateDssp(Object[], int, Object, boolean, boolean, boolean, int) - Method in class org.jmol.dssx.DSSP
- calculateDssrProperty(String) - Method in class org.jmol.modelset.ModelSet
- calculateDSSRStructure(Viewer, BS) - Method in interface org.jmol.api.JmolAnnotationParser
- calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.AnnotationParser
- calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.DSSR1
- calculateDssx(Lst<Bond>, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModel
- calculatedVolume - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- calculatedVolume - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- calculateElectronDensity() - Method in class org.jmol.quantum.MOCalculation
- calculateFormalCharges(BS) - Method in class org.jmol.viewer.Viewer
- calculateFractionalPoint(float, P3, P3, float, float, P3) - Method in class org.jmol.jvxl.data.VolumeData
- calculateGeodesicSurface(BS, float) - Method in interface org.jmol.jvxl.api.MeshDataServer
- calculateGeodesicSurface(BS, float) - Method in class org.jmol.shapesurface.Isosurface
- calculateHydrogens(BS, int[], Lst<Atom>, int) - Method in class org.jmol.modelset.AtomCollection
-
get a list of potential H atom positions based on elemental valence and formal charge
- calculateMad(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
- calculateMolecularDipole(int, BS) - Method in class org.jmol.modelset.ModelSet
- calculateMolecularDipole(BS) - Method in class org.jmol.viewer.Viewer
- calculatePartialCharges(BS) - Method in class org.jmol.viewer.Viewer
- calculatePartialCharges(Bond[], int[], Atom[], int[], BS, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
-
assign partial charges ala MMFF94
- calculatePartialCharges(ModelSet, BS, BS) - Method in class org.jmol.minimize.Minimizer
- calculatePointGroup(BS) - Method in class org.jmol.modelset.ModelSet
- calculatePointGroupForFirstModel(BS, boolean, boolean, String, int, float, T3[], P3, String) - Method in class org.jmol.modelset.ModelSet
- calculatePolymers(Group[], int, int, BS) - Method in class org.jmol.modelset.ModelSet
- calculateQCoefs(double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
determine simple linear combination assuming simple -3 to 3 no more than two dimensions.
- calculateR0(double, double, double, double, double) - Static method in class org.jmol.minimize.forcefield.CalculationsUFF
- calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.AminoPolymer
- calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.BioPolymer
- calculateRunsFourOrMore(AlphaPolymer.Code[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
- calculateStraightness() - Method in class org.jmol.viewer.Viewer
- calculateStraightnessAll() - Method in class org.jmol.modelset.ModelSet
- calculateStraightnessAll() - Method in class org.jmol.modelsetbio.BioExt
- calculateStraightnessAll() - Method in class org.jmol.modelsetbio.BioModelSet
- calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
- calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
- calculateStructures(boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModel
- calculateStructures(BS, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
- calculateStructures(BS, boolean, boolean, int) - Method in class org.jmol.viewer.Viewer
- calculateStructuresAllExcept(BS, boolean, boolean, boolean, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
-
allows rebuilding of PDB structures; also accessed by ModelManager from Eval
- calculateStruts(BS, BS) - Method in class org.jmol.modelset.ModelSet
-
see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.
- calculateStruts(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- calculateStruts(BS, BS) - Method in class org.jmol.viewer.Viewer
- calculateStruts(ModelSet, BS, BS, Lst<Atom>, float, int, boolean) - Static method in class org.jmol.modelsetbio.BioExt
-
Algorithm of George Phillips phillips@biochem.wisc.edu originally a contribution to pyMol as struts.py; adapted here by Bob Hanson for Jmol 1/2010 Return a vector of support posts for rapid prototyping models along the lines of George Phillips for Pymol except on actual molecular segments (biopolymers), not PDB chains (which may or may not be continuous).
- calculateSurface(BS, float) - Method in class org.jmol.modelset.AtomCollection
- calculateSurface(BS, float) - Method in class org.jmol.viewer.Viewer
- calculateVolume(BS, VDW) - Method in class org.jmol.modelset.AtomCollection
- calculateVolumeOrArea(MeshData, BS, boolean, boolean) - Static method in class org.jmol.jvxl.data.MeshData
- calculateVolumeOrArea(IsosurfaceMesh, boolean) - Method in class org.jmol.shapesurface.Isosurface
- Calculation - Class in org.jmol.minimize.forcefield
- Calculation() - Constructor for class org.jmol.minimize.forcefield.Calculation
- calculationNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
The number of the calculation being interpreted.
- calculationNumber - Variable in class org.jmol.adapter.readers.quantum.QchemReader
-
The number of the job being interpreted.
- calculations - Variable in class org.jmol.minimize.forcefield.Calculations
- Calculations - Class in org.jmol.minimize.forcefield
- Calculations(ForceField, MinAtom[], MinBond[], MinAngle[], MinTorsion[], MinPosition[], Lst<MMConstraint>) - Constructor for class org.jmol.minimize.forcefield.Calculations
- CalculationsMMFF - Class in org.jmol.minimize.forcefield
- CalculationsMMFF(ForceField, Map<Object, Object>, MinAtom[], MinBond[], MinAngle[], MinTorsion[], MinPosition[], Lst<MMConstraint>) - Constructor for class org.jmol.minimize.forcefield.CalculationsMMFF
- CalculationsUFF - Class in org.jmol.minimize.forcefield
- CalculationsUFF(ForceField, Map<Object, Object>, MinAtom[], MinBond[], MinAngle[], MinTorsion[], MinPosition[], Lst<MMConstraint>) - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF
- calculationType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- calculationType - Variable in class org.jmol.jvxl.readers.Parameters
- calculationType - Variable in class org.jmol.quantum.MOCalculation
- calcUnitCell(double[]) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- calcUnitCellMinMax() - Method in class org.jmol.modelset.ModelSet
- calcValue - Variable in class org.openscience.jmol.app.janocchio.Measure
- calcVertexPoint(int, int, int, int, P3) - Method in class org.jmol.jvxl.calc.MarchingCubes
- calcVoxelPlaneDistance(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
- calcVoxelVertexVectors() - Method in class org.jmol.jvxl.calc.MarchingCubes
- callbacks - Variable in class org.jmol.util.GenericApplet
- camera - Variable in class org.jmol.viewer.TransformManager
- cameradepth - Static variable in class org.jmol.script.T
- cameraDepth - Variable in class org.jmol.modelset.Orientation
- cameraDepth - Variable in class org.jmol.thread.MoveToThread
- cameraDepth - Variable in class org.jmol.viewer.TransformManager
- cameraDepthSetting - Variable in class org.jmol.viewer.TransformManager
- cameraDistance - Variable in class org.jmol.export.___Exporter
- cameraDistance - Variable in class org.jmol.viewer.TransformManager
- cameraDistanceFromCenter - Variable in class org.jmol.viewer.TransformManager
- cameraPosition - Variable in class org.jmol.export.___Exporter
- cameraScaleFactor - Variable in class org.jmol.viewer.TransformManager
- cameraSetting - Variable in class org.jmol.viewer.TransformManager
- cameraX - Variable in class org.jmol.modelset.Orientation
- cameraX - Variable in class org.jmol.thread.MoveToThread
- cameraY - Variable in class org.jmol.modelset.Orientation
- cameraY - Variable in class org.jmol.thread.MoveToThread
- canAdd(Bridge) - Method in class org.jmol.dssx.Bridge
- canBeNormalized(V3d) - Static method in class org.jmol.minimize.Util
- canBeSquared(double) - Static method in class org.jmol.minimize.Util
- canCapCylinders - Variable in class org.jmol.export.__CartesianExporter
- cancel - Static variable in class org.jmol.script.T
- cancel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- cancel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- cancel() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- cancelFileThread() - Method in class org.jmol.script.ScriptEval
- cancelPressed() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Responds to cancel being press- or equivalent eg window closed.
- cancelSorting() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- canDo(int) - Method in class org.jmol.viewer.StateManager
- canDoLineTo() - Method in interface org.jmol.api.GenericGraphics
- canDoLineTo() - Method in class org.jmol.awt.AwtG2D
- canDoLineTo() - Method in class org.jmol.awtjs2d.JsG2D
- canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
- canDownsample - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- canImport(JComponent, DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- canIncrement() - Method in class org.jmol.script.SV
- CANONICAL_DC_LIST - Static variable in class org.jmol.quantum.QS
- CANONICAL_DS_LIST - Static variable in class org.jmol.quantum.QS
- CANONICAL_FC_LIST - Static variable in class org.jmol.quantum.QS
- CANONICAL_FS_LIST - Static variable in class org.jmol.quantum.QS
- canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- canonicalSeitzList - Static variable in class org.jmol.symmetry.SpaceGroup
- canonizeAlphaDigit(char) - Static method in class org.jmol.api.JmolAdapter
- canonizeAlternateLocationID(char) - Static method in class org.jmol.api.JmolAdapter
- canonizeInsertionCode(char) - Static method in class org.jmol.api.JmolAdapter
- canSkipLoad - Variable in class org.jmol.modelset.AtomCollection
- canvas - Variable in class org.jmol.awtjs2d.Platform
- canvas - Variable in class org.jmol.console.ImageDialog
- cap - Static variable in class org.jmol.script.T
- capCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- capData(P4, float) - Method in class org.jmol.jvxl.data.VolumeData
- capMap - Variable in class org.jmol.util.MeshCapper
-
initialization only
- capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- capper - Variable in class org.jmol.util.MeshSlicer
- cappingObject - Variable in class org.jmol.shape.Mesh
- cappingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
- capPlanesPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- capture - Static variable in class org.jmol.script.T
- capture() - Method in class org.jmol.scriptext.CmdExt
- captureParams - Variable in class org.jmol.viewer.Viewer
- CapVertex(T3, int) - Constructor for class org.jmol.util.MeshCapper.CapVertex
- carbohydrate - Static variable in class org.jmol.script.T
- CARBOHYDRATE - Enum constant in enum org.jmol.c.STR
- CarbohydrateMonomer - Class in org.jmol.modelsetbio
- CarbohydrateMonomer() - Constructor for class org.jmol.modelsetbio.CarbohydrateMonomer
- CarbohydratePolymer - Class in org.jmol.modelsetbio
- CarbohydratePolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.CarbohydratePolymer
- cardinalityOf(BS) - Static method in class org.jmol.util.BSUtil
-
cardinality = "total number of set bits"
- cartesianDistance - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- cartesianOffset - Variable in class org.jmol.symmetry.UnitCell
- cartesianProduct(T3, T3) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
dual-purpose function for cross products, proper rotations, and improper rotations
- CARTN_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CARTN_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CARTN_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
- cartoon - Static variable in class org.jmol.script.T
- Cartoon - Class in org.jmol.shapebio
- Cartoon() - Constructor for class org.jmol.shapebio.Cartoon
- CARTOON - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_cylindrical_helices - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_discrete_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_dumbbell_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_dumbbell_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_dumbbell_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_fancy_helices - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_fancy_sheets - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_flat_cycles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_flat_sheets - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_helix_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_highlight_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_ladder_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_ladder_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_ladder_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_loop_cap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_loop_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_loop_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_nucleic_acid_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_nucleic_acid_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_nucleic_acid_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_oval_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_oval_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_oval_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_power_b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_putty_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_putty_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_putty_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_putty_scale_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_putty_scale_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_putty_scale_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_putty_transform - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_rect_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_rect_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_refine - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_refine_normals - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_refine_tips - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_ring_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_ring_finder - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_ring_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_ring_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_ring_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_ring_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_round_helices - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_sampling - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_side_chain_helper - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_smooth_cycles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_smooth_first - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_smooth_last - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_smooth_loops - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_throw - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_trace_atoms - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_tube_cap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_tube_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_tube_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoon_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cartoonbaseedges - Static variable in class org.jmol.script.T
- cartoonBaseEdges - Variable in class org.jmol.renderbio.NucleicRenderer
- cartoonBaseEdges - Variable in class org.jmol.viewer.GlobalSettings
- cartoonblockheight - Static variable in class org.jmol.script.T
- cartoonBlockHeight - Variable in class org.jmol.viewer.GlobalSettings
- cartoonblocks - Static variable in class org.jmol.script.T
- cartoonBlocks - Variable in class org.jmol.renderbio.NucleicRenderer
- cartoonBlocks - Variable in class org.jmol.viewer.GlobalSettings
- cartoonColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- cartoonFancy - Variable in class org.jmol.viewer.GlobalSettings
- cartoonLadderMode - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- cartoonladders - Static variable in class org.jmol.script.T
- cartoonLadders - Variable in class org.jmol.renderbio.NucleicRenderer
- cartoonLadders - Variable in class org.jmol.viewer.GlobalSettings
- CartoonRenderer - Class in org.jmol.renderbio
- CartoonRenderer() - Constructor for class org.jmol.renderbio.CartoonRenderer
- cartoonribose - Static variable in class org.jmol.script.T
- cartoonRibose - Variable in class org.jmol.renderbio.NucleicRenderer
- cartoonRibose - Variable in class org.jmol.viewer.GlobalSettings
- cartoonrockets - Static variable in class org.jmol.script.T
- cartoonRockets - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- cartoonRockets - Variable in class org.jmol.viewer.GlobalSettings
- cartoons - Variable in class org.jmol.dialog.FilePreview
- cartoonsfancy - Static variable in class org.jmol.script.T
- cartoonsFancy - Variable in class org.jmol.renderbio.BioShapeRenderer
- cartoonsteps - Static variable in class org.jmol.script.T
- cartoonSteps - Variable in class org.jmol.renderbio.NucleicRenderer
- cartoonSteps - Variable in class org.jmol.viewer.GlobalSettings
- cartoonTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- cartoonTypes - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- casecmd - Static variable in class org.jmol.script.T
- CastepDensityReader - Class in org.jmol.jvxl.readers
- CastepDensityReader() - Constructor for class org.jmol.jvxl.readers.CastepDensityReader
- CastepReader - Class in org.jmol.adapter.readers.xtal
-
CASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer "q={1/4 1/4 0}" "q=ALL" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example note: following was never implemented? -- following this with ".1" ".2" etc.
- CastepReader() - Constructor for class org.jmol.adapter.readers.xtal.CastepReader
- catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
- catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
- catalogUnit(Viewer, float[][], String, float, BS, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
-
Carried out for each unit
- catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
- catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
-
Returns a Lst
- catchcmd - Static variable in class org.jmol.script.T
- cationLookupTable - Static variable in class org.jmol.util.Elements
- cavity - Static variable in class org.jmol.script.T
- cavity_cull - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cavityRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- cavityRadius - Variable in class org.jmol.jvxl.readers.Parameters
- cb - Variable in class org.jmol.dialog.Dialog
- CB - Static variable in class org.jmol.minimize.forcefield.MMFFAngleCalc
- cB_ - Variable in class org.jmol.util.SimpleUnitCell
- cbAntialias - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- cbAxesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- cbClearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- CBK - Enum in org.jmol.c
- CBK() - Constructor for enum org.jmol.c.CBK
- cbl - Variable in class org.jmol.viewer.StatusManager
- cbMeasureAngstroms - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- cbOpenFilePreview - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- cbPerspectiveDepth - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- cbShowAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- cbShowBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- CC_ATOM_CHARGE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CC_ATOM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CC_ATOM_SYM - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CC_ATOM_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CC_ATOM_X_IDEAL - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CC_ATOM_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CC_ATOM_Y_IDEAL - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CC_ATOM_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CC_ATOM_Z_IDEAL - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CC_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CCDC_GEOM_BOND_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- cchScript - Variable in class org.jmol.script.ScriptCompiler
- cchToken - Variable in class org.jmol.script.ScriptCompiler
- cd - Static variable in class org.jmol.script.T
- cd(String) - Method in class org.jmol.viewer.Viewer
- ce - Variable in class org.jmol.util.ColorEncoder
- ce - Variable in class org.jmol.viewer.ColorManager
- cell - Static variable in class org.jmol.script.T
- cell() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- cell() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- Cell - Class in org.jmol.awtjs.swing
- Cell(JComponent, GridBagConstraints) - Constructor for class org.jmol.awtjs.swing.Cell
- CELL - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- CELL_TYPE_CONVENTIONAL - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- CELL_TYPE_MAGNETIC_PARENT - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CELL_TYPE_MAGNETIC_STANDARD - Static variable in class org.jmol.adapter.readers.cif.CifReader
- CELL_TYPE_PRIMITIVE - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- cell0 - Variable in class org.jmol.render.UccageRenderer
- cell1 - Variable in class org.jmol.render.UccageRenderer
- cellLattice - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
- cellParameterType - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- cellParamNames - Static variable in class org.jmol.api.JmolAdapter
- cellParams - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
- cellParams - Variable in class org.jmol.adapter.readers.xtal.MagresReader
- cellRange - Variable in class org.jmol.symmetry.SymmetryInfo
- cellSelectionEnabled - Variable in class org.jmol.awtjs.swing.JTable
- celOn - Variable in class org.jmol.util.Shader
- celPower - Variable in class org.jmol.util.Shader
- celRGB - Variable in class org.jmol.util.Shader
- celshading - Static variable in class org.jmol.script.T
- celshadingpower - Static variable in class org.jmol.script.T
- celZ - Variable in class org.jmol.util.Shader
- center - Variable in class org.jmol.export.___Exporter
- center - Variable in class org.jmol.jvxl.readers.Parameters
- center - Variable in class org.jmol.jvxl.readers.SurfaceReader
- center - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
- center - Variable in class org.jmol.modelset.Orientation
- center - Variable in class org.jmol.navigate.Navigator
- center - Static variable in class org.jmol.renderspecial.DipolesRenderer
- center - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- center - Static variable in class org.jmol.script.T
- center - Variable in class org.jmol.shapespecial.Dipole
- center - Variable in class org.jmol.shapespecial.Ellipsoid
- center - Variable in class org.jmol.shapespecial.Polyhedra
- center - Variable in class org.jmol.shapespecial.Polyhedron
- center - Variable in class org.jmol.shapesurface.Isosurface
- center - Variable in class org.jmol.symmetry.PointGroup
- center - Variable in class org.jmol.symmetry.UnitCellIterator
- center - Variable in class org.jmol.thread.MoveToThread
- center - Variable in class org.jmol.util.BZone
- center - Variable in class org.jmol.util.Modulation
- center - Static variable in class org.jmol.viewer.JC
- center - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- center() - Method in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- CENTER - Static variable in class org.jmol.awtjs.swing.BorderLayout
- CENTER - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
- CENTER - Static variable in class org.jmol.awtjs.swing.SwingConstants
- centerat - Static variable in class org.jmol.script.T
- centerAt() - Method in class org.jmol.scriptext.CmdExt
- centerAt(int, int, P3) - Method in class org.jmol.viewer.TransformManager
- centerAtomIndex - Variable in class org.jmol.modelkit.ModelKit
- centerAtomIndex - Variable in class org.jmol.symmetry.PointGroup
- centerDialog() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- centerDialog() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Centers the dialog on the screen.
- centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- centerDipole() - Method in class org.jmol.shapespecial.Dipole
- centerDistance - Variable in class org.jmol.modelkit.ModelKit
- centerI - Variable in class org.jmol.geodesic.EnvelopeCalculation
- centering - Variable in class org.jmol.symmetry.SymmetryOperation
- centerParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- centerParameter(int, Object[]) - Method in class org.jmol.script.ScriptParam
- centerParameterForModel(int, int, Object[]) - Method in class org.jmol.script.ScriptParam
- centerPoint - Variable in class org.jmol.modelkit.ModelKit
- centers - Variable in class org.jmol.shapespecial.Polyhedra
- centers - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- centerStart - Variable in class org.jmol.navigate.Navigator
- centerT - Variable in class org.jmol.geodesic.EnvelopeCalculation
- centralAtom - Variable in class org.jmol.shapespecial.Polyhedron
- centralize() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- centroid - Static variable in class org.jmol.script.T
- centroidPacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- centroidPacked - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- cfiStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- cgdLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- CgdReader - Class in org.jmol.adapter.readers.xtal
-
A reader for TOPOS systre file Crystal Graph Data format.
- CgdReader() - Constructor for class org.jmol.adapter.readers.xtal.CgdReader
- cgo - Static variable in class org.jmol.script.T
- cgo() - Method in class org.jmol.scriptext.IsoExt
- CGO - Class in org.jmol.shapecgo
- CGO() - Constructor for class org.jmol.shapecgo.CGO
- cgo_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_dot_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_dot_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_ellipsoid_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_line_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_line_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_ray_width_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_shader_ub_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_shader_ub_flags - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_shader_ub_normal - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_sphere_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgo_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cgoMesh - Variable in class org.jmol.rendercgo.CGORenderer
- cgoMesh - Variable in class org.jmol.shapecgo.CGO
- CGOMesh - Class in org.jmol.shapecgo
- CGOMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapecgo.CGOMesh
- CGORenderer - Class in org.jmol.rendercgo
-
Something like a PyMOL Compiled Graphical Object, but more interesting!
- CGORenderer() - Constructor for class org.jmol.rendercgo.CGORenderer
- cH - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- ch1 - Variable in class org.jmol.modelset.LabelToken
- chain - Variable in class org.jmol.modelset.Group
-
required
- chain - Static variable in class org.jmol.script.T
- Chain - Class in org.jmol.modelset
-
A Model is a collection of Chains of Groups of Atoms.
- Chain(Model, int, int) - Constructor for class org.jmol.modelset.Chain
- CHAIN - Enum constant in enum org.jmol.c.PAL
- CHAIN - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- chainAtomCount - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- chainAtomCounts - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- chainAtomMap - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- chaincasesensitive - Static variable in class org.jmol.script.T
- chainCaseSensitive - Variable in class org.jmol.viewer.GlobalSettings
- chainCaseSpecified - Variable in class org.jmol.viewer.Viewer
- chainCheck - Variable in class org.jmol.smiles.SmilesGenerator
- chainCount - Variable in class org.jmol.modelset.Model
- chainID - Variable in class org.jmol.adapter.readers.more.Mol2Reader
- chainID - Variable in class org.jmol.adapter.smarter.Atom
- chainID - Variable in class org.jmol.modelset.Chain
-
chainID is either the integer form of a single character or a pointer into a map held in Viewer that allows retrieval of a longer string
- chainList - Variable in class org.jmol.viewer.Viewer
- chainMap - Variable in class org.jmol.viewer.Viewer
- chainno - Static variable in class org.jmol.script.T
- chainNo - Variable in class org.jmol.modelset.Chain
-
chainNo is for information purposes only; retrieved by {atoms}.chainNo
- chainOf - Variable in class org.jmol.modelset.ModelLoader
- chains - Variable in class org.jmol.modelset.Model
- chainSum - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- chainToUpper(int) - Method in class org.jmol.modelset.AtomCollection
- CHANGEABLE_MASK - Static variable in class org.jmol.util.C
- changeableColixMap - Variable in class org.jmol.util.GData
- changeColixArgb(int, int) - Method in class org.jmol.util.GData
- CHAR - Static variable in class org.jmol.shapecgo.CGOMesh
- characters(char[], int, int) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- charAt(int) - Method in class org.jmol.script.ScriptCompiler
- charge - Variable in class org.jmol.smiles.SmilesAtom
- charge - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- CHARGE_OFFSET - Static variable in class org.jmol.modelset.Atom
- chargesFound - Variable in class org.jmol.adapter.readers.simple.MopacReader
- ChargesOnly - Variable in class org.jmol.popup.JmolPopup
- chargeSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- chargeTag - Variable in class org.jmol.adapter.readers.quantum.OrcaReader
- chargeTag - Variable in class org.jmol.adapter.readers.simple.OrcaReader
- chargeType - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- chars - Variable in class org.jmol.adapter.readers.xml.XmlReader
- chButtonGroup - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- check - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
- check - Static variable in class org.jmol.script.T
- check - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- check() - Method in class org.jmol.smiles.SmilesMeasure
- check(boolean, boolean) - Method in class org.jmol.renderbio.BioMeshRenderer
- check(int, int, int, int, long, long) - Method in class org.jmol.viewer.MouseState
- CHECK_DIMS - Static variable in interface org.jmol.api.JmolScriptManager
- CHECK1 - Static variable in class org.jmol.thread.JmolThread
- CHECK2 - Static variable in class org.jmol.thread.JmolThread
- CHECK3 - Static variable in class org.jmol.thread.JmolThread
- checkAction(ActionEvent) - Method in class org.jmol.console.ScriptEditor
- checkAims(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkAlchemy(String) - Static method in class org.jmol.adapter.smarter.Resolver
- checkAll - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- checkAllFieldsPresent(String[], int, boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
- checkAllocColixes() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- checkAndRemoveFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkAromaticDefined(Node[], BS, BS) - Static method in class org.jmol.smiles.SmilesAromatic
-
Set aromatic atoms based on predefined BOND_AROMATIC definitions.
- checkAtomArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.VolumeFileReader
-
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
- checkAxisOrder(int, V3, T3) - Method in class org.jmol.symmetry.PointGroup
- checkBasis(BS, BS, BS) - Method in class org.jmol.symmetry.SpaceGroupFinder
- checkBetaSheetAlphaHelixOverlap(AlphaPolymer.Code[], float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
- checkBgColixLength(short, int) - Method in class org.jmol.shape.Labels
- checkBinary(String) - Method in class org.jmol.jvxl.readers.PmeshReader
- checkBioType(String, int) - Method in class org.jmol.smiles.SmilesParser
- checkBlock() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
looking for tags here.
- checkBondArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- checkBondDistance(Atom, Atom, float, float) - Method in class org.jmol.adapter.readers.cif.CifReader
- checkBondlengths() - Method in class org.jmol.adapter.readers.simple.FAHReader
- checkBondToR(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
Checks to see if we have a bond to R and, if so, adds this R atom as a key to its attached atom
- checkBoolean(String) - Method in class org.jmol.popup.JmolPopup
- checkBoundsMinMax(P3, P3) - Method in class org.jmol.shape.Shape
- checkBoxListener - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- CheckBoxMenuItemAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
- checkBrace(SmilesSearch, char, char) - Method in class org.jmol.smiles.SmilesParser
- checkBridge(Bridge, boolean, int, int) - Method in class org.jmol.dssx.DSSP
-
check to see if another bridge exists offset by n1 and n2 from the two ends of a bridge
- checkBridges(Lst<?>, BS, Lst<?>, BS, BS) - Static method in class org.jmol.smiles.SmilesAromatic
- checkBulge(Bridge, boolean, int) - Method in class org.jmol.dssx.DSSP
- checkButton - Variable in class org.jmol.console.ScriptEditor
- checkButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- checkByteCount - Variable in class org.jmol.shape.Mesh
- checkCalculationType() - Method in class org.jmol.quantum.MOCalculation
- checkCarbohydrate(String) - Static method in class org.jmol.modelsetbio.BioResolver
- checkCastepVaspSiesta(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkCharge(String, int, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
- checkChirality(SmilesSearch, String, int, SmilesAtom) - Static method in class org.jmol.smiles.SmilesStereo
- checkcir - Static variable in class org.jmol.script.T
- checkCIR - Variable in class org.jmol.viewer.GlobalSettings
- checkCIR(boolean) - Method in class org.jmol.viewer.Viewer
-
Check to see if the resolver is working
- checkClick(TouchPoint, List<Event>, boolean) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
- checkClickAction(int, int, long, int) - Method in class org.jmol.viewer.ActionManager
- checkColixLength(short, int) - Method in class org.jmol.shape.AtomShape
- checkCommand() - Method in class org.openscience.jmol.app.InputScannerThread
- checkCommand() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- checkComment() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- checkContinue() - Method in class org.jmol.script.ScriptEval
-
checks to see if there is a pause condition, during which commands can still be issued, but with the ! first.
- checkContour(MarchingSquares.Triangle, int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- checkCoordinatesChanged() - Method in class org.jmol.viewer.Viewer
- checkCp(ContactPair, ContactPair, int, int) - Static method in class org.jmol.shapesurface.Contact
- checkCrystal(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkCube(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkCurrentLineForScript() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkCurrentRule(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Check this atom "A" vs a challenger "B" against the current rule.
- checkCutoff(int, int, int, float[]) - Static method in class org.jmol.jvxl.data.MeshData
- checkDiameter(int) - Method in class org.jmol.renderbio.BioMeshRenderer
- checkDimensionType(float[]) - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
- checkDistance(P3, P3, float, float, int, int, int, P3) - Method in interface org.jmol.api.SymmetryInterface
- checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.symmetry.Symmetry
- checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.symmetry.UnitCell
- checkDragWheelAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
- checkDuplicate(Lst<P3>, int, int, int) - Static method in class org.jmol.symmetry.UnitCell
- checkedSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- checkElementSelected(char) - Method in class org.jmol.awt.Mouse
- checkEne(BS, BS, int, int, int, BS) - Method in class org.jmol.symmetry.CIPData
-
Look for a path that contains this ene in a fully conjugated pattern
- checkExplicit(String) - Method in class org.jmol.shape.MeshCollection
- checkExtension(int) - Method in class org.jmol.script.ScriptEval
- checkExtension(File) - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
- checkFacet(P3[], int, int[], int, V3, P4, V3, V3, Map<Integer, Object[]>, Map<String, Object>, float, BS, Object[]) - Method in class org.jmol.shapespecial.Polyhedra
-
Clean out overlapping triangles based on normals and cross products.
- checkFAH(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- checkFileExists(String, boolean, String, int, boolean) - Method in class org.jmol.script.ScriptEval
- checkFileStart(String) - Static method in class org.jmol.adapter.smarter.Resolver
- checkFilter(Atom, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkFilterAssembly(String, Map<String, Object>) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- checkFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkFirstAtom(Node) - Method in class org.jmol.smiles.SmilesGenerator
-
Don't start with H or central cumulene (in case there is symmetry)
- checkFloatRange(float, float, float) - Static method in class org.jmol.viewer.Viewer
- checkFlowCommand(String) - Method in class org.jmol.script.ScriptCompiler
- checkFlowEnd(int, String, int, boolean) - Method in class org.jmol.script.ScriptCompiler
- checkFlowEndBrace() - Method in class org.jmol.script.ScriptCompiler
-
process a pending explicit right brace }
- checkFlowStartBrace(boolean) - Method in class org.jmol.script.ScriptCompiler
- checkFoldingXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkForceEndIf(int) - Method in class org.jmol.script.ScriptFlowContext
- checkForCoordinate(boolean) - Method in class org.jmol.script.ScriptTokenParser
- checkForFreq() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- checkForItemSelector(boolean) - Method in class org.jmol.script.ScriptTokenParser
- checkFormalCharges(Lst<SmilesAtom>, int, boolean) - Method in class org.jmol.inchi.InChIJNI
- checkForResidualBFactors(SymmetryInterface) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- checkFrankclicked(int, int) - Method in class org.jmol.viewer.ShapeManager
- checkFront(short, short, short) - Method in class org.jmol.render.MeshRenderer
- checkFusedRings(Lst<SmilesRing>, int[], Lst<BS>) - Static method in class org.jmol.smiles.SmilesAromatic
-
Add fused rings based on the Hueckel 4n+2 rule.
- checkGenNBO(String[], String) - Static method in class org.jmol.adapter.smarter.Resolver
- checkGouraud(short, short, short, short, short, short) - Method in class org.jmol.g3d.Graphics3D
- checkGreater - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- checkGromacs(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkHallOperators() - Method in class org.jmol.symmetry.SpaceGroup
- checkHalt(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
- checkHalt(String, boolean) - Method in class org.jmol.api.JmolViewer
- checkHalt(String, boolean) - Method in class org.jmol.script.ScriptManager
- checkHalt(String, boolean) - Method in class org.jmol.viewer.Viewer
- checkHandedness(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPData
-
Determine the ordered CIP winding of this atom.
- checkHaveXMLUtil() - Static method in class org.jmol.jvxl.data.JvxlCoder
- checkHeaderContains(String) - Static method in class org.jmol.adapter.smarter.Resolver
- checkHeaderRecords(String, String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkHKL(T3) - Method in class org.jmol.script.ScriptParam
-
Note - this check does not allow a 0 for h, k, or l.
- checkHover() - Method in class org.jmol.viewer.ActionManager
- checkHueckelAromatic(int, Node[], BS, BS, int, int[]) - Static method in class org.jmol.smiles.SmilesAromatic
-
For each atom in the ring, look up a unique combination of covalent bond count, valence, and charge for each atom and use that as a key into the PI_COUNTS array.
- checkID(String) - Method in class org.jmol.shapespecial.Ellipsoids
- checkID(String) - Method in class org.jmol.shapespecial.Polyhedra
- checkImpliedScriptCmd - Variable in class org.jmol.script.ScriptCompiler
- checkIn(String, Object) - Static method in class org.jmol.util.GenericApplet
- checking - Variable in class org.jmol.console.ScriptEditor.EditorTextPane
- checking - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- checkingCommand - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- checkInheritedShapes() - Method in class org.jmol.viewer.ShapeManager
-
starting with Jmol 13.1.13, isosurfaces can use "property color" to inherit the color of the underlying atoms.
- checkInMotion(int) - Method in class org.jmol.viewer.Viewer
- checkInsideOut(int, int, int) - Method in class org.jmol.jvxl.readers.MapFileReader
- checkInterrupted(JmolThread) - Method in class org.jmol.thread.JmolThread
- checkIntRange(int, int, int) - Static method in class org.jmol.viewer.Viewer
- checkJ(String) - Method in class org.jmol.modelset.Measurement
- checkJSONContains(String) - Static method in class org.jmol.adapter.smarter.Resolver
- checkJSpecView(boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- checkKey(String) - Method in class org.jmol.popup.GenericPopup
- checkKey(String, boolean) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Filter keys only for this model.
- checkKey(String, String, String) - Method in class org.jmol.viewer.PropertyManager
- checkLast(int) - Method in class org.jmol.script.ScriptParam
- checkLastModel() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
sets continuing and doProcessLines
- checkLatticeOnly - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- checkLength(int) - Method in class org.jmol.script.ScriptParam
- checkLength(int) - Method in class org.jmol.scriptext.ScriptExt
- checkLength23() - Method in class org.jmol.script.ScriptParam
- checkLength34() - Method in class org.jmol.script.ScriptParam
- checkLengthErrorPt(int, int) - Method in class org.jmol.script.ScriptParam
- checkLine() - Method in class org.jmol.adapter.readers.molxyz.MolReader
- checkLine() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
- checkLine() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- checkLine() - Method in class org.jmol.adapter.readers.more.GromacsReader
- checkLine() - Method in class org.jmol.adapter.readers.more.JcampdxReader
- checkLine() - Method in class org.jmol.adapter.readers.more.MdCrdReader
- checkLine() - Method in class org.jmol.adapter.readers.more.MdTopReader
- checkLine() - Method in class org.jmol.adapter.readers.more.Mol2Reader
- checkLine() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.AdfReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.CsfReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.DgridReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Reads a Collection of AtomSets from a BufferedReader.
- checkLine() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.PsiReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- checkLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.AmpacReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.FAHReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.InputReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.MopacReader
- checkLine() - Method in class org.jmol.adapter.readers.simple.OrcaReader
- checkLine() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.AimsReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.CgdReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.DmolReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
Valid blocks include [calculation] [atoms] [magres]; all magres entries must be prefaced with a corresponding unit; Use of < > instead of [ ] is allowed.
- checkLine() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- checkLine() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
- checkLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkLineContinuation() - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
- checkLineForScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkLineStarts(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkLoadAndRun(String, Object, String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- checkLogic(SmilesSearch, String, SmilesAtom, SmilesBond, SmilesAtom, boolean, boolean, int[]) - Method in class org.jmol.smiles.SmilesParser
- checkM2() - Method in class org.jmol.viewer.TransformManager4D
- checkMap(Map<String, ?>, String, boolean, Lst<Object>, Object, int, boolean) - Method in class org.jmol.viewer.PropertyManager
- checkMap(Map<String, BS>, String, BS) - Method in class org.jmol.modelsetbio.BioModelSet
-
Ensure that if two models have the same name or number, we appropriately OR their bitsets.
- checkMatchBond(SmilesAtom, SmilesAtom, SmilesBond, int, int, Edge) - Method in class org.jmol.smiles.SmilesSearch
- checkMemory() - Static method in class org.jmol.util.Logger
- checkMenuUpdate() - Method in class org.jmol.viewer.Viewer
- checkMesh(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- checkMeshBB(Shape[], int, BoxInfo) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- checkMinAttachedAngle(Atom, float, V3, V3, boolean) - Static method in class org.jmol.modelset.ModelSet
- checkMinimization() - Method in class org.jmol.viewer.Viewer
- checkMinZ(Atom, int[]) - Method in class org.jmol.modelset.Group
- checkModelTrigger - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- checkMol(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkMopacGraphf(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkMOs() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- checkMotionRendering(int) - Method in class org.jmol.viewer.Viewer
-
check motion for rendering during mouse movement, spin, vibration, and animation
- checkMotionRotateZoom(int, int, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
- checkNboLine() - Method in class org.jmol.adapter.readers.quantum.MOReader
- checkNested(SmilesSearch, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesParser
- checkNewDotsArray() - Method in class org.jmol.geodesic.EnvelopeCalculation
- checkNewGroup(JmolAdapter, int, String, int, char, boolean, boolean) - Method in class org.jmol.modelset.ModelLoader
- checkNewModel() - Method in class org.jmol.modelkit.ModelKit
- checkNewSetCommand() - Method in class org.jmol.script.ScriptCompiler
- checkNoe(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- checkNoEmptyModel() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- checkNotPDB() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- checkNucleicObject(BS, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- checkObject(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- checkObjectClicked(boolean, int, int, BS) - Method in class org.jmol.modelset.Text
- checkObjectClicked(int, int, int) - Method in class org.jmol.viewer.Viewer
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Labels
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Shape
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Sticks
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.TextShape
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Draw
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Ellipsoids
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapesurface.Isosurface
- checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.viewer.ShapeManager
- checkObjectDragged(int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
- checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Labels
- checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Shape
- checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shapespecial.Draw
- checkObjectDragged(int, int, int, int, int, BS, int) - Method in class org.jmol.viewer.ShapeManager
- checkObjectHovered(int, int) - Method in class org.jmol.viewer.Viewer
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Frank
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Shape
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Sticks
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.TextShape
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Draw
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
- checkObjectHovered(int, int, BS) - Method in class org.jmol.shapesurface.Isosurface
- checkObjectHovered(int, int, BS, boolean) - Method in class org.jmol.viewer.ShapeManager
- checkOdyssey(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkOperation(Quat, T3, int) - Method in class org.jmol.symmetry.PointGroup
- checkOption(Object) - Static method in class org.openscience.jmol.app.webexport.WebPanel
- checkOption2(String, String) - Method in class org.jmol.viewer.Viewer
- checkOptional(byte[], byte, int, int) - Static method in class org.jmol.modelsetbio.Monomer
- checkOptions(CommandLine, Options) - Method in class org.openscience.jmol.app.JmolApp
- checkOrbitalType(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- checkOut(String) - Static method in class org.jmol.util.GenericApplet
- checkPacked(int, Map<String, Object>, SB) - Method in class org.jmol.scriptext.CmdExt
-
Process FILL and PACKED and all their variants.
- checkPaused(Viewer) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.CifReader
- checkPDBModelField(int, int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- checkPeriodic(P3) - Static method in class org.jmol.util.SimpleUnitCell
-
check atom position for range [0, 1) allowing for rounding
- checkPhiPsi(float[], float, float) - Static method in class org.jmol.modelsetbio.AminoPolymer
- checkPoint(T3) - Method in class org.jmol.export._IdtfExporter
- checkPoint(Point3fi) - Method in class org.jmol.modelset.MeasurementPending
- checkPoints(BS) - Method in class org.jmol.shapesurface.PMeshWriter
- checkPolyHedralWinding(Node, Node[]) - Method in class org.jmol.smiles.SmilesStereo
- checkPressedAction(int, int, long) - Method in class org.jmol.viewer.ActionManager
- checkPrimitiveAtom(SmilesAtom, int) - Method in class org.jmol.smiles.SmilesSearch
- checkPrimitiveBond(SmilesBond, int, int, Edge) - Method in class org.jmol.smiles.SmilesSearch
- checkPrivateKey(double) - Method in class org.jmol.viewer.Viewer
-
Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet.
- checkPropertyParameter(String) - Method in interface org.jmol.api.JmolPropertyManager
- checkPropertyParameter(String) - Method in class org.jmol.viewer.PropertyManager
- checkPropertyParameter(String) - Method in class org.jmol.viewer.Viewer
- checkPt(float[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
-
two values -- v1, and v2, which need not be ordered v1 < v2.
- checkRasmolHydrogenBond(AminoMonomer, BioPolymer, int, P3, BS, Lst<Bond>, int[][], boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
- checkReleaseAction(int, int, long, boolean) - Method in class org.jmol.viewer.ActionManager
- checkRemark() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
- checkRemark() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- checkResize(String) - Method in class org.jmol.script.ScriptManager
- checkResume(String) - Method in class org.jmol.script.ScriptManager
- checkRings(Lst<BS>, int[], int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- checkScript(int) - Method in class org.jmol.console.ScriptEditor
- checkScriptExecution(String, boolean) - Method in class org.jmol.script.ScriptManager
- checkScriptSilent(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- checkScriptSilent(String) - Method in class org.jmol.script.ScriptEval
-
a method for just checking a script
- checkSecurity(String) - Method in class org.jmol.viewer.FileManager
- checkSelect(Map<String, SV>, T[]) - Method in interface org.jmol.api.JmolScriptEvaluator
- checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptEval
-
Check a map for a WHERE phrase
- checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.viewer.Viewer
- checkShades(int) - Method in class org.jmol.util.Shader
- checkSkip(T, int) - Method in class org.jmol.script.ScriptMathProcessor
- checkSlab(int, T3, float, float, BS) - Method in class org.jmol.util.MeshSlicer
- checkSpecial - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- checkSpecial1(int, String[], String) - Static method in class org.jmol.adapter.smarter.Resolver
- checkSpecial2(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkSpecialParameterSyntax() - Method in class org.jmol.script.ScriptCompiler
-
Check for special parameters, including: +, -, \, *, /, &, |, =, period, or [, single or double quote, command-specific parameters, $....
- checkSpecialVoxel(P3, P3, P3) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- checkStack(Lst<String>) - Method in class org.jmol.viewer.StateManager
- checkStandardDeviation(V3[], V3, int, float) - Static method in class org.jmol.smiles.SmilesAromatic
-
calculates a dot-product standard deviation and reports if it is below a cutoff
- checkStepping(String) - Method in class org.jmol.script.ScriptManager
- checkStereochemistry() - Method in class org.jmol.smiles.SmilesSearch
- checkStereoChemistry(SmilesSearch, VTemp) - Method in class org.jmol.smiles.SmilesStereo
- checkStereochemistryAll(boolean, SimpleNode, int, int, SimpleNode, SimpleNode, SimpleNode, SimpleNode, SimpleNode, SimpleNode, VTemp) - Static method in class org.jmol.smiles.SmilesStereo
- checkStereoForAtom(SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesStereo
- checkStereoPairs(SimpleNode, int, SimpleNode[], int, boolean) - Method in class org.jmol.smiles.SmilesGenerator
- checkStringLength(int) - Method in class org.jmol.shape.Labels
- checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
- checkSubclassSymmetry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- checkSum - Variable in class org.jmol.jvxl.readers.BCifDensityReader
- checkSupercell(Viewer, SymmetryInterface, BS, int, P3) - Method in class org.jmol.symmetry.SpaceGroupFinder
-
Look for a supercell and adjust lattice down if necessary.
- checkSymmetry() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- checkTickTemps() - Method in class org.jmol.render.FontLineShapeRenderer
- checkTimer - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- checkTimer(String, boolean) - Static method in class org.jmol.util.Logger
- checkToken(int) - Method in class org.jmol.script.ScriptParam
- checkTranslucent(boolean) - Method in interface org.jmol.api.JmolRendererInterface
- checkTranslucent(boolean) - Method in class org.jmol.export.Export3D
- checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
- checkTriangles(boolean, BS, BS) - Method in class org.jmol.shapesurface.PMeshWriter
- checkTwoAtomAction(Point3fi, int) - Method in class org.jmol.viewer.ActionManager
- checkType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- checkUndoEnabled() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- checkUnitCell(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkUnitCell(SymmetryInterface, P3, P3) - Static method in class org.jmol.util.SimpleUnitCell
- checkUnitCellItem(String[], String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- checkUnitCellOffset() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- checkUnitCellParams() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- checkUnquotedFileName() - Method in class org.jmol.script.ScriptCompiler
- checkUserAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
- checkVisible() - Method in class org.jmol.modelset.Atom
- checkWien2k(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkWinding(MeshCapper.CapVertex, MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
-
Check for CCW winding.
- checkWithin(T3, Lst<P3>, float, boolean) - Static method in class org.jmol.shape.Mesh
- checkXSF(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
- checkXYZlist(String) - Method in class org.jmol.symmetry.SpaceGroup
- CHEM_COMP_BOND_AROMATIC_FLAG - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CHEM_COMP_BOND_ATOM_ID_1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CHEM_COMP_BOND_ATOM_ID_2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CHEM_COMP_BOND_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CHEM_COMP_BOND_VALUE_ORDER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CHEM_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- CHEM_COMP_NAME - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- chemappsPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
- chemCompBondFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- chemCompFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- chemFileProperty - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- chemFileProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CHEMFLAG - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- chemical - Static variable in class org.jmol.script.T
- CHEMICAL_SHIFT_ANISOTROPY_FACTOR - Static variable in class org.jmol.util.Tensor
- chemicalName - Variable in class org.jmol.adapter.readers.cif.CifReader
- chemicalshift - Static variable in class org.jmol.script.T
- CHequation - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- CHequation - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- chFirst - Variable in class org.jmol.script.ScriptCompiler
- ChimeMessenger - Class in org.jmol.viewer
-
A legacy Chime-compatible messenger.
- ChimeMessenger() - Constructor for class org.jmol.viewer.ChimeMessenger
- chiralClass - Variable in class org.jmol.smiles.SmilesStereo
- chirality - Static variable in class org.jmol.script.T
- chiralOrder - Variable in class org.jmol.smiles.SmilesStereo
- chiralPath - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
ASCII-encoded priority string
- chk - Variable in class org.jmol.script.ScriptContext
- chk - Variable in class org.jmol.script.ScriptError
- chk - Variable in class org.jmol.script.ScriptMathProcessor
- chk - Variable in class org.jmol.scriptext.ScriptExt
- choice - Variable in class org.jmol.dialog.Dialog
- chooseBestBoundBox() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- chooser - Variable in class org.jmol.dialog.FilePreview
- chop(String) - Static method in class org.jmol.viewer.StateCreator
- chord - Variable in class org.jmol.util.ContactPair
- chpt0 - Variable in class org.jmol.script.ScriptFunction
- CHRG - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- Cif2DataParser - Class in org.jmol.adapter.readers.cif
-
Fully implemented 2016.12.1 see http://journals.iucr.org/j/issues/2016/01/00/aj5269/index.html Will deliver JSON versions of the data while file reading and Java List/Map structures when called by x = getProperty("cifInfo", filename) Validated using the test-data suite by John Bollinger (John.Bollinger@stjude.org) found at https://github.com/COMCIFS/cif_api
- Cif2DataParser() - Constructor for class org.jmol.adapter.readers.cif.Cif2DataParser
- Cif2Reader - Class in org.jmol.adapter.readers.cif
-
Preliminary Cif2 reader.
- Cif2Reader() - Constructor for class org.jmol.adapter.readers.cif.Cif2Reader
- cif2StartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- cifData - Variable in class org.jmol.jvxl.readers.BCifDensityReader
- CifDensityReader - Class in org.jmol.jvxl.readers
-
CIF density reader.
- CifDensityReader() - Constructor for class org.jmol.jvxl.readers.CifDensityReader
- cifLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- cifParser - Variable in class org.jmol.adapter.readers.cif.CifReader
- cifParser - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- CifReader - Class in org.jmol.adapter.readers.cif
-
A true line-free CIF file reader for CIF files.
- CifReader() - Constructor for class org.jmol.adapter.readers.cif.CifReader
- CifReader.Parser - Interface in org.jmol.adapter.readers.cif
-
Allows checking specific blocks e.g.
- CIFWriter - Class in org.jmol.adapter.writers
-
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
- CIFWriter() - Constructor for class org.jmol.adapter.writers.CIFWriter
- cip - Variable in class org.jmol.symmetry.Symmetry
- CIP_CHIRALITY_AXIAL_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_CANTDETERMINE - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_EZ_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_m_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_M_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_MASK - Static variable in class org.jmol.modelset.Atom
- CIP_CHIRALITY_NAME_MASK - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_NAME_OFFSET - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_NONE - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_OFFSET - Static variable in class org.jmol.modelset.Atom
- CIP_CHIRALITY_p_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_P_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_PSEUDO_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_r_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_R_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_RULE_MASK - Static variable in class org.jmol.modelset.Atom
- CIP_CHIRALITY_RULE_OFFSET - Static variable in class org.jmol.modelset.Atom
- CIP_CHIRALITY_s_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_S_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_seqcis_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_seqCis_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_seqtrans_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_seqTrans_FLAG - Static variable in class org.jmol.viewer.JC
- CIP_CHIRALITY_UNKNOWN - Static variable in class org.jmol.viewer.JC
- CIP_MASK - Static variable in class org.jmol.modelset.Atom
- CIPAtom() - Constructor for class org.jmol.symmetry.CIPChirality.CIPAtom
- cipChirality - Variable in class org.jmol.smiles.SmilesAtom
- CIPChirality - Class in org.jmol.symmetry
-
A fully validated relatively efficient implementation of Cahn-Ingold-Prelog rules for assigning R/S, M/P, and E/Z stereochemical descriptors.
- CIPChirality() - Constructor for class org.jmol.symmetry.CIPChirality
- CIPChirality.CIPAtom - Class in org.jmol.symmetry
- CIPData - Class in org.jmol.symmetry
-
A helper class to handle application-specific analysis and store information needed by CIPChirality and CIPDataSmiles.
- CIPData() - Constructor for class org.jmol.symmetry.CIPData
- CIPDataSmiles - Class in org.jmol.symmetry
-
A subclass that allows Jmol processing of SMILES using "...smiles...".find("SMILES","chirality")
- CIPDataSmiles() - Constructor for class org.jmol.symmetry.CIPDataSmiles
- CIPDataTracker - Class in org.jmol.symmetry
-
An optional class to track digraph paths to decisions.
- CIPDataTracker() - Constructor for class org.jmol.symmetry.CIPDataTracker
- CIPDataTracker.CIPTracker - Class in org.jmol.symmetry
- ciprule - Static variable in class org.jmol.script.T
- ciprule6full - Static variable in class org.jmol.script.T
- cipRule6Full - Variable in class org.jmol.viewer.GlobalSettings
- CIPTracker(int, CIPChirality.CIPAtom, CIPChirality.CIPAtom, int, int, boolean) - Constructor for class org.jmol.symmetry.CIPDataTracker.CIPTracker
- cirChecked - Variable in class org.jmol.viewer.Viewer
- circle - Static variable in class org.jmol.script.T
- CIRCLE - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- CIRCLE_FRACTION - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- circle3d - Variable in class org.jmol.g3d.Graphics3D
- circleNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- CircleRenderer - Class in org.jmol.g3d
-
Implements flat circle drawing/filling routines.
- CircleRenderer() - Constructor for class org.jmol.g3d.CircleRenderer
- CIRCULARPLANE - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- CITATION_TITLE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- citationFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
- cJvxlEdgeNaN - Variable in class org.jmol.jvxl.readers.SurfaceReader
- clamp_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- clash - Static variable in class org.jmol.script.T
- classBase - Static variable in class org.jmol.adapter.smarter.Resolver
- clauseAlternateSpec() - Method in class org.jmol.script.ScriptTokenParser
-
check for %x or % (null alternate)
- clauseAnd() - Method in class org.jmol.script.ScriptTokenParser
- clauseAtomSpec() - Method in class org.jmol.script.ScriptTokenParser
- clauseCell(int) - Method in class org.jmol.script.ScriptTokenParser
- clauseChainSpec(int) - Method in class org.jmol.script.ScriptTokenParser
-
[:] [chars] [:] ["chars"] [:] [*] [:] [0-9] [:] [?] [:] (empty chain)
- clauseComparator(boolean) - Method in class org.jmol.script.ScriptTokenParser
- clauseConnected(boolean) - Method in class org.jmol.script.ScriptTokenParser
- clauseDefine(boolean, boolean) - Method in class org.jmol.script.ScriptTokenParser
- clauseItemSelector() - Method in class org.jmol.script.ScriptTokenParser
- clauseModelSpec() - Method in class org.jmol.script.ScriptTokenParser
-
process /1 /1.1 / * or just /
- clauseNot() - Method in class org.jmol.script.ScriptTokenParser
- clauseOr(boolean) - Method in class org.jmol.script.ScriptTokenParser
- clausePrimitive() - Method in class org.jmol.script.ScriptTokenParser
- clauseResidueSpec() - Method in class org.jmol.script.ScriptTokenParser
- clauseResNameSpec() - Method in class org.jmol.script.ScriptTokenParser
-
[a] or just a
- clauseSequenceSpec() - Method in class org.jmol.script.ScriptTokenParser
- clauseSubstructure() - Method in class org.jmol.script.ScriptTokenParser
- clauseWithin(boolean) - Method in class org.jmol.script.ScriptTokenParser
- clean() - Method in class org.jmol.shape.MeshCollection
- clean() - Method in class org.jmol.shapecgo.CGO
- clean() - Method in class org.jmol.shapespecial.Draw
- clean(byte[]) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
-
remove all new-line characters, and terminate this message with a single \n.
- clean(float) - Method in class org.jmol.adapter.writers.XtlWriter
- clean_electro_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cleanFace(P3[]) - Method in class org.jmol.util.BZone
- cleanKey(String) - Method in class org.jmol.adapter.readers.more.AFLOWReader
-
cleans key to just letters and digits
- cleanLine() - Method in class org.jmol.adapter.readers.simple.InputReader
- cleanMatrix(M3) - Method in class org.jmol.symmetry.PointGroup.Operation
- cleanMatrix(Matrix) - Method in class org.jmol.adapter.readers.cif.Subsystem
- cleanPattern(String) - Static method in class org.jmol.smiles.SmilesParser
- cleanScriptComments(String) - Method in class org.jmol.script.ScriptCompiler
-
allows for three kinds of comments.
- cleanSingletons(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
PyMOL does not display cartoons or traces for single-residue runs.
- cleanSmiles(String) - Method in interface org.jmol.api.SmilesMatcherInterface
- cleanSmiles(String) - Method in class org.jmol.smiles.SmilesMatcher
- cleanUp() - Static method in class org.openscience.jmol.app.webexport.WebExport
- clear - Static variable in class org.jmol.script.T
- clear() - Method in interface org.jmol.api.GenericMouseInterface
- clear() - Method in interface org.jmol.api.JmolDataManager
- clear() - Method in class org.jmol.awt.Mouse
- clear() - Method in class org.jmol.awtjs2d.Mouse
- clear() - Method in class org.jmol.g3d.Graphics3D
- clear() - Method in class org.jmol.jvxl.data.JvxlData
- clear() - Method in class org.jmol.minimize.forcefield.ForceField
- clear() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- clear() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
- clear() - Method in class org.jmol.minimize.Minimizer
- clear() - Method in class org.jmol.multitouch.ActionManagerMT
- clear() - Method in class org.jmol.shape.Measures
- clear() - Static method in exception org.jmol.smiles.InvalidSmilesException
- clear() - Method in class org.jmol.smiles.SmilesSearch
- clear() - Method in class org.jmol.util.CommandHistory
-
clears the history.
- clear() - Method in class org.jmol.util.GData
- clear() - Method in class org.jmol.util.MeshCapper.CapVertex
-
Free all links.
- clear() - Method in class org.jmol.util.MeshCapper
- clear() - Method in class org.jmol.util.TempArray
- clear() - Method in class org.jmol.viewer.ActionManager
- clear() - Method in class org.jmol.viewer.AnimationManager
- clear() - Method in class org.jmol.viewer.DataManager
- clear() - Method in class org.jmol.viewer.FileManager
- clear() - Method in class org.jmol.viewer.GlobalSettings
- clear() - Method in class org.jmol.viewer.SelectionManager
- clear() - Method in class org.jmol.viewer.TransformManager
- clear() - Method in class org.openscience.jmol.app.HistoryFile
- clear() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- clear() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- clear(boolean) - Method in interface org.jmol.api.JmolScriptManager
- clear(boolean) - Method in class org.jmol.script.ScriptManager
- clear(boolean) - Method in class org.jmol.shapespecial.Dipoles
- clear(int) - Method in interface org.jmol.api.JmolRepaintManager
- clear(int) - Method in class org.jmol.render.RepaintManager
- clear(String) - Method in class org.jmol.shape.Mesh
- clear(String) - Method in class org.jmol.shapecgo.CGOMesh
- clear(String) - Method in class org.jmol.shapespecial.DrawMesh
- clear(Map<String, Object>) - Static method in class org.jmol.thread.TimeoutThread
- clear(BS, Atom, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
- clear(GlobalSettings) - Method in class org.jmol.viewer.StateManager
- clearAllMeasurements() - Method in class org.jmol.viewer.Viewer
- clearAndCachePngjFile(FileManager, String[]) - Method in class org.jmol.io.JmolUtil
- clearAtomConstraints() - Method in class org.jmol.modelkit.ModelKit
- clearAtomSets() - Method in class org.jmol.viewer.Viewer
- clearBfactorRange() - Method in class org.jmol.modelset.AtomCollection
- clearBindings() - Method in class org.jmol.viewer.ActionManager
- clearBioPolymers() - Method in class org.jmol.modelsetbio.BioModel
- clearBsFound(int) - Method in class org.jmol.smiles.SmilesSearch
- clearBuffer() - Method in class org.jmol.g3d.Platform3D
- clearButton - Variable in class org.jmol.console.ScriptEditor
- clearButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- clearButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- clearCache() - Method in class org.jmol.modelset.ModelSet
- clearCache() - Method in class org.jmol.util.ColorEncoder
- clearClickCount() - Method in class org.jmol.viewer.Viewer
- clearCommandWatcherThread() - Method in class org.jmol.script.ScriptManager
- clearConsole() - Method in class org.jmol.viewer.StatusManager
- clearContent() - Method in class org.jmol.console.ScriptEditor.EditorDocument
-
Removes all content of the script window, and add a new prompt.
- clearContent() - Method in class org.jmol.console.ScriptEditor.EditorTextPane
- clearContent() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
-
Removes all content of the script window, and add a new prompt.
- clearContent(String) - Method in class org.jmol.console.GenericConsole
- clearContent(String) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
- clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- clearDataFrameReference(int) - Method in class org.jmol.modelset.ModelSet
- clearDB(int) - Method in class org.jmol.modelset.ModelSet
- clearDefinedVariableAtomSets() - Method in class org.jmol.script.ScriptEval
- clearExceptions() - Method in class org.jmol.smiles.SmilesMatcher
- clearFontCache() - Method in class org.jmol.g3d.Graphics3D
- clearFontCache() - Static method in class org.jmol.g3d.TextRenderer
- clearFontCache() - Method in class org.jmol.util.GData
- clearForces() - Method in class org.jmol.minimize.forcefield.ForceField
- clearFunctions() - Method in class org.jmol.viewer.Viewer
- clearGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- clearHighlight() - Method in class org.jmol.console.ScriptEditor.EditorDocument
- clearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- clearInButton - Variable in class org.jmol.console.GenericConsole
- clearKeyBuffer() - Method in class org.jmol.awt.Mouse
- clearKeyBuffer() - Method in class org.jmol.awtjs2d.Mouse
- clearLastModelSet() - Method in class org.jmol.modelkit.ModelKitPopup
- clearLineCache() - Method in class org.jmol.g3d.LineRenderer
- clearListener(AbstractButton) - Method in class org.jmol.awt.AwtPopupHelper
- clearListeners(Object[]) - Method in class org.jmol.awt.AwtPopupHelper
- clearMap() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- clearMeasurements() - Method in class org.jmol.api.JmolViewer
- clearMeasurements() - Method in class org.jmol.viewer.Viewer
- clearMesh(String) - Method in class org.jmol.shape.Mesh
- clearMinimization() - Method in class org.jmol.viewer.Viewer
- clearModelDependentObjects() - Method in class org.jmol.viewer.Viewer
- clearMouseInfo() - Method in class org.jmol.viewer.ActionManager
- clearOrbitals() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- clearOutButton - Variable in class org.jmol.console.GenericConsole
- clearPixel(int, int) - Method in class org.jmol.g3d.Pixelator
- clearPixel(int, int) - Method in class org.jmol.g3d.PixelatorT
- clearQueue() - Method in interface org.jmol.api.JmolScriptManager
- clearQueue() - Method in class org.jmol.script.ScriptManager
- clearReaderData() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- clearRepaintManager(int) - Method in class org.jmol.viewer.Viewer
- clearRule4Lists() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Clear Rule 4b information if Rule-5 pseudochiral centers have been found, as that could change the order of descriptors in the Mata list.
- clearScreenBuffer() - Method in class org.jmol.g3d.Platform3D
- clearScreenBufferThreaded() - Method in class org.jmol.g3d.Platform3D
- clearScriptQueue() - Method in class org.jmol.viewer.Viewer
- clearSelection() - Method in class org.jmol.api.JmolViewer
- clearSelection() - Method in class org.jmol.awtjs.swing.JTable
- clearSelection() - Method in class org.jmol.viewer.Viewer
- clearSelection(boolean) - Method in class org.jmol.viewer.SelectionManager
- clearSg() - Method in class org.jmol.shapesurface.Isosurface
- clearSg() - Method in class org.jmol.shapesurface.MolecularOrbital
- clearShapeManager(Error) - Method in class org.jmol.script.ScriptParallelProcessor
- clearShapeRenderers() - Method in class org.jmol.viewer.Viewer
- clearSmallRingEZ(SimpleNode[], Lst<int[]>) - Method in class org.jmol.symmetry.CIPChirality
-
Remove E/Z designations for small-rings double bonds (IUPAC 2013.P-93.5.1.4.1).
- clearSortingState() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- clearSpin() - Method in class org.jmol.viewer.TransformManager
- clearState(boolean) - Method in class org.jmol.script.ScriptEval
- clearStateStack() - Method in class org.jmol.viewer.StateManager
- clearStructures() - Method in class org.jmol.modelsetbio.AlphaPolymer
- clearStructures() - Method in class org.jmol.modelsetbio.BioPolymer
- clearTBuffer() - Method in class org.jmol.g3d.Platform3D
- clearTemp() - Method in class org.jmol.viewer.StateCreator
- clearTempPoints() - Method in class org.jmol.util.TempArray
- clearTempScreens() - Method in class org.jmol.util.TempArray
- clearThreads() - Method in class org.jmol.viewer.TransformManager
- clearThreads() - Method in class org.jmol.viewer.Viewer
- clearTimeout(String) - Method in class org.jmol.viewer.Viewer
- clearTimeouts() - Method in class org.jmol.viewer.Viewer
- clearType(String, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- clearUnitCell() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- clearV(MeshCapper.CapVertex) - Static method in class org.jmol.util.MeshCapper
- clearVibration() - Method in class org.jmol.viewer.TransformManager
- clearViewerSelection() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- clearVisibleSets() - Method in class org.jmol.modelset.AtomCollection
- click(HTMLElement, HTMLWindowEvent) - Method in interface org.jmol.awtjs.swing.SwingController
-
Fired from clicking an element such as a button or check box or table entry, or from entering text in a text box.
- CLICK - Enum constant in enum org.jmol.c.CBK
- CLICK - Static variable in class org.jmol.multitouch.ActionManagerMT
- CLICK - Static variable in class org.jmol.viewer.binding.Binding
- CLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- clickabilityFlags - Variable in class org.jmol.modelset.Atom
- clickable - Static variable in class org.jmol.script.T
- clickableMax - Static variable in class org.jmol.viewer.ShapeManager
- clickAction - Variable in class org.jmol.viewer.ActionManager
- clicked - Variable in class org.jmol.viewer.ActionManager
- clicked(long, int, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
- CLICKED - Static variable in class org.jmol.awtjs.Event
- clickedCount - Variable in class org.jmol.viewer.ActionManager
- clickToSetElement - Variable in class org.jmol.modelkit.ModelKit
-
Except for H atoms, do not allow changes to elements just by clicking them.
- client - Variable in class org.jmol.modelset.MeasurementData
- client - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- clientService - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- clientThread - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- clipboard - Static variable in class org.jmol.script.T
- clipCode(int) - Method in class org.jmol.util.GData
- clipCode(int, int, int) - Method in class org.jmol.export.Export3D
- clipCode3(int, int, int) - Method in class org.jmol.util.GData
- clipImageOrPasteText(String) - Method in class org.jmol.api.JmolViewer
- clipImageOrPasteText(String) - Method in class org.jmol.viewer.OutputManager
- clipImageOrPasteText(String) - Method in class org.jmol.viewer.OutputManagerAwt
- clipImageOrPasteText(String) - Method in class org.jmol.viewer.OutputManagerJS
- clipImageOrPasteText(String) - Method in class org.jmol.viewer.Viewer
- clipped - Variable in class org.jmol.g3d.CylinderRenderer
- cList - Variable in class org.jmol.awtjs.swing.Container
- cList - Variable in class org.jmol.shapecgo.CGOMesh
- clone() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- clone() - Method in class org.jmol.adapter.smarter.Structure
- clone() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
- clone() - Method in class org.jmol.util.Vibration
- cloneAtomSetWithBonds(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- cloneFirstAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- cloneLastAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- cloneLastAtomSet(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- cloneLastAtomSetFromPoints(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- cloneUnitCell(UnitCell) - Static method in class org.jmol.symmetry.UnitCell
- cloneV() - Method in class org.jmol.util.MeshCapper.CapVertex
- close() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- close() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- close() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- close() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- close() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- close() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- close(Object) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- closeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CloseAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
- closeButton - Variable in class org.jmol.console.ScriptEditor
- closeButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- closeButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- closeMe() - Method in interface org.jmol.api.GenericImageDialog
- closeMe() - Method in class org.jmol.console.ImageDialog
- closePreview() - Method in class org.jmol.dialog.Dialog
- closeReader() - Method in class org.jmol.jvxl.readers.BCifDensityReader
- closeReader() - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
- closeReader() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- closeReader() - Method in class org.jmol.jvxl.readers.SurfaceReader
- closeReader() - Method in class org.jmol.jvxl.readers.VolumeDataReader
- closeReader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
- closeReaderSFR() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- closeSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
- closest - Variable in class org.jmol.modelset.ModelSet
- closest(P3, P3[]) - Method in class org.jmol.util.BZone
- closestAtom - Variable in class org.jmol.shape.Sticks
- closeStream() - Method in class org.jmol.util.JSONWriter
- closeTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
- cm - Variable in class org.jmol.viewer.Viewer
- cM - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- cMapSourceBRIX - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cMapSourceCCP4 - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cMapSourceChempyBrick - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cMapSourceCrystallographic - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cMapSourceDesc - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cMapSourceFLD - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cMapSourceGeneralPurpose - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cMapSourceGRD - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cMapSourceObsolete - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cMapSourceVMDPlugin - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- cmd(String) - Method in class org.jmol.util.BZone
- cmdAnimation() - Method in class org.jmol.script.ScriptEval
- cmdAssignAddAtoms(String, P3[], BS, String, String, boolean) - Method in class org.jmol.modelkit.ModelKit
-
MODELKIT ADD @3 ...
- cmdAssignAtom(int, P3, String, String, boolean) - Method in class org.jmol.modelkit.ModelKit
-
A versatile method that allows changing element, setting charge, setting position, adding or deleting an atom by clicking or dragging or via the MODELKIT ASSIGN ATOM command.
- cmdAssignBond(int, char, String) - Method in class org.jmol.modelkit.ModelKit
- cmdAssignConnect(int, int, char, String) - Method in class org.jmol.modelkit.ModelKit
- cmdAssignDeleteAtoms(BS) - Method in class org.jmol.modelkit.ModelKit
-
Delete all atoms that are equivalent to this atom.
- cmdAssignMoveAtoms(BS, int, P3, boolean) - Method in class org.jmol.modelkit.ModelKit
-
Move all atoms that are equivalent to this atom PROVIDED that they have the same symmetry-invariant properties.
- cmdAssignSpaceGroup(BS, String, int) - Method in class org.jmol.modelkit.ModelKit
-
Assign a given space group, currently only "P1"
- cmdAxes(int) - Method in class org.jmol.script.ScriptEval
- cmdBackground(int) - Method in class org.jmol.script.ScriptEval
- cmdBind() - Method in class org.jmol.script.ScriptEval
- cmdBondorder() - Method in class org.jmol.script.ScriptEval
- cmdBoundbox(int) - Method in class org.jmol.script.ScriptEval
- cmdCD() - Method in class org.jmol.script.ScriptEval
- cmdCenter(int) - Method in class org.jmol.script.ScriptEval
- cmdColor() - Method in class org.jmol.script.ScriptEval
- cmdDefine() - Method in class org.jmol.script.ScriptEval
- cmdDelay() - Method in class org.jmol.script.ScriptEval
- cmdDelete() - Method in class org.jmol.script.ScriptEval
- cmdDisplay(boolean) - Method in class org.jmol.script.ScriptEval
- cmdDots(int) - Method in class org.jmol.script.ScriptEval
- cmdEcho(int) - Method in class org.jmol.script.ScriptEval
- cmdExt - Variable in class org.jmol.script.ScriptExpr
- CmdExt - Class in org.jmol.scriptext
- CmdExt() - Constructor for class org.jmol.scriptext.CmdExt
- cmdFile() - Method in class org.jmol.script.ScriptEval
- cmdFixed() - Method in class org.jmol.script.ScriptEval
- cmdFlow(int, boolean, Lst<T[]>) - Method in class org.jmol.script.ScriptEval
- cmdFlowSwitch(ContextToken, int) - Method in class org.jmol.script.ScriptEval
- cmdFont(int, float) - Method in class org.jmol.script.ScriptEval
- cmdFor(int, boolean) - Method in class org.jmol.script.ScriptEval
- cmdFrank(int) - Method in class org.jmol.script.ScriptEval
- cmdFunc() - Method in class org.jmol.script.ScriptEval
- cmdGetProperty() - Method in class org.jmol.script.ScriptEval
- cmdGoto(boolean) - Method in class org.jmol.script.ScriptEval
- cmdHbond() - Method in class org.jmol.script.ScriptEval
- cmdHelp() - Method in class org.jmol.script.ScriptEval
- cmdHistory(int) - Method in class org.jmol.script.ScriptEval
- cmdHover() - Method in class org.jmol.script.ScriptEval
- cmdLabel(int, BS) - Method in class org.jmol.script.ScriptEval
- cmdLoad() - Method in class org.jmol.script.ScriptEval
- cmdLog() - Method in class org.jmol.script.ScriptEval
- cmdLoop() - Method in class org.jmol.script.ScriptEval
- cmdMessage() - Method in class org.jmol.script.ScriptEval
- cmdModel(int) - Method in class org.jmol.script.ScriptEval
-
ONE difference between FRAME and MODEL: model 1 sets model NAMED one in the case of PDB frame 1 always sets the first model
- cmdMove() - Method in class org.jmol.script.ScriptEval
- cmdMoveto() - Method in class org.jmol.script.ScriptEval
- cmdPause() - Method in class org.jmol.script.ScriptEval
- cmdPrint() - Method in class org.jmol.script.ScriptEval
- cmdPrompt() - Method in class org.jmol.script.ScriptEval
- cmdpt0 - Variable in class org.jmol.script.ScriptFunction
- cmdReset() - Method in class org.jmol.script.ScriptEval
- cmdRestore() - Method in class org.jmol.script.ScriptEval
- cmdRestrict() - Method in class org.jmol.script.ScriptEval
- cmdReturn(SV) - Method in class org.jmol.script.ScriptEval
- cmdRotate(boolean, boolean) - Method in class org.jmol.script.ScriptEval
- cmdRotateAtoms(BS, P3[], float) - Method in class org.jmol.modelkit.ModelKit
- cmds - Variable in class org.jmol.rendercgo.CGORenderer
- cmds - Variable in class org.jmol.shapecgo.CGOMesh
- cmdSave() - Method in class org.jmol.script.ScriptEval
- cmdScale(int) - Method in class org.jmol.script.ScriptEval
- cmdScript(int, String, String) - Method in class org.jmol.script.ScriptEval
- cmdSelect(int) - Method in class org.jmol.script.ScriptEval
- cmdSelectionHalos(int) - Method in class org.jmol.script.ScriptEval
- cmdSet() - Method in class org.jmol.script.ScriptEval
- cmdSetEcho(int) - Method in class org.jmol.script.ScriptEval
- cmdSetLabel(String) - Method in class org.jmol.script.ScriptEval
- cmdSetPicking() - Method in class org.jmol.script.ScriptEval
- cmdSetPickingStyle() - Method in class org.jmol.script.ScriptEval
- cmdSlab(boolean) - Method in class org.jmol.script.ScriptEval
- cmdSsbond() - Method in class org.jmol.script.ScriptEval
- cmdStructure() - Method in class org.jmol.script.ScriptEval
- cmdSubset() - Method in class org.jmol.script.ScriptEval
- cmdSync() - Method in class org.jmol.script.ScriptEval
- cmdThrow() - Method in class org.jmol.script.ScriptEval
- cmdTimeout(int) - Method in class org.jmol.script.ScriptEval
- cmdTranslate(boolean) - Method in class org.jmol.script.ScriptEval
- cmdUnbind() - Method in class org.jmol.script.ScriptEval
- cmdUndoRedo(int) - Method in class org.jmol.script.ScriptEval
- cmdUnitcell(int) - Method in class org.jmol.script.ScriptEval
- cmdVector() - Method in class org.jmol.script.ScriptEval
- cmdVibration() - Method in class org.jmol.script.ScriptEval
- cmdWireframe() - Method in class org.jmol.script.ScriptEval
- cmdZap(boolean) - Method in class org.jmol.script.ScriptEval
- cmdZoom(boolean) - Method in class org.jmol.script.ScriptEval
- cmeshes - Variable in class org.jmol.shapecgo.CGO
- cmi - Variable in class org.jmol.viewer.AnimationManager
-
current model index
- CML - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- CML_NAMESPACE_URI - Static variable in class org.jmol.adapter.smarter.Resolver
- CMLWriter - Class in org.jmol.adapter.writers
-
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
- CMLWriter() - Constructor for class org.jmol.adapter.writers.CMLWriter
- cnmrPeaks - Variable in class org.jmol.popup.JmolPopup
- code - Variable in class org.jmol.adapter.readers.cif.Subsystem
- code - Variable in enum org.jmol.c.FIL
- code - Variable in class org.jmol.i18n.Language
- code - Variable in enum org.jmol.util.Edge.EnumBondOrder
- Code() - Constructor for enum org.jmol.modelsetbio.AlphaPolymer.Code
- codeBase - Variable in class org.jmol.util.GenericApplet
- codePath - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- coef - Variable in class org.jmol.g3d.SphereRenderer
- coef - Variable in class org.jmol.jvxl.readers.IsoMOReader
- coef - Variable in class org.jmol.quantum.SlaterData
- COEF_INDICES - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- coef1 - Static variable in class org.jmol.quantum.NciCalculation
- coef2 - Static variable in class org.jmol.quantum.NciCalculation
- coef3 - Static variable in class org.jmol.quantum.NciCalculation
- coefCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- coefCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- coeffs - Variable in class org.jmol.quantum.MOCalculation
- coefs - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
- coefs - Variable in class org.jmol.jvxl.readers.IsoMOReader
- coefs - Variable in class org.jmol.quantum.MOCalculation
- coefs - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- col - Static variable in class org.jmol.script.T
- col2key - Variable in class org.jmol.adapter.readers.cif.CifReader
- colix - Variable in class org.jmol.adapter.smarter.Bond
- colix - Variable in class org.jmol.export.Export3D
- colix - Variable in class org.jmol.modelset.Bond
- colix - Variable in class org.jmol.modelset.Measurement
- colix - Variable in class org.jmol.modelset.MeasurementData
- colix - Variable in class org.jmol.modelset.Text
- colix - Variable in class org.jmol.render.ShapeRenderer
- colix - Variable in class org.jmol.renderbio.NucleicRenderer
- colix - Variable in class org.jmol.renderbio.RocketRenderer
- colix - Variable in class org.jmol.shape.Measures
- colix - Variable in class org.jmol.shape.MeshCollection
- colix - Variable in class org.jmol.shapespecial.Dipole
- colix - Variable in class org.jmol.shapespecial.Dipoles
- colix - Variable in class org.jmol.shapespecial.Ellipsoid
- colix - Variable in class org.jmol.shapespecial.Polyhedron
- colix - Variable in class org.jmol.util.MeshSurface
- colix - Variable in class org.jmol.viewer.Connection
- colix0 - Variable in class org.jmol.rendercgo.CGORenderer
- colix1 - Variable in class org.jmol.rendercgo.CGORenderer
- colix2 - Variable in class org.jmol.rendercgo.CGORenderer
- colixA - Variable in class org.jmol.g3d.CylinderRenderer
- colixA - Variable in class org.jmol.render.FontLineShapeRenderer
- colixA - Variable in class org.jmol.renderspecial.DipolesRenderer
- colixAtom - Variable in class org.jmol.modelset.Atom
- colixB - Variable in class org.jmol.g3d.CylinderRenderer
- colixB - Variable in class org.jmol.render.FontLineShapeRenderer
- colixB - Variable in class org.jmol.renderspecial.DipolesRenderer
- colixBack - Variable in class org.jmol.renderbio.BioShapeRenderer
- colixBack - Variable in class org.jmol.util.MeshSurface
- colixBackgroundContrast - Variable in class org.jmol.viewer.ColorManager
- colixCurrent - Variable in class org.jmol.util.GData
- colixEdge - Variable in class org.jmol.shapespecial.Polyhedron
- colixEndcap - Variable in class org.jmol.g3d.CylinderRenderer
- colixes - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- colixes - Variable in class org.jmol.render.AxesRenderer
- colixes - Variable in class org.jmol.renderbio.BioShapeRenderer
- colixes - Variable in class org.jmol.shape.AtomShape
- colixesBack - Variable in class org.jmol.renderbio.BioShapeRenderer
- colixesBack - Variable in class org.jmol.shapebio.BioShape
- colixHash - Static variable in class org.jmol.util.C
- colixHighlight - Variable in class org.jmol.shape.Halos
- colixMax - Static variable in class org.jmol.util.C
- colixRubberband - Variable in class org.jmol.viewer.ColorManager
- colixSelection - Variable in class org.jmol.shape.Halos
- collapsed - Static variable in class org.jmol.script.T
- collapsed - Variable in class org.jmol.shapespecial.Polyhedron
- COLLECTION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
String for prefix/resource identifier for the collection area.
- collectionName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- colon - Static variable in class org.jmol.script.T
- color - Variable in enum org.jmol.c.STR
- color - Variable in class org.jmol.jvxl.data.JvxlData
- color - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
- color - Static variable in class org.jmol.script.T
- color - Variable in class org.jmol.shape.Mesh
- color - Variable in class org.jmol.shape.MeshCollection
- color - Variable in class org.jmol.util.BZone
- color - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- Color - Class in org.jmol.awtjs.swing
- Color() - Constructor for class org.jmol.awtjs.swing.Color
- COLOR - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- COLOR - Static variable in class org.jmol.shape.Echo
- COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
- COLOR_BACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- COLOR_BLACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- COLOR_FRONT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- color4(short) - Method in class org.jmol.export._PovrayExporter
- colorArrayed - Variable in class org.jmol.shapesurface.PMeshWriter
- colorByPhase - Variable in class org.jmol.jvxl.readers.Parameters
- colorBySets - Variable in class org.jmol.jvxl.readers.Parameters
- colorBySign - Variable in class org.jmol.jvxl.readers.Parameters
- colorCellRenderer - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- colorCellRenderer - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- colorCommand - Variable in class org.jmol.shape.Mesh
- colorCommand(SimpleAttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- colorData - Variable in class org.jmol.viewer.ColorManager
- colorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
- colorDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- colorDensity - Variable in class org.jmol.jvxl.calc.MarchingCubes
- colorDensity - Variable in class org.jmol.jvxl.data.JvxlData
- colorDensity - Variable in class org.jmol.jvxl.readers.Parameters
- colorDensity - Variable in class org.jmol.shape.Mesh
- colorEncoder - Variable in class org.jmol.jvxl.readers.Parameters
- colorEncoder - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- ColorEncoder - Class in org.jmol.util
- ColorEncoder(ColorEncoder, Viewer) - Constructor for class org.jmol.util.ColorEncoder
- colorFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
- colorFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
- colorFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
- colorFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
- colorIndex(float, int) - Static method in class org.jmol.util.ColorEncoder
- colorIndexRepeat(float, int) - Static method in class org.jmol.util.ColorEncoder
- colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
- ColorManager - Class in org.jmol.viewer
- ColorManager(Viewer, GData) - Constructor for class org.jmol.viewer.ColorManager
- colorNeg - Variable in class org.jmol.jvxl.readers.Parameters
- colorNegLCAO - Variable in class org.jmol.jvxl.readers.Parameters
- colorPhase - Variable in class org.jmol.jvxl.readers.Parameters
- colorPhased - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- colorPhases - Static variable in class org.jmol.jvxl.readers.SurfaceReader
- colorPos - Variable in class org.jmol.jvxl.readers.Parameters
- colorPosLCAO - Variable in class org.jmol.jvxl.readers.Parameters
- colorPtr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- colorPtr - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- colorrasmol - Static variable in class org.jmol.script.T
- colorRgb - Variable in class org.jmol.jvxl.readers.Parameters
- colors - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- colorscheme - Static variable in class org.jmol.script.T
- colorScheme - Variable in class org.jmol.jvxl.data.JvxlData
- colorSchemes - Static variable in class org.jmol.util.ColorEncoder
- colorSchemeTranslucent - Variable in class org.jmol.jvxl.readers.Parameters
- colorSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- colorSettingClamped(Lst<Object>, P3) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- colorsExplicit - Variable in class org.jmol.util.MeshSurface
- colorShape(int, int, boolean) - Method in class org.jmol.script.ScriptEval
- colorSolid - Variable in class org.jmol.shapesurface.PMeshWriter
- colorType - Variable in class org.jmol.shape.Mesh
- colorType - Variable in class org.jmol.shapesurface.Isosurface
- colorVertices(short, BS, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
color a specific set of vertices a specific color
- colspan - Variable in class org.jmol.awtjs.swing.Cell
- column - Variable in class org.openscience.jmol.app.janocchio.TableSorter.Directive
- columnComparators - Variable in class org.openscience.jmol.app.janocchio.TableSorter
- ColumnSelectionModel - Interface in org.jmol.awtjs.swing
- combineModulation(String, float, float) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
Retrieve cataloged displacement and add in this component, returning a new double[3].
- combineSurfaces(Lst<ContactPair>, int, int, float[], Object, boolean, boolean) - Method in class org.jmol.shapesurface.Contact
- comma - Static variable in class org.jmol.script.T
- command - Static variable in class org.jmol.script.T
- command - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- commandDelay - Static variable in class org.jmol.script.CommandWatcherThread
- commandExpected() - Method in class org.jmol.script.ScriptTokenParser
- commandHistory - Variable in class org.jmol.viewer.Viewer
- CommandHistory - Class in org.jmol.util
-
Implements a queue for a bash-like command history.
- CommandHistory() - Constructor for class org.jmol.util.CommandHistory
-
Creates a new instance using the default size (100)
- commandHistoryLevelMax - Static variable in class org.jmol.script.ScriptEval
- commandLineOptions - Variable in class org.jmol.export.___Exporter
- commandList - Variable in class org.jmol.util.CommandHistory
-
Array of commands.
- commandLoop(boolean) - Method in class org.jmol.script.ScriptEval
- commandOptions - Variable in class org.jmol.viewer.Viewer
- commands - Static variable in class org.jmol.script.T
- commands - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- commands - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- commandStart - Variable in class org.jmol.script.ScriptFlowContext
- commandWatcherThread - Variable in class org.jmol.script.ScriptManager
- CommandWatcherThread - Class in org.jmol.script
- CommandWatcherThread() - Constructor for class org.jmol.script.CommandWatcherThread
- commensurateSection1 - Variable in class org.jmol.adapter.readers.cif.MSRdr
- comment - Variable in class org.jmol.script.ScriptCompiler
- commentChar - Variable in class org.jmol.export.___Exporter
- COMPARABLE_COMAPRATOR - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- comparator - Static variable in class org.jmol.script.T
- compare - Static variable in class org.jmol.script.T
- compare() - Method in class org.jmol.scriptext.CmdExt
-
Compares one set of atoms to another, generating the matrix that takes that maps the first set's coordinates to the second's.
- compare(Object[], Object[]) - Method in class org.jmol.shapespecial.Polyhedra
- compare(Object[], Object[]) - Method in class org.jmol.smiles.PolyhedronStereoSorter
-
Comparison is by torsion angle, as set previously and passed in as Float a[1] and b[1].
- compare(Object, Object) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
- compare(Object, Object) - Method in class org.jmol.util.EigenSort
- compare(String[], String[]) - Method in class org.jmol.modelsetbio.BioResolver
- compare(Map<String, Object>, Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
- compare(Option, Option) - Method in class org.openscience.jmol.app.JmolApp.OptSort
- compare(TextString, TextString) - Method in class org.jmol.g3d.TextString
- compare(MeshData.SSet, MeshData.SSet) - Method in class org.jmol.jvxl.data.MeshData.SortSet
- compare(Atom, Atom) - Method in class org.jmol.modelset.AtomCollection.AtomSorter
- compare(SlaterData, SlaterData) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
- compare(SV, SV) - Method in class org.jmol.script.SV.Sort
- compare(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.MeshCapperSorter
- compareAtoms(int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- compareAtoms(int, int) - Method in interface org.jmol.api.PymolAtomReader
- compareFloat(int, float, float) - Method in class org.jmol.script.ScriptExpr
- compareFloatData(int, float[], int, float) - Method in class org.jmol.script.ScriptExpr
- compareInt(int, int, int) - Method in class org.jmol.script.ScriptExpr
- compareLikeUnlike(BS, BS) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
- compareRule1a(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Looking for phantom atom (atom number 0) or element number
- compareRule1b(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Looking for root distance -- duplicate atoms only.
- compareRule2(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Chapter 9 Rule 2.
- compareRule3(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Chapter 9 Rule 3.
- compareRule4b5(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Compare the better R-ref or S-ref list for A with the same for B.
- compareRule6(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Just look for match with the Rule 6 reference atom index
- compareRules4ac(CIPChirality.CIPAtom, String) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Chapter 9 Rules 4a and 4c.
- compareString(int, int, String) - Method in class org.jmol.script.ScriptExpr
- compareStringValues(int, String, String) - Method in class org.jmol.script.ScriptExpr
- compareTo(Object) - Method in class org.openscience.jmol.app.janocchio.TableSorter.Row
- compareTo(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Used in Array.sort when an atom is set and Collection.sort when determining the Mata like/unlike sequence for Rules 4b and 5.
- compareTo(Measure) - Method in class org.openscience.jmol.app.janocchio.Measure
- compile(String, boolean) - Method in interface org.jmol.api.JmolPatternMatcher
- compile(String, boolean) - Method in class org.jmol.util.PatternMatcher
- compile(String, String, boolean, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptCompiler
- compile(Viewer, String, char, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
-
Compiles a set of tokens for each primitive element of a label.
- compile0(boolean) - Method in class org.jmol.script.ScriptCompiler
- compileCommand() - Method in class org.jmol.script.ScriptCompiler
- compileExpr(String) - Method in class org.jmol.viewer.Viewer
- compileExpression() - Method in class org.jmol.script.ScriptTokenParser
- compileExpressions() - Method in class org.jmol.script.ScriptTokenParser
- compiler - Variable in class org.jmol.script.ScriptEval
- compiler - Variable in class org.jmol.script.ScriptFlowContext
- compiler - Variable in class org.jmol.viewer.Viewer
- compileScript(String, String, boolean) - Method in class org.jmol.script.ScriptEval
- compileScriptFile(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- compileScriptFile(String, boolean) - Method in class org.jmol.script.ScriptEval
- compileScriptString(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- compileScriptString(String, boolean) - Method in class org.jmol.script.ScriptEval
- compileSelect(SV[]) - Method in class org.jmol.viewer.PropertyManager
- completeCommand(String) - Method in class org.jmol.console.GenericConsole
- completeCommand(Map<String, ?>, boolean, boolean, String, int) - Static method in class org.jmol.script.T
- compnd - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- compnd(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- component - Variable in class org.jmol.awtjs.swing.Cell
- component - Variable in class org.jmol.smiles.SmilesAtom
- Component - Class in org.jmol.awtjs.swing
- Component(String) - Constructor for class org.jmol.awtjs.swing.Component
- componentCount - Variable in class org.jmol.smiles.SmilesParser
- componentHidden(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- componentMoved(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- componentParenCount - Variable in class org.jmol.smiles.SmilesParser
- componentResized(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- componentShown(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- compositions - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.Calculations
- compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
- compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFAngleCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFDistanceCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFESCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFOOPCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFSBCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFTorsionCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFVDWCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFAngleCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFDistanceCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFOOPCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFTorsionCalc
- compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFVDWCalc
- comSSMat - Variable in class org.jmol.adapter.readers.cif.MSCifParser
- concatList(SV, SV, boolean) - Static method in class org.jmol.script.SV
- CONE - Static variable in class org.jmol.shapecgo.CGOMesh
- cone_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- conect() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- coneNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- CONF_TYPE_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- configuration - Static variable in class org.jmol.script.T
- configuration() - Method in class org.jmol.scriptext.CmdExt
- configurationPtr - Variable in class org.jmol.adapter.readers.cif.CifReader
- configurationPtr - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- configurationSelected - Variable in class org.jmol.popup.JmolPopup
- confirm(String, String) - Method in interface org.jmol.api.GenericPlatform
- confirm(String, String) - Method in class org.jmol.awt.Platform
- confirm(String, String) - Method in class org.jmol.awtjs2d.Platform
- confirm(String, String) - Method in class org.jmol.viewer.Viewer
- conformationIndex - Variable in class org.jmol.adapter.readers.cif.CifReader
- conformationIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- connect - Static variable in class org.jmol.script.T
- connect(float[][]) - Method in class org.jmol.modelset.ModelSet
- connect(int) - Method in class org.jmol.scriptext.CmdExt
- connect_bonded - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- connect_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- connect_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- connectAll(int, boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- connectAllBad(int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- connected - Static variable in class org.jmol.script.T
- connectedAtoms - Variable in class org.jmol.shape.Mesh
- Connection - Class in org.jmol.viewer
- Connection(int, int, short, short, int, float, int) - Constructor for class org.jmol.viewer.Connection
- connections - Variable in class org.jmol.adapter.writers.MOLWriter
- connections - Variable in class org.jmol.shape.MeshCollection
- connections - Variable in class org.jmol.smiles.SmilesParser
- connections - Variable in class org.jmol.viewer.Connections
- Connections - Class in org.jmol.viewer
- Connections(Viewer) - Constructor for class org.jmol.viewer.Connections
- connectivity - Variable in class org.jmol.smiles.SmilesAtom
- connectLast - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- connectNBO(int, String) - Method in class org.jmol.adapter.readers.quantum.NBOParser
- connectNBO(String) - Method in class org.jmol.viewer.Viewer
- connectNextAtomIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- connectNextAtomSet - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- connectorFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- connectorFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- connectors - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- console - Variable in class org.jmol.console.ImageDialog
- console - Static variable in class org.jmol.script.T
- console - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- console() - Method in class org.jmol.scriptext.CmdExt
- consoleAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ConsoleAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
- consoleButton - Variable in class org.jmol.console.ScriptEditor
- consoleDoc - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- ConsoleDocument() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- consoleFontScale - Variable in class org.jmol.viewer.Viewer
- consoleframe - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- consoleGetImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Method in interface org.jmol.api.js.JmolToJSmolInterface
- consoleMessage(String) - Method in class org.jmol.util.GenericApplet
- ConsoleTextArea - Class in org.openscience.jmol.app.jmolpanel.console
- ConsoleTextArea(boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
- ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
- consoleTextPane - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- ConsoleTextPane(AppConsole) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- ConsoleWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
- constrain(P3, P3, boolean) - Method in class org.jmol.modelkit.ModelKit.Constraint
- constrainQuadratic(double, double, double, int) - Method in class org.jmol.minimize.forcefield.Calculations
- constraint - Variable in class org.jmol.modelkit.ModelKit
- constraint - Static variable in class org.jmol.script.T
- Constraint(P3, int, Object[]) - Constructor for class org.jmol.modelkit.ModelKit.Constraint
- constraintEnergy(int) - Method in class org.jmol.minimize.forcefield.Calculations
- constraintMap - Variable in class org.jmol.minimize.Minimizer
- constraints - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
- constraints - Variable in class org.jmol.minimize.Minimizer
- constraintsByType - Variable in class org.jmol.minimize.forcefield.Calculations
- constructBitSetPolyhedron(Atom) - Method in class org.jmol.shapespecial.Polyhedra
- constructBondsPolyhedron(Atom, int) - Method in class org.jmol.shapespecial.Polyhedra
- constructCoupleButtonPanel() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- constructCoupleTable() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- constructDismissButtonPanel() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- constructDismissButtonPanel() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- constructDismissButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- constructMeasurementButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- constructMeasurementTable() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- constructNoeButtonPanel() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- constructNoeTable() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- constructRadiusPolyhedron(Atom, AtomIndexIterator) - Method in class org.jmol.shapespecial.Polyhedra
- constructUnitCellPolygon(Atom, boolean) - Method in class org.jmol.shapespecial.Polyhedra
- contact - Static variable in class org.jmol.script.T
- contact() - Method in class org.jmol.scriptext.IsoExt
- Contact - Class in org.jmol.shapesurface
- Contact() - Constructor for class org.jmol.shapesurface.Contact
- contactPair - Variable in class org.jmol.jvxl.readers.AtomDataReader
- contactPair - Variable in class org.jmol.jvxl.readers.Parameters
- ContactPair - Class in org.jmol.util
- ContactPair(Atom[], int, int, float, float, float, float) - Constructor for class org.jmol.util.ContactPair
- ContactRenderer - Class in org.jmol.rendersurface
- ContactRenderer() - Constructor for class org.jmol.rendersurface.ContactRenderer
- contactType - Variable in class org.jmol.util.ContactPair
- container - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- Container - Class in org.jmol.awtjs.swing
- Container(String) - Constructor for class org.jmol.awtjs.swing.Container
- contains(int, int) - Method in class org.jmol.util.Rectangle
- contentPane - Variable in class org.jmol.awtjs.swing.JDialog
- context - Variable in class org.jmol.awtjs2d.Platform
- context - Variable in class org.jmol.script.ScriptProcess
- context - Static variable in class org.jmol.script.T
- CONTEXT_DELAY - Static variable in class org.jmol.script.ScriptEval
- CONTEXT_HOLD_QUEUE - Static variable in class org.jmol.script.ScriptEval
- contextCount - Static variable in class org.jmol.script.ScriptContext
- contextdepthmax - Static variable in class org.jmol.script.T
- contextDepthMax - Static variable in class org.jmol.script.ScriptEval
- contextFunctions - Variable in class org.jmol.script.ScriptParam
- contextPath - Variable in class org.jmol.script.ScriptContext
- contextPath - Variable in class org.jmol.script.ScriptEval
- ContextToken - Class in org.jmol.script
- ContextToken() - Constructor for class org.jmol.script.ContextToken
- contextVariables - Variable in class org.jmol.script.ContextToken
- contextVariables - Variable in class org.jmol.script.ScriptCompiler
- contextVariables - Variable in class org.jmol.script.ScriptParam
- CONTINUE - Static variable in class org.jmol.script.ScriptCompiler
- continuecmd - Static variable in class org.jmol.script.T
- continueWith(String) - Method in class org.jmol.adapter.readers.cif.CifReader
- continuing - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- contour - Static variable in class org.jmol.script.T
- CONTOUR_BITSET - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_COLIX - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_COLOR - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_FDATA - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_NPOLYGONS - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
- CONTOUR_POINTS - Static variable in class org.jmol.jvxl.data.JvxlCoder
- CONTOUR_VALUE - Static variable in class org.jmol.jvxl.data.JvxlCoder
- contourColixes - Variable in class org.jmol.jvxl.data.JvxlData
- contourColixes - Variable in class org.jmol.jvxl.readers.Parameters
- contourColixes - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- contourColixes - Variable in class org.jmol.shapesurface.PMeshWriter
- contourColors - Variable in class org.jmol.jvxl.data.JvxlData
- contourFromZero - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contourFromZero - Variable in class org.jmol.jvxl.readers.Parameters
- contourIncrements - Variable in class org.jmol.jvxl.readers.Parameters
- contourIndex - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
- contourlines - Static variable in class org.jmol.script.T
- contourPlaneMaximumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contourPlaneMinimumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contours - Static variable in class org.jmol.script.T
- contoursDiscrete - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contoursDiscrete - Variable in class org.jmol.jvxl.readers.Parameters
- contourType - Variable in class org.jmol.jvxl.calc.MarchingCubes
- contourType - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contourType - Variable in class org.jmol.jvxl.readers.Parameters
- contourValues - Variable in class org.jmol.jvxl.data.JvxlData
- contourValues - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- contourValuesUsed - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contourValuesUsed - Variable in class org.jmol.jvxl.data.JvxlData
- ContourVertex(P3) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
- contourVertexCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
- contourVertexCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
- contourVertexes - Variable in class org.jmol.jvxl.calc.MarchingSquares
- CONTRACTIONS - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- ControlEnterTextArea() - Constructor for class org.jmol.console.AppletConsole.ControlEnterTextArea
- controlHermites - Variable in class org.jmol.renderbio.BioMeshRenderer
- controlHermites - Variable in class org.jmol.renderspecial.DrawRenderer
- controlPoints - Variable in class org.jmol.modelsetbio.BioPolymer
- controlPoints - Variable in class org.jmol.renderbio.BioShapeRenderer
- controlPointScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
- converged - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
- convertPointFromScreen(Object, P3) - Method in interface org.jmol.api.GenericPlatform
- convertPointFromScreen(Object, P3) - Static method in class org.jmol.awt.Display
- convertPointFromScreen(Object, P3) - Method in class org.jmol.awt.Platform
- convertPointFromScreen(Object, P3) - Static method in class org.jmol.awtjs2d.Display
- convertPointFromScreen(Object, P3) - Method in class org.jmol.awtjs2d.Platform
- convertToMegabytes(long) - Static method in class org.jmol.popup.GenericPopup
- CONVEX_HULL_MAX - Static variable in class org.jmol.shapespecial.Polyhedra
- coord - Variable in class org.jmol.minimize.MinAtom
- coord - Static variable in class org.jmol.script.T
- coordinateInRange(int, int, T3, int, P3i) - Method in class org.jmol.shape.Shape
- coordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- coordinatesAreFractional - Variable in class org.jmol.script.ScriptParam
-
set in getPointOrPlane
- coordinatesAreFractional - Variable in class org.jmol.symmetry.SymmetryInfo
- coordinatesAreFractional(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- coordinatesAreFractional(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the boolean whether coordinates are fractional.
- coordinatesArePrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- coords - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- coords - Variable in class org.jmol.shapespecial.Dipole
- coordSaved - Variable in class org.jmol.minimize.forcefield.ForceField
- coordSaved - Variable in class org.jmol.minimize.Minimizer
- copy() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- copy() - Method in class org.jmol.util.Point3fi
- copy(BS) - Static method in class org.jmol.util.BSUtil
- copy2(BS, BS) - Static method in class org.jmol.util.BSUtil
- copyandUnzip(String, String, String) - Method in class org.openscience.jmol.app.webexport.WebPanel
-
Based on code available at Java2s.com
- copyBinaryFile(String, String) - Method in class org.openscience.jmol.app.webexport.WebPanel
- copyColixTranslucency(short, short) - Static method in class org.jmol.util.C
- copyImageAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CopyImageAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
- copyImageActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- copyInvert(BS, int) - Static method in class org.jmol.util.BSUtil
- copyModulations(String, String) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
Create a new catalog entry for an atom's modulation components.
- copyright - Static variable in class org.jmol.viewer.JC
- copyScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CopyScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
- copyScriptActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- copyTensor() - Method in class org.jmol.util.Tensor
- copyTo(P3, AtomSetCollection) - Method in class org.jmol.adapter.smarter.Atom
- cordMidPoints - Variable in class org.jmol.renderbio.RocketsRenderer
- corner - Variable in class org.jmol.shape.Axes
- corners - Variable in class org.jmol.renderbio.RocketRenderer
- corners - Static variable in class org.jmol.script.T
- cos - Static variable in class org.jmol.script.T
- cosAlpha - Variable in class org.jmol.util.SimpleUnitCell
- cosASB2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- cosBeta - Variable in class org.jmol.util.SimpleUnitCell
- cosGamma - Variable in class org.jmol.util.SimpleUnitCell
- cosPhi - Variable in class org.jmol.g3d.CylinderRenderer
- cossin - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- cosTheta - Variable in class org.jmol.g3d.CylinderRenderer
- cosTolerance - Variable in class org.jmol.symmetry.PointGroup
- couldBeChiralAlkene(SimpleNode, SimpleEdge) - Method in class org.jmol.symmetry.CIPData
-
Allow double bonds only if trivalent and first-row atom.
- couldBeChiralAtom(SimpleNode) - Method in class org.jmol.symmetry.CIPData
-
Determine whether an atom is one we need to consider.
- coulomb_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- coulomb_dielectric - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- coulomb_units_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- count - Variable in class org.jmol.bspt.Element
- count - Variable in class org.jmol.modelset.Measurement
- count - Variable in class org.jmol.render.MeasuresRenderer
- count - Static variable in class org.jmol.script.T
- COUNT_MASK - Static variable in class org.jmol.viewer.binding.Binding
- countAuxDuplicates(int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Get a count of the number of duplicate nodes to the auxiliary atom.
- countData(String) - Method in class org.jmol.jvxl.readers.JvxlReader
- countData(String) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- counter - Variable in class org.jmol.script.ScriptParallelProcessor
- countGroup(int, String, String) - Method in class org.jmol.modelset.ModelLoader
- countPlusIndices - Variable in class org.jmol.modelset.Measurement
- countsXYZ - Variable in class org.jmol.quantum.QuantumCalculation
- coupleAddAllButton - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- coupleColourSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- CoupleColourSelectionPanel - Class in org.openscience.jmol.app.janocchio
- CoupleColourSelectionPanel(CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- coupledeleteAllButton - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- coupledeleteButton - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- coupleHeaders - Variable in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- CoupleListWindowListener() - Constructor for class org.openscience.jmol.app.janocchio.CoupleTable.CoupleListWindowListener
- CoupleParameterSelectionPanel - Class in org.openscience.jmol.app.janocchio
- CoupleParameterSelectionPanel(CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
-
Creates new form noeParameterSelectionPanel
- couples - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- coupleSelection - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- couplesWhole - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- coupleTable - Variable in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- coupleTable - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- coupleTable - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- coupleTable - Variable in class org.openscience.jmol.app.janocchio.LabelSetter
- coupleTable - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- CoupleTable - Class in org.openscience.jmol.app.janocchio
- CoupleTable(NMR_JmolPanel, JFrame) - Constructor for class org.openscience.jmol.app.janocchio.CoupleTable
-
Constructor
- CoupleTable.CoupleListWindowListener - Class in org.openscience.jmol.app.janocchio
- CoupleTable.CoupleTableModel - Class in org.openscience.jmol.app.janocchio
- coupleTableModel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- CoupleTableModel() - Constructor for class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- coupleWeight - Variable in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- coupleWeightField - Variable in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- covalentHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
- covalentradius - Static variable in class org.jmol.script.T
- covalentVersion - Static variable in class org.jmol.util.Elements
- CPK - Enum constant in enum org.jmol.c.PAL
- cpno - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- cr - Variable in class org.jmol.adapter.readers.cif.MSRdr
- create - Static variable in class org.jmol.script.T
- create(SimpleNode, CIPChirality.CIPAtom, boolean, boolean, boolean) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
- createActions() - Method in class org.jmol.viewer.ActionManager
- createAllBZs(int, boolean, String, float) - Method in class org.jmol.util.BZone
-
Starting with 1, build the Brillouin zones as polyhedra, optionally discarding the previous as we go.
- createAndShowGUI(Viewer, HistoryFile, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
- createAtomDataSet(Object, int) - Method in class org.jmol.viewer.ModelManager
- createAtomDataSet(Viewer, ModelSet, int, Object, BS) - Static method in class org.jmol.modelset.ModelLoader
- createAtomSeCollectionFromArrayData(Lst<Object>, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
- createAtomSeCollectionFromStrings(String[], SB, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
- createAtomSetCollectionFromFile(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
- createAtomSetCollectionFromFiles(String[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
- createAtomSetCollectionFromReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
-
not used in Jmol project -- will close reader
- createAtomSetCollectionFromString(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
- createAuxiliaryDescriptors(CIPChirality.CIPAtom, CIPChirality.CIPAtom[]) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
By far the most complex of the methods, this method creates a list of downstream (higher-sphere) auxiliary chirality designators, starting with those furthest from the root and moving in, toward the root.
- createBonds(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
-
Use the site bitset to check for atoms that are within +/-dx Angstroms of the specified distances in GEOM_BOND where dx is determined by the uncertainty (dx) in the record.
- createBZ(int, Object[], boolean, String, float) - Method in class org.jmol.util.BZone
-
Create a Brillouin zone.
- createCap(V3) - Method in class org.jmol.util.MeshCapper
-
Entry point when finished generating edges.
- createCartoonObject(String, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- createColorScheme(String, boolean, boolean) - Method in class org.jmol.util.ColorEncoder
- createContours(float, float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- createCube() - Method in class org.jmol.quantum.MepCalculation
- createCube() - Method in class org.jmol.quantum.MOCalculation
- createCube() - Method in class org.jmol.quantum.NciCalculation
- createCube() - Method in class org.jmol.quantum.QuantumCalculation
- CREATED - Enum constant in enum org.jmol.c.FIL
- createDFMap(int[], String, String, int) - Static method in class org.jmol.quantum.QS
- createDialog(Component) - Method in class org.jmol.dialog.FileChooser
- createDisplayAndAddStatusListener() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- createDisplayAndAddStatusListener() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- createDomNodeJS(String, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
-
totally untested, probably useless
- createEllipsoidShades() - Method in class org.jmol.util.Shader
- createExportPanel(String[], String[], String) - Method in class org.jmol.dialog.Dialog
- createFileData(String) - Method in interface org.jmol.api.JmolDataManager
- createFileData(String) - Method in class org.jmol.viewer.DataManager
- createFont3D(int, int, float, float, FontManager, Object) - Static method in class org.jmol.util.Font
- createFunction(String, String, String) - Method in class org.jmol.scriptext.IsoExt
-
for the ISOSURFACE command
- createGeodesic() - Method in class org.jmol.jvxl.readers.IsoShapeReader
- createGeodesic(int) - Static method in class org.jmol.util.Geodesic
- createGuiMap() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- createGuiMap() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- createHAtomList(Viewer, BS, BS, Map<Atom, String>, Map<String, Lst<Atom>>) - Static method in class org.jmol.quantum.NMRNoeMatrix
- createHelix(Viewer, int, int[], float[], boolean) - Static method in class org.jmol.modelsetbio.BioExt
- createImage(Object) - Method in interface org.jmol.api.GenericPlatform
-
can be ignored (return null) if platform cannot save images
- createImage(Object) - Method in class org.jmol.awt.Platform
-
could be byte[] (from ZIP file) or String (local file name) or URL
- createImage(Object) - Method in class org.jmol.awtjs2d.Platform
- createImage(Object, PlatformViewer) - Static method in class org.jmol.awt.Image
- createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolStatusListener
-
Starting with Jmol 11.8.RC5, for a context where the Jmol application is embedded in another application simply to send the returned message to the application.
- createImage(String, String, Object, int) - Method in class org.jmol.util.GenericApplet
- createImage(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- createImage(String, String, String, byte[], int) - Method in class org.jmol.viewer.StatusManager
-
offer to let application do the image creation.
- createImageStatus(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Starting with Jmol 11.8.RC5, this is just informational if type == null and null is returned, then it means "Jmol, you handle it"
- createInfoArray(SymmetryOperation, SymmetryInterface, P3, P3, String, float, int, boolean, BS) - Method in class org.jmol.symmetry.SymmetryDesc
- createIsosurface(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- createItemKeys(JmolPanel) - Method in class org.jmol.console.KeyJMenu
- createLabelMapAndIndex(Viewer, BS, String[], BS, Map<Atom, String>, Map<Atom, Integer>) - Static method in class org.jmol.quantum.NMRNoeMatrix
- createLadders(Lst<Bridge>, boolean) - Method in class org.jmol.dssx.DSSP
-
"ladder =: one or more consecutive bridges of identical type" (p.
- createLanguageList() - Method in class org.jmol.i18n.GT
- createLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
- createLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
- createLcaoLobe(V3, float, int) - Method in class org.jmol.shapesurface.Isosurface
- createLineBuffer() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- createMatrix(Viewer, BS, String[], NMRNoeMatrix.NOEParams) - Static method in class org.jmol.quantum.NMRNoeMatrix
- createMenu() - Method in class org.jmol.console.ImageDialog
- createMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create a menu for the app.
- createMenubar() - Method in class org.jmol.console.AppletConsole
- createMenubar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create the menubar for the app.
- createMenuItem(String) - Method in class org.jmol.console.AppletConsole
- createMenuItem(String) - Method in class org.jmol.console.ImageDialog
- createMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
This is the hook through which all menu items are created.
- createMesh() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
- createMesh(int, int, int, int, float, int) - Method in class org.jmol.renderbio.BioMeshRenderer
-
Cartoon meshes are triangulated objects.
- createModels(int) - Method in class org.jmol.modelset.ModelSet
- createModelSet(String, String, SB, Object, BS, boolean) - Method in class org.jmol.viewer.ModelManager
- createModelSet(JmolAdapter, Object, BS) - Method in class org.jmol.modelset.ModelLoader
- createModelSetAndReturnError(Object, boolean, SB, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
-
finally(!) we are ready to create the "model set" from the "atom set collection" - does NOT repaint
- createMonteCarloOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
- createMopacSlaters(int, int, float[], boolean) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- createMovie(Viewer, String[], int, int, int, String) - Method in interface org.jmol.api.JmolMovieCreatorInterface
-
create a movie from a set of image files
- createMovie(Viewer, String[], int, int, int, String) - Method in class org.jmol.image.AviCreator
- createNewAtomSet() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- createNextBZ(BZone, BZone, String) - Method in class org.jmol.util.BZone
- createNOEMatrix(Lst<Object>, Map<Atom, Integer>, int, int, NMRNoeMatrix.NOEParams) - Static method in class org.jmol.quantum.NMRNoeMatrix
-
Create noeMatix and indexAtomInNoeMatrix from hAtoms and indexAtomInMol.
- createOrbital() - Method in class org.jmol.jvxl.readers.IsoMOReader
- createParticle(String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- createPdfDocument(OC, Object) - Method in interface org.jmol.api.JmolPdfCreatorInterface
- createPuttyObject(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
"Putty" shapes scaled in a variety of ways.
- createRibbonObject(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
PyMOL "ribbons" could be Jmol backbone or trace, depending upon the value of PyMOL.ribbon_sampling.
- createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManager
- createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerAwt
- createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerJS
- createSet(int, int, int) - Method in class org.jmol.jvxl.data.MeshData
- createSGFromList(String, Lst<?>) - Static method in class org.jmol.symmetry.SpaceGroup
- createShapeObject(int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Create JmolObjects for each shape.
- createShapeObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create JmolObjects for all the molecular shapes; not executed for a state script.
- createShapeObjects(BS[], boolean, int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
create all objects for a given molecule or scene
- createSlaterData(int, String, String) - Method in class org.jmol.adapter.readers.quantum.DgridReader
- createSpacefillObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Create a BALLS JmolObject for each radius.
- createSpaceGroup(int, String, Object, int) - Method in interface org.jmol.api.SymmetryInterface
- createSpaceGroup(int, String, Object, int) - Static method in class org.jmol.symmetry.SpaceGroup
- createSpaceGroup(int, String, Object, int) - Method in class org.jmol.symmetry.Symmetry
- createSpaceGroupN(String) - Static method in class org.jmol.symmetry.SpaceGroup
- createSpaceGroups() - Static method in class org.jmol.symmetry.SpaceGroup
- createSphericalSlaterByType(int, int, String, double, float) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
We have the type as a string and need to translate that to exponents for x, y, z, and r.
- createStatusBar() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- createStatusBar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- createSubzonePolyhedron(BZone, String) - Method in class org.jmol.util.BZone
-
Generate the polyhedra.
- createSurfaceTool() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- createTextureFile(String, MeshSurface, int[]) - Method in class org.jmol.export._ObjExporter
-
Writes a texture file with the colors in the colixes array in a way that it can be mapped by the texture coordinates vt.
- createTheImage(Object, String, OC, Map<String, Object>, String[]) - Method in class org.jmol.viewer.OutputManager
- createToolBar() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- createToolBar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create the toolbar.
- createToolbarButton(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Create a button to go inside of the toolbar.
- createTopoMap(BS) - Method in class org.jmol.smiles.SmilesSearch
- createTraceObject(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
trace, or cartoon in the case of cartoon ladders.
- createTransferable(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- createTreeModel() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Creates the treeModel of the AtomSets available in the JmolViewer
- createVCRController(String) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Creates a VCR type set of controller inside a JPanel.
- createVoxelData() - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
-
Developer must customize this method
- createWebExport() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- createWS(String) - Method in class org.jmol.util.BZone
-
Create a Wigner-Seitz unitcell centered on {0 0 0}.
- createZip(String, String, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- createZipSet(String, String[], boolean, OC, String) - Method in class org.jmol.viewer.OutputManager
- CREATING_MODELSET - Enum constant in enum org.jmol.c.FIL
- creatingImage - Variable in class org.jmol.viewer.Viewer
- creditsAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- CreditsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
- CreditsDialog - Class in org.openscience.jmol.app.jmolpanel
- CreditsDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.CreditsDialog
- crit - Variable in class org.jmol.minimize.Minimizer
- criterion - Variable in class org.jmol.minimize.forcefield.ForceField
- criterion - Static variable in class org.jmol.script.T
- cross - Static variable in class org.jmol.renderspecial.DipolesRenderer
- cross - Static variable in class org.jmol.script.T
- cross0 - Variable in class org.jmol.renderspecial.DipolesRenderer
- cross1 - Variable in class org.jmol.renderspecial.DipolesRenderer
- crossBinary(String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- crossed - Static variable in class org.jmol.script.T
- crossEnd - Static variable in class org.jmol.renderspecial.DipolesRenderer
- crossOffset - Static variable in class org.jmol.renderspecial.DipolesRenderer
- crossWidth - Static variable in class org.jmol.renderspecial.DipolesRenderer
- crossWidthPixels - Variable in class org.jmol.renderspecial.DipolesRenderer
- crtval - Static variable in class org.jmol.shapespecial.Ellipsoid
- crtypes - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
- cryst1 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- cryst1() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- CRYSTAL - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- CRYSTAL_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- CRYSTAL_SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- CRYSTAL_SYMMETRY_TRANSFORM3 - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- crystalClass - Variable in class org.jmol.symmetry.SpaceGroup
- crystalContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- CrystalReader - Class in org.jmol.adapter.readers.xtal
-
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
- CrystalReader() - Constructor for class org.jmol.adapter.readers.xtal.CrystalReader
- crystGroup - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
- CS - Static variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
- CS2 - Static variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
- csfLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- CsfReader - Class in org.jmol.adapter.readers.quantum
-
CSF file reader based on CIF idea -- fluid property fields.
- CsfReader() - Constructor for class org.jmol.adapter.readers.quantum.CsfReader
- CTRL - Static variable in class org.jmol.viewer.binding.Binding
- CTRL_ALT - Static variable in class org.jmol.awtjs.Event
- CTRL_ALT - Static variable in class org.jmol.viewer.binding.Binding
- CTRL_MASK - Static variable in class org.jmol.awtjs.Event
- CTRL_SHIFT - Static variable in class org.jmol.awtjs.Event
- CTRL_SHIFT - Static variable in class org.jmol.viewer.binding.Binding
- cubeCountX - Variable in class org.jmol.jvxl.calc.MarchingCubes
- cubeCountY - Variable in class org.jmol.jvxl.calc.MarchingCubes
- cubeCountZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
- cubeFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- cubeIterator - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- CubeIterator - Class in org.jmol.bspt
-
Iterator used for finding all points within a box or a hemi-box
- CubeIterator(Bspt) - Constructor for class org.jmol.bspt.CubeIterator
- cubeIterators - Variable in class org.jmol.bspt.Bspf
- CubeReader - Class in org.jmol.adapter.readers.simple
-
Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.
- CubeReader - Class in org.jmol.jvxl.readers
- CubeReader() - Constructor for class org.jmol.adapter.readers.simple.CubeReader
- CubeReader() - Constructor for class org.jmol.jvxl.readers.CubeReader
- cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
- cubeVertexVectors - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- cull_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- current - Variable in class org.jmol.thread.HoverWatcherThread
- current - Variable in class org.jmol.viewer.ActionManager
- currentAtomSetIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- currentBgColor - Variable in class org.jmol.shape.TextShape
- currentBgTranslucentLevel - Variable in class org.jmol.shape.TextShape
- currentBlock - Variable in class org.jmol.adapter.readers.xtal.MagresReader
- currentChain - Variable in class org.jmol.modelset.ModelLoader
- currentChainID - Variable in class org.jmol.modelset.ModelLoader
- currentColor - Variable in class org.jmol.shape.TextShape
- currentCompnd - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- currentCursor - Variable in class org.jmol.viewer.Viewer
- currentDipole - Variable in class org.jmol.shapespecial.Dipoles
- currentDir - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- currentDirection - Variable in class org.jmol.viewer.AnimationManager
- currentFont - Variable in class org.jmol.shape.TextShape
- currentFont - Variable in class org.jmol.util.GData
- currentFrameIs(int) - Method in class org.jmol.viewer.AnimationManager
- currentFrankId - Variable in class org.jmol.popup.JmolPopup
- currentGroup3 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- currentGroup3 - Variable in class org.jmol.modelset.ModelLoader
- currentGroupInsertionCode - Variable in class org.jmol.modelset.ModelLoader
- currentGroupSequenceNumber - Variable in class org.jmol.modelset.ModelLoader
- currentIndex - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- currentIsLast() - Method in class org.jmol.viewer.AnimationManager
- currentKey - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- currentLevel - Static variable in class org.jmol.util.Geodesic
- currentlocalpath - Static variable in class org.jmol.script.T
- currentlyRendering - Variable in class org.jmol.util.GData
- currentMenuItemId - Variable in class org.jmol.popup.GenericPopup
- currentMesh - Variable in class org.jmol.shape.MeshCollection
- currentMetricsFont3d - Variable in class org.jmol.shape.Frank
- currentModelIndex - Variable in class org.jmol.modelkit.ModelKit
- currentMorphModel - Variable in class org.jmol.viewer.AnimationManager
- currentNormalOrigin - Variable in class org.jmol.export._ObjExporter
-
Wavefront OBJ refers to vertices and normals and textures by their location in the file.
- currentObject - Variable in class org.jmol.shape.TextShape
- currentPalette - Variable in class org.jmol.util.ColorEncoder
- currentPoints - Variable in class org.jmol.geodesic.EnvelopeCalculation
- currentProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- currentResno - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- currentRule - Variable in class org.jmol.symmetry.CIPChirality
-
the current rule being applied exhaustively
- currentSegmentCount - Variable in class org.jmol.util.ColorEncoder
- currentShadeIndex - Variable in class org.jmol.g3d.Graphics3D
- currentShapeID - Variable in class org.jmol.viewer.Viewer
- currentShapeState - Variable in class org.jmol.viewer.Viewer
- currentSize - Variable in class org.jmol.dialog.FilePreview.FPPanel
- currentStep - Variable in class org.jmol.minimize.forcefield.ForceField
- currentTextureOrigin - Variable in class org.jmol.export._ObjExporter
-
Wavefront OBJ refers to vertices and normals and textures by their location in the file.
- currentThread - Variable in class org.jmol.script.ScriptEval
- currentTime - Variable in class org.jmol.thread.JmolThread
- currentTranslucentLevel - Variable in class org.jmol.shape.TextShape
- currentVertexOrigin - Variable in class org.jmol.export._ObjExporter
-
Wavefront OBJ refers to vertices and normals and textures by their location in the file.
- cursor - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
- CURSOR_CROSSHAIR - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_DEFAULT - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_HAND - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_MOVE - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_WAIT - Static variable in interface org.jmol.api.GenericPlatform
- CURSOR_ZOOM - Static variable in interface org.jmol.api.GenericPlatform
- cursorPos - Variable in class org.jmol.util.CommandHistory
-
Current position of the cursor;
- curve - Static variable in class org.jmol.script.T
- CURVE - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- CUSTOM - Enum constant in enum org.jmol.c.STER
- CUSTOM - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- CUSTOM - Static variable in class org.jmol.util.ColorEncoder
- CUSTOM_CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
- CUSTOMTYPE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- CUT - Static variable in class org.jmol.quantum.MOCalculation
- cutoff - Variable in class org.jmol.jvxl.calc.MarchingCubes
- cutoff - Variable in class org.jmol.jvxl.data.JvxlData
- cutoff - Variable in class org.jmol.jvxl.readers.Parameters
- cutoff - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- cutoff - Static variable in class org.jmol.script.T
- cutoff - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- cutoffAutomatic - Variable in class org.jmol.jvxl.readers.Parameters
- cutoffField - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- cutoffFieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- cutoffLabel - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- cutoffRange - Variable in class org.jmol.jvxl.data.JvxlData
- cutoffRange - Variable in class org.jmol.jvxl.readers.Parameters
- cutoffRange - Variable in class org.jmol.shapesurface.Isosurface
- cx - Variable in class org.jmol.bspt.CubeIterator
- cx - Variable in class org.jmol.shapesurface.PMeshWriter
- CX - Variable in class org.jmol.quantum.MOCalculation
- cxyz - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
- cy - Variable in class org.jmol.bspt.CubeIterator
- CY - Variable in class org.jmol.quantum.MOCalculation
- CYAN - Static variable in class org.jmol.util.C
- cyclicFlag - Variable in class org.jmol.modelsetbio.BioPolymer
- cylinder - Static variable in class org.jmol.script.T
- CYLINDER - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
- cylinder_shader_ff_workaround - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cylinder3d - Variable in class org.jmol.g3d.Graphics3D
- cylinderBase - Static variable in class org.jmol.renderspecial.DipolesRenderer
- cylinderMatrix - Variable in class org.jmol.export._IdtfExporter
- cylinderNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- CylinderRenderer - Class in org.jmol.g3d
-
Draws shaded cylinders in 3D.
- CylinderRenderer(Graphics3D) - Constructor for class org.jmol.g3d.CylinderRenderer
- cylinders_shader_filter_faces - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- cz - Variable in class org.jmol.bspt.CubeIterator
- CZ - Variable in class org.jmol.quantum.MOCalculation
D
- d - Variable in class org.jmol.adapter.readers.cif.Subsystem
- d - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- d - Variable in class org.jmol.minimize.forcefield.Calculation
- d - Variable in class org.jmol.util.ContactPair
- d1 - Variable in class org.jmol.g3d.HermiteRenderer
- d2 - Variable in class org.jmol.g3d.HermiteRenderer
- d2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- da - Variable in class org.jmol.minimize.forcefield.Calculations
- DA_D - Static variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- DA_DA - Static variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- dAB - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- dAB2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- dash_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dash_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dash_gap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dash_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dash_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dash_round_ends - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dash_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dash_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dashDots - Variable in class org.jmol.render.FontLineShapeRenderer
- dashes - Static variable in class org.jmol.render.FontLineShapeRenderer
- data - Variable in class org.jmol.adapter.readers.cif.CifReader
- data - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- data - Variable in class org.jmol.jvxl.readers.DelPhiBinaryReader
- data - Variable in class org.jmol.jvxl.readers.IsoFxyReader
- data - Variable in class org.jmol.jvxl.readers.IsoFxyzReader
- data - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- data - Variable in class org.jmol.minimize.MinObject
- data - Variable in class org.jmol.modelset.LabelToken
- data - Static variable in class org.jmol.script.T
- data - Variable in class org.jmol.symmetry.CIPChirality
-
collected bitsets and more specialized SMILES/SMARTS searches and vwr references
- data - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- data - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule.DihedralCouple
- data - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
- data() - Method in class org.jmol.scriptext.CmdExt
- DATA_ATOM_PROP_ENTRY - Static variable in interface org.jmol.api.JmolDataManager
- DATA_LABEL - Static variable in interface org.jmol.api.JmolDataManager
- DATA_SAVE_IN_STATE - Static variable in interface org.jmol.api.JmolDataManager
- DATA_SELECTION - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_AF - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_AFF - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_AFFF - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_LAST - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_STRING - Static variable in interface org.jmol.api.JmolDataManager
- DATA_TYPE_UNKNOWN - Static variable in interface org.jmol.api.JmolDataManager
- DATA_VALUE - Static variable in interface org.jmol.api.JmolDataManager
- DataAdder - Interface in org.jmol.quantum.mo
- DataAdder11H - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical H orbital contributions
- DataAdder11H() - Constructor for class org.jmol.quantum.mo.DataAdder11H
- DataAdder13I - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical I orbital contributions
- DataAdder13I() - Constructor for class org.jmol.quantum.mo.DataAdder13I
- DataAdder7F - Class in org.jmol.quantum.mo
-
adds 7 spherical F orbital contributions
- DataAdder7F() - Constructor for class org.jmol.quantum.mo.DataAdder7F
- DataAdder9G - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds 9 spherical G orbital contributions
- DataAdder9G() - Constructor for class org.jmol.quantum.mo.DataAdder9G
- DataAdderF - Class in org.jmol.quantum.mo
-
adds 10 cartesian F orbital contributions
- DataAdderF() - Constructor for class org.jmol.quantum.mo.DataAdderF
- DataAdderG - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds 15 cartesian G orbital contributions
- DataAdderG() - Constructor for class org.jmol.quantum.mo.DataAdderG
- DataAdderH - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds 21 cartesian H orbital contributions
- DataAdderH() - Constructor for class org.jmol.quantum.mo.DataAdderH
- DataAdderI - Class in org.jmol.quantum.mo
-
change QS.MAX_TYPE_SUPPORTED if you implement this adds 28 cartesian I orbital contributions
- DataAdderI() - Constructor for class org.jmol.quantum.mo.DataAdderI
- dataAdderOK - Variable in class org.jmol.quantum.MOCalculation
- dataAdders - Variable in class org.jmol.quantum.MOCalculation
- databaseArray - Static variable in class org.jmol.viewer.JC
- databases - Static variable in class org.jmol.viewer.JC
- dataFrames - Variable in class org.jmol.modelset.Model
- dataIsReducedDensity - Variable in class org.jmol.quantum.NciCalculation
- DataManager - Class in org.jmol.viewer
- DataManager() - Constructor for class org.jmol.viewer.DataManager
- dataMax - Variable in class org.jmol.jvxl.data.JvxlData
- dataMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
- dataMean - Variable in class org.jmol.jvxl.readers.SurfaceReader
- dataMin - Variable in class org.jmol.jvxl.data.JvxlData
- dataMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
- dataOnly - Variable in class org.jmol.util.MeshSurface
- dataOnly - Variable in class org.jmol.viewer.Viewer
- dataReaders - Variable in class org.jmol.io.FilesReader
- dataScaling - Variable in class org.jmol.quantum.NciCalculation
- dataseparator - Static variable in class org.jmol.script.T
- dataSeparator - Variable in class org.jmol.viewer.GlobalSettings
- dataSourceFrame - Variable in class org.jmol.modelset.Model
- dataT - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- dataType - Variable in class org.jmol.jvxl.readers.Parameters
- dataType - Variable in class org.jmol.jvxl.readers.VolumeDataReader
- dataType - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- dataValues - Variable in class org.jmol.viewer.DataManager
- dataXYReversed - Variable in class org.jmol.jvxl.readers.Parameters
- date - Static variable in class org.jmol.viewer.JC
- db - Variable in class org.jmol.minimize.forcefield.Calculations
- dBb(BS, boolean) - Method in class org.jmol.modelset.BondCollection
- DBLCLK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- DBLCLK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- dc - Variable in class org.jmol.minimize.forcefield.Calculations
- DC - Static variable in class org.jmol.quantum.QS
- DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
- DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
- DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
- DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
- dcdFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- dclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- dd - Variable in class org.jmol.minimize.forcefield.Calculations
- ddata - Variable in class org.jmol.minimize.MinObject
- dData - Variable in class org.jmol.minimize.forcefield.Calculation
- dE - Variable in class org.jmol.minimize.forcefield.Calculation
- dE - Variable in class org.jmol.minimize.forcefield.ForceField
- DEATH - Static variable in class org.jmol.multitouch.ActionManagerMT
- debug - Static variable in class org.jmol.export._ObjExporter
-
Flag to cause debugging output to stdout.
- debug - Static variable in class org.jmol.script.T
- debug(String) - Method in class org.jmol.util.DefaultLogger
- debug(String) - Static method in class org.jmol.util.Logger
-
Writes a log at DEBUG level.
- debug(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at DEBUG level.
- debug_pick - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- debugContext - Variable in class org.jmol.adapter.readers.xml.XmlHandler
- debugging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- debugging - Static variable in class org.jmol.util.Logger
- debuggingHigh - Static variable in class org.jmol.util.Logger
- debughigh - Static variable in class org.jmol.script.T
- debugHigh - Variable in class org.jmol.script.ScriptExpr
- debugHigh - Variable in class org.jmol.script.ScriptMathProcessor
- debugPrint(String) - Method in class org.jmol.export._ObjExporter
-
Debug print utility.
- debugscript - Static variable in class org.jmol.script.T
- debugScript - Variable in class org.jmol.script.ScriptEval
- debugScript - Variable in class org.jmol.viewer.GlobalSettings
- decimal - Static variable in class org.jmol.script.T
- decode(String) - Method in class org.jmol.adapter.readers.cif.MMTFReader
- decodeAssemblyOperators(String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- decodeInchiStereo(SimpleNode[]) - Method in class org.jmol.inchi.InChIJNI
- decodeKey(Integer) - Static method in class org.jmol.minimize.MinObject
- deduceElementSymbol(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
-
The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed.
- deduceElementSymbol(String, String) - Method in class org.jmol.adapter.readers.more.GromacsReader
- deducePdbElementSymbol(boolean, String, String) - Static method in class org.jmol.adapter.readers.more.ForceFieldReader
- deepCopy(Object, boolean, boolean) - Static method in class org.jmol.script.SV
-
Copies a hash or array deeply; invoked by Jmol script x = @a where a.type == "hash" or a.type == "varray"
- deepCopySV(SV) - Static method in class org.jmol.script.SV
- DEFAULT - Static variable in class org.jmol.g3d.TriangleRenderer
- DEFAULT - Static variable in class org.jmol.smiles.SmilesStereo
- default_2fofc_map_rep - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- DEFAULT_BASIS - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JC
- DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JC
- DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JC
- default_buster_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- DEFAULT_CAMERA_DEPTH - Static variable in class org.jmol.viewer.TransformManager
- DEFAULT_CHARGE - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- DEFAULT_DRAG_DROP_SCRIPT - Static variable in class org.jmol.viewer.JC
- DEFAULT_DSSP_VERSION - Static variable in class org.jmol.modelsetbio.BioModelSet
- DEFAULT_FACECENTEROFFSET - Static variable in class org.jmol.shapespecial.Polyhedra
- default_fofc_map_rep - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JC
- DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JC
- DEFAULT_GESTURE_SWIPE_FACTOR - Static variable in class org.jmol.viewer.ActionManager
- DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JC
- DEFAULT_MAD - Static variable in class org.jmol.shapespecial.Dipoles
- DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
- DEFAULT_MAX_SIZE - Static variable in class org.jmol.util.CommandHistory
- DEFAULT_METHOD - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JC
- DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
- DEFAULT_MOUSE_DRAG_FACTOR - Static variable in class org.jmol.viewer.ActionManager
- DEFAULT_MOUSE_WHEEL_FACTOR - Static variable in class org.jmol.viewer.ActionManager
- DEFAULT_MULT - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- DEFAULT_NAV_FPS - Static variable in class org.jmol.viewer.TransformManager
- DEFAULT_OFFSETSIDE - Static variable in class org.jmol.shapespecial.Dipoles
- DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JC
- DEFAULT_PERSPECTIVE_DEPTH - Static variable in class org.jmol.viewer.TransformManager
- DEFAULT_PERSPECTIVE_MODEL - Static variable in class org.jmol.viewer.TransformManager
- default_phenix_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- default_phenix_no_fill_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- DEFAULT_PLANAR_PARAM - Static variable in class org.jmol.shapespecial.Polyhedra
-
a dot product comparison term
- default_refmac_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- DEFAULT_RHOPARAM - Variable in class org.jmol.quantum.NciCalculation
- DEFAULT_RHOPLOT_PRO - Variable in class org.jmol.quantum.NciCalculation
- DEFAULT_RHOPLOT_SCF - Variable in class org.jmol.quantum.NciCalculation
- DEFAULT_SPIN_FPS - Static variable in class org.jmol.viewer.TransformManager
- DEFAULT_SPIN_Y - Static variable in class org.jmol.viewer.TransformManager
- DEFAULT_STEREO_DEGREES - Static variable in class org.jmol.viewer.TransformManager
- DEFAULT_STRUT_RADIUS - Static variable in class org.jmol.viewer.JC
- DEFAULT_VISUAL_RANGE - Static variable in class org.jmol.viewer.TransformManager
- defaultAlignment - Variable in class org.jmol.shape.Labels
- defaultanglelabel - Static variable in class org.jmol.script.T
- defaultAngleLabel - Variable in class org.jmol.viewer.GlobalSettings
- defaultBBox - Variable in class org.jmol.modelset.ModelSet
- defaultBgcolix - Variable in class org.jmol.shape.Labels
- defaultBondingMars - Static variable in class org.jmol.util.Elements
-
Default table of bonding radii stored as a short mar ...
- defaultChoice - Static variable in class org.jmol.dialog.Dialog
- defaultcmd - Static variable in class org.jmol.script.T
- defaultColix - Variable in class org.jmol.shape.Labels
- defaultColix - Variable in class org.jmol.shapesurface.Isosurface
- defaultColorFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
- defaultColorFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultColorFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
- defaultColorFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultColorNegative - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultColorNegativeLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultColorPositive - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultColorPositiveLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultcolorscheme - Static variable in class org.jmol.script.T
- defaultContourCount - Static variable in class org.jmol.jvxl.calc.MarchingSquares
- defaultContourCount - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultCovalentMad - Variable in class org.jmol.modelset.BondCollection
- defaultCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultCutoff - Static variable in class org.jmol.jvxl.readers.SurfaceReader
- defaultdirectory - Static variable in class org.jmol.script.T
- defaultDirectory - Variable in class org.jmol.viewer.GlobalSettings
- defaultdistancelabel - Static variable in class org.jmol.script.T
- defaultDistanceLabel - Variable in class org.jmol.viewer.GlobalSettings
- defaultdrawarrowscale - Static variable in class org.jmol.script.T
- defaultDrawArrowScale - Variable in class org.jmol.viewer.GlobalSettings
- defaultdropscript - Static variable in class org.jmol.script.T
- defaultDropScript - Variable in class org.jmol.viewer.GlobalSettings
- defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
- defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
- defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultFontId - Variable in class org.jmol.shape.Labels
- defaultFontId - Variable in class org.jmol.shapespecial.Draw
- defaultFontId0 - Variable in class org.jmol.shapespecial.Draw
- defaultFontName - Static variable in class org.jmol.shape.Frank
- defaultFontSize - Static variable in class org.jmol.shape.Frank
- defaultFontSize - Variable in class org.jmol.shapespecial.Draw
- defaultFontStyle - Static variable in class org.jmol.shape.Frank
- defaultFormat - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.MyStatusListener
- defaultGroupCount - Static variable in class org.jmol.modelset.ModelLoader
- defaultHeight - Variable in class org.jmol.awtjs.swing.JDialog
- defaultlabelpdb - Static variable in class org.jmol.script.T
- defaultLabelPDB - Variable in class org.jmol.viewer.GlobalSettings
- defaultLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- defaultlabelxyz - Static variable in class org.jmol.script.T
- defaultLabelXYZ - Variable in class org.jmol.viewer.GlobalSettings
- defaultlattice - Static variable in class org.jmol.script.T
- defaultloadfilter - Static variable in class org.jmol.script.T
- defaultLoadFilter - Variable in class org.jmol.viewer.GlobalSettings
- defaultloadscript - Static variable in class org.jmol.script.T
- defaultLoadScript - Variable in class org.jmol.viewer.GlobalSettings
- defaultLobeCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
- DefaultLogger - Class in org.jmol.util
-
Default implementation of the logger.
- DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
- defaultMacroDirectory - Static variable in class org.jmol.viewer.JC
- defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.SurfaceReader
- defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.SurfaceReader
- defaultMepCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultMepMax - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultMepMin - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultMessage - Variable in class org.jmol.console.GenericConsole
- defaultMode - Variable in class org.jmol.viewer.TransformManager
- defaultOffset - Variable in class org.jmol.shape.Labels
- defaultON - Static variable in class org.jmol.script.T
- defaultOptimadeFieldsStr - Static variable in class org.jmol.viewer.JC
- defaultOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultOrbitalCutoffOld - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultPaletteID - Variable in class org.jmol.shape.Labels
- defaultPointer - Variable in class org.jmol.shape.Labels
- defaultQMElectronDensityCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultQMOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultRotationRadius - Variable in class org.jmol.modelset.Model
- defaults - Static variable in class org.jmol.script.T
- defaultScaleToScreen(float) - Method in class org.jmol.viewer.TransformManager
- defaultSolventRadius - Static variable in class org.jmol.jvxl.readers.Parameters
- defaultStructure - Variable in class org.jmol.modelsetbio.BioModel
- defaultstructuredssp - Static variable in class org.jmol.script.T
- defaultStructureDSSP - Variable in class org.jmol.viewer.GlobalSettings
- defaultTickInfo - Variable in class org.jmol.shape.Measures
- defaulttorsionlabel - Static variable in class org.jmol.script.T
- defaultTorsionLabel - Variable in class org.jmol.viewer.GlobalSettings
- defaulttranslucent - Static variable in class org.jmol.script.T
- defaultTranslucent - Variable in class org.jmol.viewer.GlobalSettings
- defaultvdw - Static variable in class org.jmol.script.T
- defaultVdw - Variable in class org.jmol.viewer.Viewer
- defaultWidth - Variable in class org.jmol.awtjs.swing.JDialog
- defaultZPos - Variable in class org.jmol.shape.Labels
- defer_builds_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- defer_updates - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- deferred - Variable in class org.jmol.awt.AwtSwingComponent
- define - Static variable in class org.jmol.script.T
- define(JmolMeasurementClient, ModelSet) - Method in class org.jmol.modelset.MeasurementData
-
called by the client to generate a set of measurements
- define(MeasurementData, int) - Method in class org.jmol.shape.Measures
- defineAll(int, Measurement, boolean, boolean, boolean) - Method in class org.jmol.shape.Measures
- defineAtoms(String, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- defineAtomSet(String) - Method in class org.jmol.script.ScriptEval
- defineAtomSets(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- defineCenterAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- DefineCenterAction() - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction
- definedAtomSets - Variable in class org.jmol.viewer.Viewer
- defineMeasurement(int, Measurement, boolean) - Method in class org.jmol.shape.Measures
- defineSets() - Method in class org.jmol.script.ScriptEval
-
support for @xxx or define xxx commands
- definesStereo() - Method in class org.jmol.smiles.SmilesAtom
-
for InChI or any other system that self-defines stereochemistry.
- DEG_TO_RAD - Static variable in class org.jmol.minimize.forcefield.Calculations
- DEG_TO_RAD - Static variable in class org.jmol.minimize.Util
- degree - Variable in class org.jmol.smiles.SmilesAtom
- degrees - Variable in class org.jmol.navigate.Navigator
- DEGREES - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- degreesPerRadian - Static variable in class org.jmol.export.___Exporter
- degreesPerRadian - Static variable in class org.jmol.viewer.TransformManager
- degreeStep - Variable in class org.jmol.navigate.Navigator
- degtorad - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- delay - Static variable in class org.jmol.script.T
- DELAY_INTERRUPT_MS - Static variable in class org.jmol.script.ScriptEval
- delaymaximumms - Static variable in class org.jmol.script.T
- delayMaximumMs - Variable in class org.jmol.viewer.GlobalSettings
- delayScript(int) - Method in class org.jmol.script.ScriptEval
- delete - Static variable in class org.jmol.script.T
- delete() - Method in class org.openscience.jmol.app.webexport.JmolInstance
- delete(BS) - Method in class org.jmol.modelset.Atom
- deleteAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- deleteAllBonds() - Method in class org.jmol.modelset.ModelSet
- deleteAllBonds2() - Method in class org.jmol.modelset.BondCollection
- deleteAllButton - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- deleteAtomReferences() - Method in class org.jmol.modelset.Bond
- deleteAtoms - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- deleteAtoms(int) - Method in class org.jmol.shapespecial.DrawMesh
- deleteAtoms(int, int) - Method in class org.jmol.geodesic.EnvelopeCalculation
- deleteAtoms(int, BS, BS) - Method in class org.jmol.modelset.StateScript
- deleteAtoms(BS) - Method in class org.jmol.modelset.ModelSet
- deleteAtoms(BS) - Method in class org.jmol.modelsetbio.BioResolver
-
called from org.jmol.modelsetbio.resolver when adding hydrogens.
- deleteAtoms(BS) - Method in class org.jmol.viewer.SelectionManager
- deleteAtoms(BS, boolean) - Method in class org.jmol.viewer.Viewer
- deleteAtomsInVariables(BS) - Method in interface org.jmol.api.JmolScriptEvaluator
- deleteAtomsInVariables(BS) - Method in class org.jmol.script.ScriptEval
- deleteAtomTensors(BS) - Method in class org.jmol.modelset.AtomCollection
- deleteBits(BS, BS) - Static method in class org.jmol.util.BSUtil
-
this one slides deleted bits out of a pattern.
- deleteBond(Bond) - Method in class org.jmol.modelset.Atom
- deleteBondAt(int) - Method in class org.jmol.modelset.Atom
- deleteBonds(BS) - Method in class org.jmol.viewer.Viewer
- deleteBonds(BS, boolean) - Method in class org.jmol.modelset.ModelSet
- deleteButton - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- deleteConnections(float, float, int, BS, BS, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
- deleteContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- DELETED - Enum constant in enum org.jmol.c.FIL
- deleteDipole(Dipole) - Method in class org.jmol.shapespecial.Dipoles
- deleteI(int) - Method in class org.jmol.shape.Measures
- deleteInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
- deleteLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
- deleteLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
- deleteM(Measurement) - Method in class org.jmol.shape.Measures
- deleteMeasurement(int) - Method in class org.jmol.api.JmolViewer
- deleteMeasurement(int) - Method in class org.jmol.viewer.Viewer
- deleteMesh() - Method in class org.jmol.shape.MeshCollection
- deleteMeshElement(int) - Method in class org.jmol.shapecgo.CGO
- deleteMeshElement(int) - Method in class org.jmol.shapespecial.Draw
- deleteMeshI(int) - Method in class org.jmol.shape.MeshCollection
- deleteMeshKey(String) - Method in class org.jmol.shape.MeshCollection
- deleteModel(int, BS, BS) - Method in class org.jmol.modelset.ModelSet
- deleteModelAtoms(int, int, int, BS) - Method in class org.jmol.viewer.Viewer
- deleteModelAtoms(int, int, BS) - Method in interface org.jmol.api.JmolDataManager
- deleteModelAtoms(int, int, BS) - Method in class org.jmol.modelset.AtomCollection
- deleteModelAtoms(int, int, BS) - Method in class org.jmol.viewer.DataManager
- deleteModelBonds(int) - Method in class org.jmol.modelset.ModelSet
- deleteModels(int) - Method in class org.jmol.shapecgo.CGO
- deleteModels(int) - Method in class org.jmol.shapespecial.Draw
- deleteModels(int, BS) - Method in class org.jmol.viewer.Viewer
-
called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1
- deleteModels(BS) - Method in class org.jmol.modelset.ModelSet
- deleteO(Object) - Method in class org.jmol.shape.Measures
- deletePolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
- deleteSaved(String) - Method in class org.jmol.viewer.StateManager
- deleteSavedType(String) - Method in class org.jmol.viewer.StateManager
- deleteShapeAtoms(Object[], BS) - Method in class org.jmol.viewer.ShapeManager
- deleteUnneededAtoms() - Method in class org.jmol.modelsetbio.BioResolver
-
Delete hydrogen atoms that are still in bsAddedHydrogens, because they were not actually added.
- deleteVdwDependentShapes(BS) - Method in class org.jmol.viewer.ShapeManager
- deleteWidget(int) - Method in class org.openscience.jmol.app.webexport.JmolInstance
- DELPHI_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.viewer.FileManager
- DelPhiBinaryReader - Class in org.jmol.jvxl.readers
- DelPhiBinaryReader() - Constructor for class org.jmol.jvxl.readers.DelPhiBinaryReader
- delta - Variable in class org.jmol.minimize.forcefield.Calculation
- delta - Variable in class org.jmol.thread.MoveToThread.Slider
- delta2 - Variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
- delta2 - Variable in class org.jmol.util.Modulation
- deltaElectro - Static variable in class org.jmol.quantum.NMRCalculation
-
Calculate an H-X-X-H or C-X-X-H coupling constant.
- demoBZ(Object[], boolean) - Method in class org.jmol.util.BZone
- density - Static variable in class org.jmol.script.T
- DEPR_FD_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DEPR_FD_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DEPR_FO_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DEPR_FO_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DEPR_FU_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DEPR_FU_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- deprecatedparam - Static variable in class org.jmol.script.T
- depth - Variable in class org.jmol.export.Export3D
- depth - Variable in class org.jmol.g3d.SphereRenderer
- depth - Static variable in class org.jmol.script.T
- depth - Variable in class org.jmol.util.GData
- depth_cue - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- depth1 - Variable in class org.jmol.g3d.HermiteRenderer
- depthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
- depthByPixels(int) - Method in class org.jmol.viewer.Viewer
- depthDelta - Variable in class org.jmol.navigate.Navigator
- depthPercent - Variable in class org.jmol.navigate.Navigator
- depthPercentSetting - Variable in class org.jmol.viewer.TransformManager
- depthPlane - Variable in class org.jmol.viewer.TransformManager
- depthStart - Variable in class org.jmol.navigate.Navigator
- depthToPercent(int) - Method in class org.jmol.viewer.TransformManager
- depthValue - Variable in class org.jmol.viewer.TransformManager
- depthZ - Variable in class org.jmol.export.___Exporter
- desc - Variable in class org.jmol.symmetry.Symmetry
- DESCENDER - Static variable in class org.jmol.util.MeshCapper
- descending - Variable in class org.openscience.jmol.app.janocchio.TableSorter.Arrow
- DESCENDING - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- descent - Variable in class org.jmol.modelset.Text
- descent - Variable in class org.jmol.render.LabelsRenderer
- descent - Variable in class org.jmol.util.Font
- descr - Variable in class org.jmol.minimize.forcefield.AtomType
- DeselectallAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.DeselectallAction
- desiredModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- desiredQ - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- desiredQpt - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- desiredSpaceGroupIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- desiredVibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- destroy() - Method in interface org.jmol.api.JmolAppletInterface
- destroy() - Method in class org.jmol.g3d.Graphics3D
- destroy() - Method in class org.jmol.util.GData
- destroy() - Method in class org.jmol.util.GenericApplet
- destroy() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- destroy() - Method in interface org.openscience.jmol.app.JmolPlugin
- destroyConsole() - Method in class org.jmol.console.GenericConsole
- detachAppletAction - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- DetachAppletAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.DetachAppletAction
- details - Variable in class org.jmol.smiles.SmilesStereo
- detectExplosion() - Method in class org.jmol.minimize.forcefield.ForceField
- determineAtomSetCollectionReader(Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
-
the main resolver method.
- determineSpaceGroup(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
- determineSpaceGroupIndex(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
- determineSpaceGroupN(String) - Static method in class org.jmol.symmetry.SpaceGroup
- determineSpaceGroupNA(String, float[]) - Static method in class org.jmol.symmetry.SpaceGroup
- determineSpaceGroupNS(String, SpaceGroup) - Static method in class org.jmol.symmetry.SpaceGroup
- determineSurfaceFileType(BufferedReader) - Static method in class org.jmol.viewer.FileManager
-
Try to determine a surface file type based on its header.
- determineUniqueAxis(float, float, float, float, float, float) - Static method in class org.jmol.symmetry.SpaceGroup
- df - Static variable in class org.openscience.jmol.app.janocchio.Measure
- DF_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- dfact2 - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
- dfBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- dfCoefMaps - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- dfCoefMaps - Variable in class org.jmol.adapter.writers.QCJSONWriter
- dfCoefMaps - Variable in class org.jmol.jvxl.readers.IsoMOReader
- dfCoefMaps - Variable in class org.jmol.quantum.MOCalculation
- dFixed - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- DFT_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- dgridContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- DgridReader - Class in org.jmol.adapter.readers.quantum
-
A reader for Dgrid BASISFILE data.
- DgridReader() - Constructor for class org.jmol.adapter.readers.quantum.DgridReader
- diagonal - Variable in class org.openscience.jmol.app.surfacetool.Slice
- Diagonalise() - Method in class org.jmol.quantum.NMRNoeMatrix
- diagonalReferenceAxis - Variable in class org.jmol.symmetry.HallRotationTerm
- dialog - Variable in class org.jmol.dialog.FileChooser
- Dialog - Class in org.jmol.dialog
- Dialog() - Constructor for class org.jmol.dialog.Dialog
- Dialog.ExportChoiceListener - Class in org.jmol.dialog
- Dialog.QualityListener - Class in org.jmol.dialog
- Dialog.TypeFilter - Class in org.jmol.dialog
- dialogAsk(String, String, Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
- dialogAsk(String, String, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
-
Ask for new file name when saving or opening a file in Java and saving a file in JavaScript.
- dialogLocation - Variable in class org.jmol.dialog.FileChooser
- dialogSize - Variable in class org.jmol.dialog.FileChooser
- dialogType - Variable in class org.jmol.dialog.Dialog
- diameter - Variable in class org.jmol.g3d.CylinderRenderer
- diameter - Variable in class org.jmol.jvxl.data.JvxlData
- diameter - Variable in class org.jmol.render.MeshRenderer
- diameter - Variable in class org.jmol.renderspecial.DipolesRenderer
- diameter - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- diameter - Variable in class org.jmol.renderspecial.VectorsRenderer
- diameter - Static variable in class org.jmol.script.T
- diameter - Variable in class org.jmol.shape.Mesh
- diameter - Variable in class org.jmol.shapespecial.Draw
- diameter0 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- diameterBeg - Variable in class org.jmol.renderbio.BioShapeRenderer
- diameterEnd - Variable in class org.jmol.renderbio.BioShapeRenderer
- diameterMid - Variable in class org.jmol.renderbio.BioShapeRenderer
- diameterP - Variable in class org.jmol.geodesic.EnvelopeCalculation
- diff - Variable in class org.openscience.jmol.app.janocchio.Measure
- diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.util.Rgb16
- diffuseFactor - Variable in class org.jmol.util.Shader
- diffusepercent - Static variable in class org.jmol.script.T
- diffusePercent - Variable in class org.jmol.util.Shader
- dihedral_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dihedral_label_position - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dihedral_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- DihedralCouple(Atom[], boolean) - Constructor for class org.openscience.jmol.app.janocchio.NmrMolecule.DihedralCouple
- dihedralList - Variable in class org.jmol.thread.SpinThread
- dim - Variable in class org.jmol.bspt.Node
- dimension - Variable in class org.jmol.util.SimpleUnitCell
- Dimension - Class in org.jmol.awtjs.swing
- Dimension(int, int) - Constructor for class org.jmol.awtjs.swing.Dimension
- dimMax - Variable in class org.jmol.bspt.Bspf
- dimMax - Variable in class org.jmol.bspt.Bspt
- dimSize - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- DIPOLAR_FACTOR - Static variable in class org.jmol.quantum.NMRCalculation
- dipole - Static variable in class org.jmol.script.T
- dipole() - Method in class org.jmol.scriptext.IsoExt
- Dipole - Class in org.jmol.shapespecial
- Dipole() - Constructor for class org.jmol.shapespecial.Dipole
- DIPOLE - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- DIPOLE_TYPE_ATOMS - Static variable in class org.jmol.shapespecial.Dipole
- DIPOLE_TYPE_BOND - Static variable in class org.jmol.shapespecial.Dipole
- DIPOLE_TYPE_MOLECULAR - Static variable in class org.jmol.shapespecial.Dipole
- DIPOLE_TYPE_POINTS - Static variable in class org.jmol.shapespecial.Dipole
- DIPOLE_TYPE_POINTVECTOR - Static variable in class org.jmol.shapespecial.Dipole
- DIPOLE_TYPE_UNKNOWN - Static variable in class org.jmol.shapespecial.Dipole
- dipoleCount - Variable in class org.jmol.shapespecial.Dipoles
- dipoleInfo - Variable in class org.jmol.shapespecial.Dipole
- dipoles - Variable in class org.jmol.shapespecial.Dipoles
- Dipoles - Class in org.jmol.shapespecial
- Dipoles() - Constructor for class org.jmol.shapespecial.Dipoles
- dipolescale - Static variable in class org.jmol.script.T
- dipoleScale - Variable in class org.jmol.viewer.GlobalSettings
- DipolesRenderer - Class in org.jmol.renderspecial
- DipolesRenderer() - Constructor for class org.jmol.renderspecial.DipolesRenderer
- dipoleValue - Variable in class org.jmol.shapespecial.Dipole
- dipoleValue - Variable in class org.jmol.shapespecial.Dipoles
- dipoleVectorScale - Variable in class org.jmol.renderspecial.DipolesRenderer
- direct - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- direction - Static variable in class org.jmol.script.T
- direction - Variable in class org.openscience.jmol.app.janocchio.TableSorter.Directive
- Directive(int, int) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter.Directive
- directLatticeVectors - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- directLatticeVectorsFirst - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
-
CRYSTAL 17 moves directLatticeVectors before LATTICE PARAMETERS
- DISABLE - Static variable in class org.jmol.shapecgo.CGOMesh
- disableField(int) - Method in class org.jmol.adapter.readers.cif.CifReader
-
used for turning off fractional or nonfractional coord.
- disablepopupmenu - Static variable in class org.jmol.script.T
- disablePopupMenu - Variable in class org.jmol.viewer.GlobalSettings
- discardLinesUntilBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardLinesUntilContains(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardLinesUntilContains(String) - Method in interface org.jmol.api.JmolJDXMOLReader
- discardLinesUntilContains2(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardLinesUntilContains2(String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
- discardLinesUntilNonBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardLinesUntilNonBlank() - Method in interface org.jmol.api.JmolJDXMOLReader
- discardLinesUntilStartsWith(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardPreviousAtoms() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- discardTempData(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- discardTempData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- discardTempData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- discardTempData(boolean) - Method in class org.jmol.shapesurface.Isosurface
- discardTempDataSR(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- discrete - Static variable in class org.jmol.script.T
- DISCRETESTATE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- DISORDER_ASSEMBLY - Static variable in class org.jmol.adapter.readers.cif.CifReader
- DISORDER_GROUP - Static variable in class org.jmol.adapter.readers.cif.CifReader
- disorderAssembly - Variable in class org.jmol.adapter.readers.cif.CifReader
- disorderMap - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- disorderMapMax - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- DISP_SAW_AX - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DISP_SAW_AY - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DISP_SAW_AZ - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DISP_SAW_C - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DISP_SAW_W - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- DISP_SPEC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.CmdExt
-
The command dispatcher for the set of commands extended by this class.
- dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.IsoExt
- dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.ScriptExt
- dispatchCommands(boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
- displacement - Static variable in class org.jmol.script.T
- display - Variable in class org.jmol.dialog.FilePreview
- display - Variable in class org.jmol.i18n.Language
- display - Static variable in class org.jmol.script.T
- display - Variable in class org.jmol.viewer.Viewer
- display - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- display - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- display(ModelSet, BS, int, boolean) - Method in class org.jmol.viewer.SelectionManager
- Display - Class in org.jmol.awt
-
methods required by Jmol that access java.awt.Component private to org.jmol.awt
- Display - Class in org.jmol.awtjs2d
-
methods required by Jmol that access java.awt.Component private to org.jmol.awt
- Display() - Constructor for class org.jmol.awt.Display
- Display() - Constructor for class org.jmol.awtjs2d.Display
- displayAtoms(BS, boolean, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
- displayBonds(BondSet, boolean) - Method in class org.jmol.modelset.BondCollection
- displaycellparameters - Static variable in class org.jmol.script.T
- displayCellParameters - Variable in class org.jmol.viewer.GlobalSettings
- displayConsole() - Method in class org.jmol.console.GenericConsole
- displayed - Static variable in class org.jmol.script.T
- displayLoadErrors - Variable in class org.jmol.viewer.Viewer
- displayLoadErrorsSave - Variable in class org.jmol.script.ScriptContext
- displayMaxX - Variable in class org.jmol.util.GData
- displayMaxX2 - Variable in class org.jmol.util.GData
- displayMaxY - Variable in class org.jmol.util.GData
- displayMaxY2 - Variable in class org.jmol.util.GData
- displayMinX - Variable in class org.jmol.util.GData
- displayMinX2 - Variable in class org.jmol.util.GData
- displayMinY - Variable in class org.jmol.util.GData
- displayMinY2 - Variable in class org.jmol.util.GData
- DisplayPanel - Class in org.openscience.jmol.app.jmolpanel
- DisplayPanel(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel
- DisplayPanel.CheckBoxMenuItemAction - Class in org.openscience.jmol.app.jmolpanel
-
Action calling evalStringQuiet(<action> + CheckBoxState)
- DisplayPanel.DefineCenterAction - Class in org.openscience.jmol.app.jmolpanel
- DisplayPanel.HomeAction - Class in org.openscience.jmol.app.jmolpanel
- DisplayPanel.MoveToAction - Class in org.openscience.jmol.app.jmolpanel
-
Action calling moveTo()
- DisplayPanel.SetStatusAction - Class in org.openscience.jmol.app.jmolpanel
-
Action calling setStatus()
- displaySpeed - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- displayType - Variable in class org.jmol.shapesurface.Contact
- displayWhileRenderingCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- displayWithinDistance2 - Variable in class org.jmol.shape.MeshCollection
- displayWithinPoints - Variable in class org.jmol.shape.MeshCollection
- dispose() - Method in interface org.jmol.api.GenericMouseInterface
- dispose() - Method in interface org.jmol.api.JmolAppConsoleInterface
- dispose() - Method in interface org.jmol.api.JmolGestureServerInterface
- dispose() - Method in interface org.jmol.api.JmolScriptEditorInterface
- dispose() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- dispose() - Method in class org.jmol.api.JmolViewer
- dispose() - Method in class org.jmol.awt.FileDropper
- dispose() - Method in class org.jmol.awt.Mouse
- dispose() - Method in class org.jmol.awtjs.swing.JDialog
- dispose() - Method in class org.jmol.awtjs2d.Mouse
- dispose() - Method in class org.jmol.console.GenericConsole
- dispose() - Method in class org.jmol.console.JmolConsole
- dispose() - Method in class org.jmol.console.ScriptEditor
- dispose() - Method in class org.jmol.consolejs.AppletConsole
- dispose() - Method in class org.jmol.modelkit.ModelKit
- dispose() - Method in class org.jmol.multitouch.ActionManagerMT
- dispose() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
- dispose() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- dispose() - Method in class org.jmol.multitouch.jni.JmolJniClientAdapter
- dispose() - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- dispose() - Method in class org.jmol.viewer.ActionManager
- dispose() - Method in class org.jmol.viewer.Viewer
-
end of life for this viewer
- dispose() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- dispose() - Static method in class org.openscience.jmol.app.webexport.WebExport
- dispose(JFrame, boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- dispose(SC) - Method in class org.jmol.awt.AwtPopupHelper
- dispose(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
- dispose(SC) - Method in interface org.jmol.popup.PopupHelper
- dispose(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
Remove this component's HTML5 equivalent and clear references to it.
- disposeGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
- disposeGraphics(Object) - Static method in class org.jmol.awt.Image
- disposeGraphics(Object) - Method in class org.jmol.awt.Platform
- disposeGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
- disposeMenu() - Method in class org.jmol.awtjs.swing.JPopupMenu
- disregardNeighbors - Variable in class org.jmol.geodesic.EnvelopeCalculation
- dist_counter - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- distance - Variable in class org.jmol.adapter.smarter.Bond
- distance - Variable in class org.jmol.jvxl.readers.Parameters
- distance - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
- distance - Static variable in class org.jmol.script.T
- distance_exclusion - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- distance2 - Variable in class org.jmol.symmetry.UnitCellIterator
- distance2(double[], double[]) - Static method in class org.jmol.minimize.Util
- distance2V(V3d, V3d) - Static method in class org.jmol.minimize.Util
- distancefactor - Static variable in class org.jmol.script.T
- distanceMatrix - Variable in class org.jmol.quantum.NMRNoeMatrix
- distanceMode - Variable in class org.jmol.quantum.MepCalculation
- distancePointToPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
- distanceRef - Variable in class org.jmol.shapespecial.Polyhedra
- distanceRef - Variable in class org.jmol.shapespecial.Polyhedron
- distances - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- distanceSqrd(NMRNoeMatrix.NOEAtom, NMRNoeMatrix.NOEAtom) - Method in class org.jmol.quantum.NMRNoeMatrix
- distanceSquared - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- distanceTolerance - Variable in class org.jmol.symmetry.PointGroup
- distanceTolerance2 - Variable in class org.jmol.symmetry.PointGroup
- distanceToMappingPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
- distanceVerticalToPlane(float, float, P3, P3, P3) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- distinguishAndPropagateGroup(int, Chain, String, int, int, int) - Method in class org.jmol.modelset.ModelLoader
- distinguishAndPropagateGroup(Chain, String, int, int, int, int[], Atom[]) - Method in class org.jmol.modelsetbio.BioResolver
- div - Static variable in class org.jmol.script.T
- div12(M4, int) - Static method in class org.jmol.symmetry.SymmetryOperation
- divide - Static variable in class org.jmol.script.T
- divisor - Variable in class org.jmol.symmetry.SymmetryOperation
- DIVISOR_MASK - Static variable in class org.jmol.symmetry.SymmetryOperation
- DIVISOR_OFFSET - Static variable in class org.jmol.symmetry.SymmetryOperation
- dList - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- dm - Variable in class org.jmol.viewer.Viewer
- dmax - Variable in class org.jmol.jvxl.readers.MapFileReader
- dMax - Static variable in class org.jmol.quantum.NciCalculation
- dmean - Variable in class org.jmol.jvxl.readers.MapFileReader
- dmesh - Variable in class org.jmol.renderspecial.DrawRenderer
- dmeshes - Variable in class org.jmol.shapespecial.Draw
- dmin - Variable in class org.jmol.jvxl.readers.MapFileReader
- dmolContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- DmolReader - Class in org.jmol.adapter.readers.xtal
- DmolReader() - Constructor for class org.jmol.adapter.readers.xtal.DmolReader
- dna - Static variable in class org.jmol.script.T
- DNA - Enum constant in enum org.jmol.c.STR
- DNA_MASK - Static variable in class org.jmol.viewer.JC
- doAction(Object) - Method in class org.jmol.console.GenericConsole
- doAction(MeasurementData, String, int) - Method in class org.jmol.shape.Measures
- doAddHydrogens - Variable in class org.jmol.jvxl.readers.AtomDataReader
- doAddHydrogens - Variable in class org.jmol.modelset.ModelLoader
- doApplySymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doCache - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- doCache - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- doCalcArea - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- doCalculateTroughs - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- doCap - Variable in class org.jmol.util.MeshSlicer
- doCap0 - Variable in class org.jmol.renderbio.BioMeshRenderer
- doCap1 - Variable in class org.jmol.renderbio.BioMeshRenderer
- doCentralize - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doCentroidUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doCentroidUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- doCheckAtom(int) - Method in class org.jmol.smiles.SmilesSearch
- doCheckUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doClear - Variable in class org.jmol.util.MeshSlicer
- doClose(boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- doClose(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- doColor - Variable in class org.jmol.rendercgo.CGORenderer
- doConvertToFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- Document - Interface in org.jmol.awtjs.swing
- documentBase - Variable in class org.jmol.util.GenericApplet
- doDebug - Variable in class org.jmol.quantum.QuantumCalculation
- doDelay(int) - Method in class org.jmol.script.ScriptEval
- doDisplace - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
- doDrop(PropertyChangeEvent) - Method in class org.jmol.awt.FileDropper
- doEndMove - Variable in class org.jmol.thread.MoveToThread
- doEval(String) - Method in class org.jmol.util.GenericApplet
-
return RAW JAVASCRIPT OBJECT, NOT A STRING
- doFinalize() - Method in class org.jmol.symmetry.SymmetryOperation
- doFinalTransform() - Method in class org.jmol.thread.MoveToThread
- doFixPeriodic - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- doFont() - Method in class org.jmol.console.ScriptEditor
- doFormatText - Variable in class org.jmol.modelset.Text
- doFullMolecular - Variable in class org.jmol.jvxl.readers.Parameters
- doGetModel(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doGetVibration(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doGhost - Variable in class org.jmol.util.MeshSlicer
- doHalt() - Method in class org.jmol.console.ScriptEditor
- doHaveJDX() - Method in class org.jmol.viewer.Viewer
- doHighlight(int, int, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor.EditorDocument
- doItAll(File) - Method in class org.jmol.quantum.NMRNoeMatrix
- doIterate - Variable in class org.jmol.jvxl.data.VolumeData
- doJustify - Variable in class org.jmol.render.MeasuresRenderer
- dollarsign - Static variable in class org.jmol.script.T
- doLogLevel(boolean) - Static method in class org.jmol.util.Logger
-
Indicates if the level is logged.
- domains - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- domains - Static variable in class org.jmol.script.T
- doMenuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
- doMenuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
- doMinimize - Variable in class org.jmol.modelset.ModelLoader
- domObj - Variable in class org.jmol.adapter.readers.xml.XmlReader
- DOMReader - Class in org.jmol.io
- DOMReader() - Constructor for class org.jmol.io.DOMReader
- DOMResolve(Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
-
a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page.
- doNavStep(int) - Method in class org.jmol.navigate.Navigator
- done - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- done - Variable in class org.jmol.dssx.DSSP
- done - Variable in class org.jmol.symmetry.UnitCellIterator
- doneHere - Variable in class org.jmol.multitouch.ActionManagerMT
- doneHere - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- doNew() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- DONOR - Enum constant in enum org.jmol.c.HB
- doNormalize - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- doNormalize - Variable in class org.jmol.symmetry.SpaceGroup
- doNormalize - Variable in class org.jmol.symmetry.SymmetryOperation
-
"normalization" is the process of adjusting symmetry operator definitions such that the center of geometry of a molecule is within the 555 unit cell for each operation.
- dontsave - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- doOpen() - Method in class org.jmol.console.ScriptEditor
- doOverWrite(JFileChooser, File) - Static method in class org.jmol.dialog.Dialog
- doPackUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doPackUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- doPause() - Method in class org.jmol.console.ScriptEditor
- doPointer - Variable in class org.jmol.render.LabelsRenderer
- doPoly(Object, int[], int[], int, boolean) - Method in class org.jmol.awtjs2d.JsG2D
- doPopPush - Variable in class org.jmol.script.ScriptDelayThread
- doPopup(int, int) - Method in class org.jmol.viewer.ActionManager
- doPreSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
- doPreSymmetry() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- doPreSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doPreviewAction(boolean) - Method in class org.jmol.dialog.FilePreview
- doProcessLines - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doReadMolecularOrbitals - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doRender - Variable in class org.jmol.render.MeshRenderer
- doReport - Variable in class org.jmol.dssx.DSSP
- doReport() - Method in class org.jmol.script.ScriptEval
- doReportProperty(String) - Static method in class org.jmol.viewer.GlobalSettings
- doResize - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- doResume() - Method in class org.jmol.console.ScriptEditor
- doRun() - Method in class org.jmol.console.ScriptEditor
- doSaveSurfacePoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- doSelection() - Method in class org.jmol.script.ScriptMathProcessor
- doSelections - Variable in class org.jmol.script.ScriptMathProcessor
- doSendCallback(CBK, Object, Object[], String) - Method in class org.jmol.util.GenericApplet
- doSetBonds - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- doSetOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- doShowDocument(URL) - Method in class org.jmol.util.GenericApplet
- doShowShellType - Variable in class org.jmol.quantum.MOCalculation
- doShowStatus(String) - Method in class org.jmol.util.GenericApplet
- doSmoothProperty - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
- doSort - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- doStep() - Method in class org.jmol.console.ScriptEditor
- doStepTransform() - Method in class org.jmol.thread.MoveToThread
- doStroke(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
- doStroke(Object, boolean) - Method in class org.jmol.awt.AwtG2D
- doStroke(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
- doSymmetry - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
- doSync() - Method in class org.jmol.viewer.StatusManager
- dot - Static variable in class org.jmol.script.T
- dot_as_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_density - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_hydrogens - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_normals - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dot_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dotColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- dotCount - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- dotdensity - Static variable in class org.jmol.script.T
- dotDensity - Variable in class org.jmol.viewer.GlobalSettings
- doTrack - Variable in class org.jmol.symmetry.CIPChirality
-
are we tracking pathways for _M.CIPInfo?
- doTransform - Variable in class org.jmol.adapter.writers.CMLWriter
- doTransform - Variable in class org.jmol.adapter.writers.PDBWriter
- doTransform() - Method in class org.jmol.thread.SpinThread
- doTransform4D - Variable in class org.jmol.viewer.TransformManager
- doTranslate - Variable in class org.jmol.i18n.GT
- doTranslate - Variable in class org.jmol.util.GenericApplet
- dots - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- dots - Static variable in class org.jmol.script.T
- dots() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Provide an indent for clarity in debugging messages
- Dots - Class in org.jmol.shapespecial
- Dots() - Constructor for class org.jmol.shapespecial.Dots
- dotscale - Static variable in class org.jmol.script.T
- dotScale - Variable in class org.jmol.renderspecial.DotsRenderer
- dotScale - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- dotScale - Variable in class org.jmol.viewer.GlobalSettings
- dotsConvexMaps - Variable in class org.jmol.geodesic.EnvelopeCalculation
- dotsConvexMax - Variable in class org.jmol.geodesic.EnvelopeCalculation
- dotSolvent - Variable in class org.jmol.viewer.GlobalSettings
- dotsOrDashes - Variable in class org.jmol.render.FontLineShapeRenderer
- DotsRenderer - Class in org.jmol.renderspecial
- DotsRenderer() - Constructor for class org.jmol.renderspecial.DotsRenderer
- dotsselectedonly - Static variable in class org.jmol.script.T
- dotsSelectedOnly - Variable in class org.jmol.viewer.GlobalSettings
- dotsurface - Static variable in class org.jmol.script.T
- dotSurface - Variable in class org.jmol.viewer.GlobalSettings
- dotted - Static variable in class org.jmol.script.T
- DOTWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
- DOUBLE - Enum constant in enum org.jmol.c.STER
- DOUBLE - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- DOUBLE - Static variable in class org.jmol.viewer.binding.Binding
- doubleprecision - Static variable in class org.jmol.script.T
- doublePrecision - Variable in class org.jmol.viewer.GlobalSettings
-
setting doublePrecision will also toggle legacyJavaFloat to doublePrecision in order to avoid any rounding
- doubleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- doUpdatePreview(File) - Method in class org.jmol.dialog.FilePreview
-
Update preview
- doUseIterator - Variable in class org.jmol.jvxl.readers.AtomDataReader
- DOWN - Static variable in class org.jmol.viewer.binding.Binding
- DownLoadWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
- downsample - Static variable in class org.jmol.script.T
- downsample2d(int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
- downsample2dZ(int[], int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
- downsampleFactor - Variable in class org.jmol.jvxl.readers.Parameters
- downsampleFactor - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- downsampleFullSceneAntialiasing(boolean) - Method in class org.jmol.g3d.Graphics3D
- downsampleRemainders - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- dPlane - Variable in class org.jmol.util.MeshSlicer
- DRAG - Static variable in class org.jmol.viewer.binding.Binding
- DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- dragAction - Variable in class org.jmol.viewer.ActionManager
- dragAtomIndex - Variable in class org.jmol.viewer.ActionManager
- dragBinding - Variable in class org.jmol.viewer.ActionManager
- DragBinding - Class in org.jmol.viewer.binding
- DragBinding() - Constructor for class org.jmol.viewer.binding.DragBinding
- DRAGDROP - Enum constant in enum org.jmol.c.CBK
- dragEnter(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
- dragExit(DropTargetEvent) - Method in class org.jmol.awt.FileDropper
- dragged - Variable in class org.jmol.viewer.ActionManager
- dragged(long, int, int) - Method in class org.jmol.awtjs2d.Mouse
- DRAGGED - Static variable in class org.jmol.awtjs.Event
- dragGesture - Variable in class org.jmol.viewer.ActionManager
- dragMinimizeAtom(int) - Method in class org.jmol.viewer.Viewer
- dragOver(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
- dragselected - Static variable in class org.jmol.script.T
- dragSelected - Variable in class org.jmol.viewer.GlobalSettings
- dragSelected(int, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
-
change actual coordinates of selected atoms from set dragSeleted TRUE or set PICKING DRAGSELECTED Basically, set dragSelected adds new functionality to Jmol with alt-drag and alt-shift drag, and set picking dragSelected replaces the standard mouse drag with a move action and also adds rotate and z-shift options.
- dragSelectedMode - Variable in class org.jmol.viewer.ActionManager
- drange - Variable in class org.jmol.jvxl.readers.MapFileReader
- draw - Static variable in class org.jmol.script.T
- draw() - Method in class org.jmol.scriptext.IsoExt
- Draw - Class in org.jmol.shapespecial
- Draw() - Constructor for class org.jmol.shapespecial.Draw
- DRAW_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
- draw_frames - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- draw_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- Draw.EnumDrawType - Enum in org.jmol.shapespecial
- draw000 - Variable in class org.jmol.render.FontLineShapeRenderer
- drawArrowScale - Variable in class org.jmol.shapespecial.DrawMesh
- drawAtom(Atom, float) - Method in interface org.jmol.api.JmolRendererInterface
- drawAtom(Atom, float) - Method in class org.jmol.export.___Exporter
- drawAtom(Atom, float) - Method in class org.jmol.export.__CartesianExporter
- drawAtom(Atom, float) - Method in class org.jmol.export.__RayTracerExporter
- drawAtom(Atom, float) - Method in class org.jmol.export.Export3D
- drawAtom(Atom, float) - Method in class org.jmol.g3d.Graphics3D
- drawBanana(Atom, Atom, V3, int) - Method in class org.jmol.render.SticksRenderer
- drawBond(int) - Method in class org.jmol.render.SticksRenderer
- drawBond(P3, P3, short, short, byte, short, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.export.Export3D
- drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.g3d.Graphics3D
- drawCap - Variable in class org.jmol.renderspecial.VectorsRenderer
- drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.___Exporter
- drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.__CartesianExporter
- drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
- drawCircle(short, int, int, int, int, boolean) - Method in class org.jmol.export.Export3D
-
draws a simple circle (draw circle)
- drawCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
- drawCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- drawCylinder(P3, P3, short, short, byte, int, int) - Method in class org.jmol.export.___Exporter
- drawCylinder(P3, P3, short, short, byte, int, int) - Method in class org.jmol.export.__CartesianExporter
-
bond order -1 -- single bond, Cartesian bond order -2 -- multiple bond, Cartesian
- drawCylinder(P3, P3, short, short, byte, int, int) - Method in class org.jmol.export.__RayTracerExporter
- drawDashedCylinder(JmolRendererInterface, int, int, int, int, int, int, int[], int, short, short, int, boolean, P3i) - Static method in class org.jmol.render.FontLineShapeRenderer
- drawDashedLineBits(int, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.export.Export3D
- drawDashedLineBits(int, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- drawData - Variable in class org.jmol.modelkit.ModelKit
- drawEdge(int, int, boolean, T3, T3, P3i, P3i) - Method in class org.jmol.render.MeshRenderer
- drawEdges - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- drawEdges - Variable in class org.jmol.shapespecial.Polyhedra
- drawEdges(short, P3, P3, P3, int) - Method in class org.jmol.renderspecial.PolyhedraRenderer
- drawEdges(P3[], P3[], int) - Method in class org.jmol.renderbio.NucleicRenderer
- drawEllipse(P3, P3, P3, boolean, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.export.Export3D
- drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
- drawEllipse(P3, P3, P3, short, boolean) - Method in class org.jmol.export.___Exporter
- drawEllipse(P3, P3, P3, short, boolean) - Method in class org.jmol.export.__CartesianExporter
- drawEllipse(P3, P3, P3, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
- drawFilledCircle(short, short, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
draws a ring and filled circle (halos, draw CIRCLE, draw handles)
- drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.___Exporter
- drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.Export3D
-
draws a screened circle ...
- drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawfontsize - Static variable in class org.jmol.script.T
- drawFontSize - Variable in class org.jmol.viewer.GlobalSettings
- drawFrameLine(String, P3, V3, float, P3, SB, String, String) - Static method in class org.jmol.symmetry.SymmetryDesc
- drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- drawHermite4(int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
- drawHermite4(int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in interface org.jmol.api.JmolRendererInterface
- drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.export.Export3D
- drawHermite7(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, short) - Method in class org.jmol.g3d.Graphics3D
- drawHLine(int, int, int, int) - Method in class org.jmol.export.Export3D
- drawHLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawhover - Static variable in class org.jmol.script.T
- drawHover - Variable in class org.jmol.viewer.GlobalSettings
- drawImage(Object, int, int, int, int, short, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.export.Export3D
- drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawImage(Object, Object, int, int, boolean) - Method in class org.jmol.viewer.Viewer
- drawImage(Object, Object, int, int, int, int) - Static method in class org.jmol.awt.Display
- drawImage(Object, Object, int, int, int, int, boolean) - Method in interface org.jmol.api.GenericPlatform
- drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awt.Platform
- drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs.Platform
- drawImage(Object, Object, int, int, int, int, boolean) - Static method in class org.jmol.awtjs2d.Display
-
Draw the completed image from rendering.
- drawImage(Object, Object, int, int, int, int, boolean) - Method in class org.jmol.awtjs2d.Platform
- drawImageDTI(Object, Object, int, int, int, int) - Static method in class org.jmol.awt.Display
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
- drawImageToBuffer(Object, Object, Object, int, int, int) - Static method in class org.jmol.awt.Image
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
- drawIndex - Variable in class org.jmol.symmetry.PointGroup
- drawInfo - Variable in class org.jmol.symmetry.PointGroup
- drawInfo(String, int, String) - Method in class org.jmol.render.UccageRenderer
- drawing - Static variable in class org.jmol.script.T
- drawLcaoCartoon(V3, V3, V3, int) - Method in class org.jmol.shapesurface.Isosurface
- drawLine(int, int, int, int, int, int) - Method in class org.jmol.render.StarsRenderer
- drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
- drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.MeasuresRenderer
- drawLine(short, short, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
- drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawLine(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawLine(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- drawLine(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- drawLine(SB, String, float, P3, P3, String) - Static method in class org.jmol.symmetry.SymmetryDesc
- drawLine2(JmolRendererInterface, int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
- drawLineAB(P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- drawLineAB(P3, P3) - Method in class org.jmol.export.Export3D
- drawLineAB(P3, P3) - Method in class org.jmol.g3d.Graphics3D
- drawLineABBits(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
- drawLineBits(short, short, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- drawLineBits(short, short, P3, P3) - Method in class org.jmol.export.Export3D
- drawLineBits(short, short, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- drawLineBits(P3, P3, short, short) - Method in class org.jmol.export.Export3D
- drawLineData(Lst<P3[]>) - Method in class org.jmol.renderspecial.DrawRenderer
- drawLinePixels(P3i, P3i, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
- drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.export.Export3D
- drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawLinePixels(P3i, P3i, int, int) - Method in class org.jmol.util.GData
- drawLineXYZ(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
- drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawLineXYZ(JmolRendererInterface, int, int, int, float, float, int, float, float, short, int) - Static method in class org.jmol.render.TextRenderer
- DrawMesh - Class in org.jmol.shapespecial
- DrawMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapespecial.DrawMesh
- drawMeshSphere(P3i) - Method in class org.jmol.render.MeshRenderer
- drawMode - Variable in class org.jmol.viewer.ActionManager
- drawpicking - Static variable in class org.jmol.script.T
- drawPicking - Variable in class org.jmol.viewer.GlobalSettings
- drawPixel(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawPixel(int, int, int) - Method in class org.jmol.export.Export3D
- drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawPixel(short, int, int, int, int) - Method in class org.jmol.export.___Exporter
- drawPixel(short, int, int, int, int) - Method in class org.jmol.export.__CartesianExporter
- drawPixel(short, int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
- drawPoint(int, boolean) - Method in class org.jmol.render.MeshRenderer
- drawPoints(int, int[], int) - Method in interface org.jmol.api.JmolRendererInterface
- drawPoints(int, int[], int) - Method in class org.jmol.export.Export3D
- drawPoints(int, int[], int) - Method in class org.jmol.g3d.Graphics3D
- drawPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
- drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
- drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
- drawQuadrilateralBits(JmolRendererInterface, short, P3, P3, P3, P3) - Method in class org.jmol.util.GData
- drawQuat(Quat, String, String, P3, float) - Static method in class org.jmol.modelsetbio.BioExt
- drawQuat(Quat, String, String, P3, float) - Static method in class org.jmol.util.Escape
- drawRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
draws a rectangle
- drawRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
-
draws a rectangle
- drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
draws a rectangle
- drawRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- drawRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- DrawRenderer - Class in org.jmol.renderspecial
- DrawRenderer() - Constructor for class org.jmol.renderspecial.DrawRenderer
- drawScript - Variable in class org.jmol.modelkit.ModelKit
- drawSegmentAB(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.BioShapeRenderer
- drawShaft - Variable in class org.jmol.renderspecial.VectorsRenderer
- drawSlicePlane(SB, int, boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- drawString(int, int, int, int, boolean, boolean, boolean, int, String) - Method in class org.jmol.render.FontLineShapeRenderer
- drawString(Object, String, int, int) - Method in interface org.jmol.api.GenericGraphics
- drawString(Object, String, int, int) - Method in class org.jmol.awt.AwtG2D
- drawString(Object, String, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- drawString(String, Font, int, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
-
draws the specified string in the current font.
- drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.export.Export3D
-
draws the specified string in the current font.
- drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
-
draws the specified string in the current font.
- drawStringNoSlab(String, Font, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
-
draws the specified string in the current font.
- drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.export.Export3D
-
draws the specified string in the current font.
- drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
-
draws the specified string in the current font.
- drawStringRotated(Object, String, int, int, double) - Method in interface org.jmol.api.GenericGraphics
- drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awt.AwtG2D
- drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awtjs2d.JsG2D
- drawSubzonePolygons(BZone) - Method in class org.jmol.util.BZone
- drawSurface(MeshSurface, short) - Method in interface org.jmol.api.JmolRendererInterface
- drawSurface(MeshSurface, short) - Method in class org.jmol.export.___Exporter
- drawSurface(MeshSurface, short) - Method in class org.jmol.export._ObjExporter
- drawSurface(MeshSurface, short) - Method in class org.jmol.export.Export3D
- drawSurface(MeshSurface, short) - Method in class org.jmol.g3d.Graphics3D
- drawTextPixel(int, int, int, int) - Method in class org.jmol.export.___Exporter
- drawTextPixel(int, int, int, int) - Method in class org.jmol.export.__CartesianExporter
- drawTextPixel(int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
- drawTextPixel(int, int, int, int) - Method in class org.jmol.export._MayaExporter
- drawTicks(int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
- drawTicks2(float, int, int, String[]) - Method in class org.jmol.render.FontLineShapeRenderer
- drawTriangle(int, MeshCapper.CapVertex, MeshCapper.CapVertex, MeshCapper.CapVertex, String) - Method in class org.jmol.util.MeshCapper
-
for debugging
- drawTriangle(P3i, short, P3i, short, P3i, short, int, int) - Method in class org.jmol.render.MeshRenderer
- drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in interface org.jmol.api.JmolRendererInterface
- drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.export.Export3D
- drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.g3d.Graphics3D
- drawTriangleBits(P3, short, P3, short, P3, short, int, int) - Method in class org.jmol.render.MeshRenderer
- drawTriangleBits(JmolRendererInterface, P3, short, P3, short, P3, short, int) - Method in class org.jmol.util.GData
- drawTriangles - Variable in class org.jmol.shape.Mesh
- drawType - Variable in class org.jmol.renderspecial.DrawRenderer
- drawType - Variable in class org.jmol.shapespecial.DrawMesh
- drawType - Variable in class org.jmol.symmetry.PointGroup
- drawTypes - Variable in class org.jmol.shapespecial.DrawMesh
- drawVector(SB, String, String, String, String, T3, T3, String) - Static method in class org.jmol.symmetry.SymmetryDesc
- drawVertexCount - Variable in class org.jmol.shapespecial.DrawMesh
- drawVertexCounts - Variable in class org.jmol.shapespecial.DrawMesh
- drawVLine(int, int, int, int) - Method in class org.jmol.export.Export3D
- drawVLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- drawZoneCenters(BZone) - Method in class org.jmol.util.BZone
- DRIVER_NONE - Static variable in class org.jmol.multitouch.ActionManagerMT
- drivingSync - Variable in class org.jmol.viewer.StatusManager
- drop(DropTargetDropEvent) - Method in class org.jmol.awt.FileDropper
- dropActionChanged(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
- dropListener - Variable in class org.jmol.awt.FileDropper
- dRot - Variable in class org.jmol.thread.MoveToThread
- DS - Static variable in class org.jmol.quantum.QS
- DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
- DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
- DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
- DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
- dSlab - Variable in class org.jmol.thread.MoveToThread
- dslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- Dsn6BinaryReader - Class in org.jmol.jvxl.readers
- Dsn6BinaryReader() - Constructor for class org.jmol.jvxl.readers.Dsn6BinaryReader
- dSpherical - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- dssp - Static variable in class org.jmol.script.T
- DSSP - Class in org.jmol.dssx
- DSSP() - Constructor for class org.jmol.dssx.DSSP
- dsspcalchydrogen - Static variable in class org.jmol.script.T
- dsspCalcHydrogen - Variable in class org.jmol.viewer.GlobalSettings
- dsspIgnoreHydrogens - Variable in class org.jmol.dssx.DSSP
- dsspTypes - Static variable in class org.jmol.modelsetbio.AlphaPolymer
- dssr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- dssr - Static variable in class org.jmol.script.T
- DSSR_PATHS - Static variable in class org.jmol.dssx.DSSR1
-
The paths to the unit id data within the structure.
- DSSR0 - Class in org.jmol.dssx
-
The original non-JSON parser for output from 3DNA web service.
- DSSR0() - Constructor for class org.jmol.dssx.DSSR0
- DSSR1 - Class in org.jmol.dssx
-
A parser for output from 3DNA web service.
- DSSR1() - Constructor for class org.jmol.dssx.DSSR1
- dssrBox - Variable in class org.jmol.modelsetbio.NucleicMonomer
- dssrBoxHeight - Variable in class org.jmol.modelsetbio.NucleicMonomer
- dssrCache - Variable in class org.jmol.modelset.Model
- dssrData - Variable in class org.jmol.modelset.AtomCollection
- dssrFrame - Variable in class org.jmol.modelsetbio.NucleicMonomer
- dssrNT - Variable in class org.jmol.modelset.Group
- dssrParser - Variable in class org.jmol.viewer.Viewer
- DTI - Enum constant in enum org.jmol.c.STER
- dTrans - Variable in class org.jmol.thread.MoveToThread
- DUMMY_ATOM - Static variable in class org.jmol.adapter.readers.cif.CifReader
- dump_binary - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dumpAll(boolean) - Static method in class org.jmol.symmetry.SpaceGroup
- dumpAllSeitz() - Static method in class org.jmol.symmetry.SpaceGroup
- dumpBasis(BS, BS, BS) - Method in class org.jmol.symmetry.SpaceGroupFinder
- dumpCanonicalSeitzList() - Method in class org.jmol.symmetry.SpaceGroup
- dumpContainer(Container, String) - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- dumpDipoles(String) - Method in class org.jmol.shapespecial.Dipoles
- dumpInfo() - Method in class org.jmol.symmetry.HallInfo
- dumpInfo() - Method in class org.jmol.symmetry.SpaceGroup
- dumpInfo() - Method in class org.jmol.symmetry.SymmetryOperation
- dumpInfo(boolean, boolean) - Method in class org.jmol.symmetry.UnitCell
- dumpInfo(int) - Method in class org.jmol.quantum.MOCalculation
- dumpInfo(String) - Method in class org.jmol.symmetry.HallRotationTerm
- dumpInfoObj() - Method in class org.jmol.symmetry.SpaceGroup
- dumping - Variable in class org.jmol.util.MeshCapper
-
for debugging
- dumpLine(P3, T3, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- dumpLine2(P3, P3, String, float, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- dumpMatrix(String, int, int[][]) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
- dumpPoint(P3, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- dumpRegion() - Method in class org.jmol.util.MeshCapper.CapVertex
-
for debugging
- dumpRingKeys(SB, Map<String, Object[]>) - Method in class org.jmol.smiles.SmilesGenerator
- dumpSeitz(M4, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- dumpStacks(String) - Method in class org.jmol.script.ScriptMathProcessor
- dumpStructure(String[][]) - Method in class org.jmol.popup.PopupResource
- dumpSummary(AminoPolymer, char[]) - Method in class org.jmol.dssx.DSSP
- dumpTags(AminoPolymer, String, BS, int) - Method in class org.jmol.dssx.DSSP
- dumpWords() - Method in class org.jmol.popup.PopupResource
- duplicateAtomProperties(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- dval(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- dVal - Variable in class org.jmol.minimize.forcefield.FFParam
- dx - Variable in class org.jmol.bspt.CubeIterator
- dx - Variable in class org.jmol.render.SticksRenderer
- dx - Variable in class org.jmol.rendercgo.CGORenderer
-
UV mapping min/max x and y
- dx - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- dx - Variable in class org.jmol.shape.Frank
- dxB - Variable in class org.jmol.g3d.CylinderRenderer
- dxBf - Variable in class org.jmol.g3d.CylinderRenderer
- dxStep - Variable in class org.jmol.render.SticksRenderer
- DXY - Variable in class org.jmol.quantum.MOCalculation
- dxyz - Variable in class org.jmol.g3d.SphereRenderer
- DXZ - Variable in class org.jmol.quantum.MOCalculation
- dy - Variable in class org.jmol.bspt.CubeIterator
- dy - Variable in class org.jmol.render.SticksRenderer
- dy - Variable in class org.jmol.rendercgo.CGORenderer
-
UV mapping min/max x and y
- dy - Variable in class org.jmol.shape.Frank
- dyB - Variable in class org.jmol.g3d.CylinderRenderer
- dyBf - Variable in class org.jmol.g3d.CylinderRenderer
- dynamic_measures - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dynamic_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dynamic_width_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dynamic_width_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dynamic_width_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- dynamicmeasurements - Static variable in class org.jmol.script.T
- dyStep - Variable in class org.jmol.render.SticksRenderer
- DYZ - Variable in class org.jmol.quantum.MOCalculation
- dz - Variable in class org.jmol.bspt.CubeIterator
- dzB - Variable in class org.jmol.g3d.CylinderRenderer
- dzBf - Variable in class org.jmol.g3d.CylinderRenderer
- dZoom - Variable in class org.jmol.thread.MoveToThread
E
- e - Variable in class org.jmol.scriptext.MathExt
- e - Variable in class org.jmol.scriptext.ScriptExt
- e - Variable in class org.jmol.scriptext.SmilesExt
- e(Object) - Static method in class org.jmol.util.Escape
- E_ANG_PER_DEBYE - Static variable in class org.jmol.shapespecial.Dipoles
- e_charge - Static variable in class org.jmol.quantum.NMRCalculation
- E_MINUS_D - Static variable in class org.jmol.quantum.MepCalculation
- E_MINUS_D_OVER_2 - Static variable in class org.jmol.quantum.MepCalculation
- e0 - Variable in class org.jmol.minimize.forcefield.ForceField
- eAD(double[]) - Static method in class org.jmol.util.Escape
- eAF(float[]) - Static method in class org.jmol.util.Escape
- eAI(int[]) - Static method in class org.jmol.util.Escape
- EANGLE - Static variable in class org.jmol.minimize.forcefield.ForceField
- eAP(T3[]) - Static method in class org.jmol.util.Escape
- eAS(String[], boolean) - Static method in class org.jmol.util.Escape
- EAST - Static variable in class org.jmol.awtjs.swing.BorderLayout
- EAST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
- eBond(BS) - Static method in class org.jmol.util.Escape
- EBOND - Static variable in class org.jmol.minimize.forcefield.ForceField
- eBS(BS) - Static method in class org.jmol.util.Escape
- eButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- ec - Variable in class org.jmol.shapespecial.Dots
- eccentricity - Static variable in class org.jmol.script.T
- eccentricityMatrix - Variable in class org.jmol.jvxl.readers.Parameters
- eccentricityMatrix - Variable in class org.jmol.jvxl.readers.SurfaceReader
- eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.Parameters
- eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.SurfaceReader
- eccentricityRatio - Variable in class org.jmol.jvxl.readers.Parameters
- eccentricityRatio - Variable in class org.jmol.jvxl.readers.SurfaceReader
- eccentricityScale - Variable in class org.jmol.jvxl.readers.Parameters
- eccentricityScale - Variable in class org.jmol.jvxl.readers.SurfaceReader
- echo - Static variable in class org.jmol.script.T
- Echo - Class in org.jmol.shape
- Echo() - Constructor for class org.jmol.shape.Echo
- ECHO - Enum constant in enum org.jmol.c.CBK
- ECHO_BOTTOM - Static variable in class org.jmol.viewer.JC
- ECHO_MIDDLE - Static variable in class org.jmol.viewer.JC
- ECHO_TOP - Static variable in class org.jmol.viewer.JC
- ECHO_XY - Static variable in class org.jmol.viewer.JC
- ECHO_XYZ - Static variable in class org.jmol.viewer.JC
- echoMessage(String) - Method in class org.jmol.viewer.Viewer
- echoNames - Static variable in class org.jmol.viewer.JC
- EchoRenderer - Class in org.jmol.render
- EchoRenderer() - Constructor for class org.jmol.render.EchoRenderer
- echoShapeActive - Variable in class org.jmol.modelset.ModelSet
- ecosASB2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- eCounts - Variable in class org.jmol.symmetry.PointGroup
- ed - Static variable in class org.jmol.script.T
- Edge - Class in org.jmol.util
- Edge() - Constructor for class org.jmol.util.Edge
- Edge(IsoSolventReader, int, int, float) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Edge
- EDGE_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
- Edge.EnumBondOrder - Enum in org.jmol.util
- edgeCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
- edgeData - Variable in class org.jmol.adapter.readers.xtal.CgdReader
- edgeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- edgeDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- edgeFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
- edgeFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
- edgeFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
- edgeFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
- edgePointIndexes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edges - Static variable in class org.jmol.script.T
- edges - Variable in class org.jmol.smiles.SmilesRing
- edges - Static variable in class org.jmol.util.BoxInfo
- EDGES_ALL - Static variable in class org.jmol.shapespecial.Polyhedra
- EDGES_FRONT - Static variable in class org.jmol.shapespecial.Polyhedra
- EDGES_NONE - Static variable in class org.jmol.shapespecial.Polyhedra
- EDGES_ONLY - Static variable in class org.jmol.shapespecial.Polyhedra
- edgesonly - Static variable in class org.jmol.script.T
- edgesOnly - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- edgeTypeTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVector - Variable in class org.jmol.jvxl.data.VolumeData
- edgeVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexes - Static variable in class org.jmol.util.TriangleData
- edgeVertexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPlanesHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPlanesLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPointers - Variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPointersHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- edgeVertexPointersLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- edit_light - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- editArea - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- editButton - Variable in class org.jmol.console.GenericConsole
- editor - Variable in class org.jmol.console.ScriptEditor
- editor_auto_dihedral - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- editor_auto_origin - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- editor_bond_cycle_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- editor_label_fragments - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- EDITOR_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- editorAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- editorDoc - Variable in class org.jmol.console.ScriptEditor.EditorTextPane
- EditorDocument() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument
- editorScrollPane - Variable in class org.openscience.jmol.app.webexport.WebPanel
- EditorTextPane - Variable in class org.jmol.console.ScriptEditor.EditorDocument
- EditorTextPane() - Constructor for class org.jmol.console.ScriptEditor.EditorTextPane
- editPane - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- eds - Static variable in class org.jmol.script.T
- edsdiff - Static variable in class org.jmol.script.T
- EELECTROSTATIC - Static variable in class org.jmol.minimize.forcefield.ForceField
- EfvetReader - Class in org.jmol.jvxl.readers
- EfvetReader() - Constructor for class org.jmol.jvxl.readers.EfvetReader
- EIG_VAL - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- EIG_VEC - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- EIG_VEC_COMPRESSED - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- eigen - Variable in class org.jmol.quantum.NciCalculation
- eigenSignMask - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- eigenSignMask - Variable in class org.jmol.util.Tensor
- EigenSort - Class in org.jmol.util
-
sort from smallest to largest absolute
- EigenSort() - Constructor for class org.jmol.util.EigenSort
- eigenValues - Variable in class org.jmol.quantum.NciCalculation
- eigenValues - Variable in class org.jmol.quantum.NMRNoeMatrix
- eigenValues - Variable in class org.jmol.util.Tensor
- eigenVectors - Variable in class org.jmol.quantum.NMRNoeMatrix
- eigenVectors - Variable in class org.jmol.util.Tensor
- eightPiSquared100 - Static variable in class org.jmol.shapebio.BioShape
- ELECRADIUS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- electroNegativities - Static variable in class org.jmol.util.Elements
- electronEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- eleLeft - Variable in class org.jmol.bspt.Node
- ELEM - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- element - Static variable in class org.jmol.script.T
- Element - Class in org.jmol.bspt
-
the internal tree is made up of elements ...
- Element() - Constructor for class org.jmol.bspt.Element
- elementCharMasks - Static variable in class org.jmol.adapter.smarter.Atom
- elementContext - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- elementCount - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- elementCounts - Variable in class org.jmol.util.JmolMolecule
- elementDefined - Variable in class org.jmol.smiles.SmilesAtom
- elementLabel - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- elementNameFromNumber(int) - Static method in class org.jmol.util.Elements
- elementNames - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- elementNames - Static variable in class org.jmol.util.Elements
- elementNumber - Variable in class org.jmol.adapter.smarter.Atom
- elementNumber - Variable in class org.jmol.smiles.SmilesAtom
- elementNumberFromName(String) - Static method in class org.jmol.util.Elements
- elementNumberFromSymbol(String, boolean) - Static method in class org.jmol.util.Elements
- elementNumberMax - Static variable in class org.jmol.util.Elements
-
one larger than the last elementNumber, same as elementSymbols.length
- elementNumberMax - Variable in class org.jmol.util.JmolMolecule
- elementPt - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- elements - Variable in class org.jmol.symmetry.PointGroup
- Elements - Class in org.jmol.util
- Elements() - Constructor for class org.jmol.util.Elements
- elementsPresent - Variable in class org.jmol.modelset.ModelSet
- elementSymbol - Variable in class org.jmol.adapter.smarter.Atom
- elementSymbolFromNumber(int) - Static method in class org.jmol.util.Elements
- elementSymbols - Static variable in class org.jmol.util.Elements
-
The default elementSymbols.
- elemisono - Static variable in class org.jmol.script.T
- elemno - Static variable in class org.jmol.script.T
- elemNo - Variable in class org.jmol.minimize.forcefield.AtomType
- elemNo - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Rule 1a nominal element number; may be fractional for Kekule issues
- elemnoMax - Variable in class org.jmol.minimize.Minimizer
- elemNos - Variable in class org.jmol.shapespecial.Polyhedron
- eleRight - Variable in class org.jmol.bspt.Node
- eleRoot - Variable in class org.jmol.bspt.Bspt
- ellipseNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- ellipsoid - Static variable in class org.jmol.script.T
- ellipsoid() - Method in class org.jmol.scriptext.CmdExt
- Ellipsoid - Class in org.jmol.shapespecial
- Ellipsoid() - Constructor for class org.jmol.shapespecial.Ellipsoid
- ELLIPSOID - Static variable in class org.jmol.shapecgo.CGOMesh
- ellipsoid_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ellipsoid_probability - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ellipsoid_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ellipsoid_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ellipsoid_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ellipsoidarcs - Static variable in class org.jmol.script.T
- ellipsoidArcs - Variable in class org.jmol.viewer.GlobalSettings
- ellipsoidarrows - Static variable in class org.jmol.script.T
- ellipsoidArrows - Variable in class org.jmol.viewer.GlobalSettings
- ellipsoidaxes - Static variable in class org.jmol.script.T
- ellipsoidAxes - Variable in class org.jmol.viewer.GlobalSettings
- ellipsoidaxisdiameter - Static variable in class org.jmol.script.T
- ellipsoidAxisDiameter - Variable in class org.jmol.viewer.GlobalSettings
- ellipsoidball - Static variable in class org.jmol.script.T
- ellipsoidBall - Variable in class org.jmol.viewer.GlobalSettings
- ellipsoiddotcount - Static variable in class org.jmol.script.T
- ellipsoidDotCount - Variable in class org.jmol.viewer.GlobalSettings
- ellipsoiddots - Static variable in class org.jmol.script.T
- ellipsoidDots - Variable in class org.jmol.viewer.GlobalSettings
- ellipsoidfill - Static variable in class org.jmol.script.T
- ellipsoidFill - Variable in class org.jmol.viewer.GlobalSettings
- ellipsoidNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- ellipsoids - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- Ellipsoids - Class in org.jmol.shapespecial
- Ellipsoids() - Constructor for class org.jmol.shapespecial.Ellipsoids
- ellipsoidSet - Variable in class org.jmol.shapespecial.Ellipsoids
- ellipsoidShades - Variable in class org.jmol.util.Shader
- EllipsoidsRenderer - Class in org.jmol.renderspecial
- EllipsoidsRenderer() - Constructor for class org.jmol.renderspecial.EllipsoidsRenderer
- elsecmd - Static variable in class org.jmol.script.T
- elseif - Static variable in class org.jmol.script.T
- EMBEDDED_SCRIPT_TAG - Static variable in class org.jmol.viewer.JC
- embeddedCrystal - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- embedScript(String) - Static method in class org.jmol.viewer.JC
- empty - Variable in class org.jmol.viewer.SelectionManager
- EMPTY_DICT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- EMPTY_DIRECTIVE - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- EMPTY_LIST - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- EMPTY_SET - Static variable in class org.jmol.geodesic.EnvelopeCalculation
- EMPTY_TUPLE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- emptyListPt - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- emptySet - Static variable in class org.jmol.util.BSUtil
- ENABLE - Static variable in class org.jmol.shapecgo.CGOMesh
- enableButton(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- enableButtons(JList<?>) - Method in class org.openscience.jmol.app.webexport.WebPanel
- enabled - Variable in class org.jmol.awtjs.swing.Component
- enabled - Variable in class org.jmol.util.ModulationSet
-
indicates state of modulated or unmodulated
- enableShell(int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
This flag must be explicitly set when a reader has been verified to properly sort G, H, I,...
- ENC_CALC_MAX_DIST - Static variable in class org.jmol.viewer.JC
- encapsulateData(String, Object, int) - Static method in class org.jmol.util.Escape
- encodeColor(short) - Static method in class org.jmol.shape.Shape
- encodeImage(int, int, Object) - Method in class org.jmol.viewer.OutputManager
-
general image encoder, allows for BufferedImage, int[], or HTML5 2D canvas
- encodeRadiusParameter(int, boolean, boolean) - Method in class org.jmol.script.ScriptEval
- end - Static variable in class org.jmol.script.T
- END - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- END - Static variable in class org.jmol.shapecgo.CGOMesh
- END_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- END_INS_CODE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- END_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- endAssignment() - Method in class org.jmol.script.ScriptMathProcessor
- endcap - Variable in class org.jmol.render.FontLineShapeRenderer
- endCapHidden - Variable in class org.jmol.g3d.CylinderRenderer
- endcaps - Variable in class org.jmol.g3d.CylinderRenderer
- endcaps - Variable in class org.jmol.render.SticksRenderer
- ENDCAPS_FLAT - Static variable in class org.jmol.util.GData
- ENDCAPS_FLAT_TO_SPHERICAL - Static variable in class org.jmol.util.GData
- ENDCAPS_HIDDEN - Static variable in class org.jmol.util.GData
- ENDCAPS_NONE - Static variable in class org.jmol.util.GData
- ENDCAPS_OPEN_TO_SPHERICAL - Static variable in class org.jmol.util.GData
- ENDCAPS_SPHERICAL - Static variable in class org.jmol.util.GData
- endcapShadeIndex - Variable in class org.jmol.g3d.CylinderRenderer
- endChainID - Variable in class org.jmol.adapter.smarter.Structure
- endCheck - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- endCheck - Static variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- endCoord - Variable in class org.jmol.shapespecial.Dipoles
- endDegrees - Variable in class org.jmol.thread.SpinThread
- endDocument() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- endDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
- endDocument() - Method in class org.jmol.adapter.readers.xml.XmlReader
- endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- endFlag - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
- endifcmd - Static variable in class org.jmol.script.T
- endIndexPending - Variable in class org.jmol.renderbio.RocketRenderer
- endInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
- endMinimization() - Method in class org.jmol.minimize.Minimizer
- endOfData - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- endOfLine - Variable in class org.jmol.script.ScriptCompiler
- endPositions - Variable in class org.jmol.thread.SpinThread
- endRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- endRendering() - Method in class org.jmol.g3d.Graphics3D
- endRendering() - Method in class org.jmol.util.GData
- endSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
- energy - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- energy - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- energy - Variable in class org.jmol.minimize.forcefield.Calculation
- energy - Variable in class org.jmol.modelset.HBond
- energy - Static variable in class org.jmol.script.T
- energy - Variable in class org.jmol.viewer.Connection
- ENERGY - Enum constant in enum org.jmol.c.PAL
- ENERGY - Static variable in class org.jmol.minimize.forcefield.ForceField
- energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- energyBond(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- energyBond(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- energyES(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- energyES(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- energyFull(boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- energyKey - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
Type of energy calculated, e.g., E(RB+HF-PW91).
- energyKey - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
The type of energy last calculated.
- energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- energyStrBnd(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- energyStretchBend(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- energyStretchBend(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- energyString - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
Calculated energy with units (if possible).
- energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- energyunits - Static variable in class org.jmol.script.T
- energyUnits - Variable in class org.jmol.adapter.readers.quantum.MOReader
- energyUnits - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- energyUnits - Variable in class org.jmol.viewer.GlobalSettings
- energyValue - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
The last calculated energy value.
- energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
- energyWithUnits - Variable in class org.jmol.adapter.readers.simple.MopacArchiveReader
- ensureCapacity(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- ensureFourier(int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
Make sure that F_n record is present.
- ensureMeshSource() - Method in class org.jmol.shapesurface.Isosurface
- enterListener - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- EnterListener - Interface in org.openscience.jmol.app.jmolpanel.console
- enterMeasurementMode(int) - Method in class org.jmol.viewer.ActionManager
- enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- enterPressed() - Method in interface org.openscience.jmol.app.jmolpanel.console.EnterListener
- enthalpy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- entities - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- entries - Variable in class org.jmol.util.Int2IntHash
- entry(long, int, int, boolean) - Method in class org.jmol.awtjs2d.Mouse
- entryCount - Variable in class org.jmol.util.Int2IntHash
- EnumBondOrder(int, String, String) - Constructor for enum org.jmol.util.Edge.EnumBondOrder
- EnumDrawType(int, String) - Constructor for enum org.jmol.shapespecial.Draw.EnumDrawType
- EnumType() - Constructor for enum org.jmol.atomdata.RadiusData.EnumType
- ENV_CALC_MAX_LEVEL - Static variable in class org.jmol.viewer.JC
- EnvelopeCalculation - Class in org.jmol.geodesic
- EnvelopeCalculation() - Constructor for class org.jmol.geodesic.EnvelopeCalculation
- envelopeRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- envelopeRadius - Variable in class org.jmol.jvxl.readers.Parameters
- eol(char) - Method in class org.jmol.script.ScriptCompiler
-
look for end-of-line character \r, \n, or ; that is not within a command such as for (var i=0;i < 10; i++)
- EOL - Static variable in class org.jmol.script.ScriptCompiler
- EOOP - Static variable in class org.jmol.minimize.forcefield.ForceField
- eP(T3) - Static method in class org.jmol.util.Escape
-
must be its own, because of the possibility of being null
- eP4(P4) - Static method in class org.jmol.util.Escape
- eq0RadioButton - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- eq0RadioButtonActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- eq1RadioButton - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- eq1RadioButtonActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- eq2RadioButton - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- eq2RadioButtonActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- eq3RadioButton - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- eq3RadioButtonActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- equalCount - Variable in class org.jmol.script.ScriptMathProcessor
- equals(Object) - Method in class org.jmol.modelset.Atom
- equals(Object) - Method in class org.jmol.script.T
- equiv - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- equivalentAtomSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
The number of equivalent atom sets.
- equivalentAtomSets - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
The number of equivalent atom sets.
- equivalentTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- errCount - Variable in class org.openscience.jmol.app.webexport.WebPanel
- error - Variable in class org.jmol.script.ScriptError
- error - Variable in class org.jmol.script.ScriptParallelProcessor
- error - Static variable in class org.jmol.script.T
- error(int) - Method in class org.jmol.script.ScriptError
- error(int) - Method in class org.jmol.script.ScriptTokenParser
- error(int) - Method in class org.jmol.scriptext.ScriptExt
- error(String) - Method in class org.jmol.util.DefaultLogger
- error(String) - Static method in class org.jmol.util.Logger
-
Writes a log at ERROR level.
- error(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at ERROR level.
- error(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- ERROR - Enum constant in enum org.jmol.c.CBK
- ERROR - Static variable in class org.jmol.script.ScriptCompiler
- ERROR(int) - Method in class org.jmol.script.ScriptCompiler
- ERROR(int, String) - Method in class org.jmol.script.ScriptCompiler
- ERROR_axisExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_backgroundModelError - Static variable in class org.jmol.script.ScriptError
- ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptError
- ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_badContext - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_badMillerIndices - Static variable in class org.jmol.script.ScriptError
- ERROR_badRGBColor - Static variable in class org.jmol.script.ScriptError
- ERROR_booleanExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_booleanOrNumberExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_booleanOrWhateverExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_cannotSet - Static variable in class org.jmol.script.ScriptError
- ERROR_colorExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_colorOrPaletteRequired - Static variable in class org.jmol.script.ScriptError
- ERROR_commandExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_commandExpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_coordinateExpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_coordinateOrNameOrExpressionRequired - Static variable in class org.jmol.script.ScriptError
- ERROR_drawObjectNotDefined - Static variable in class org.jmol.script.ScriptError
- ERROR_endOfCommandUnexpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_endOfExpressionExpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_endOfStatementUnexpected - Static variable in class org.jmol.script.ScriptError
- ERROR_expressionExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_expressionOrIntegerExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_filenameExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_fileNotFoundException - Static variable in class org.jmol.script.ScriptError
- ERROR_FLAG - Static variable in class org.jmol.util.CommandHistory
- ERROR_identifierOrResidueSpecificationExpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_incompatibleArguments - Static variable in class org.jmol.script.ScriptError
- ERROR_insufficientArguments - Static variable in class org.jmol.script.ScriptError
- ERROR_integerExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_integerOutOfRange - Static variable in class org.jmol.script.ScriptError
- ERROR_invalidArgument - Static variable in class org.jmol.script.ScriptError
- ERROR_invalidArgument - Static variable in class org.jmol.scriptext.CmdExt
- ERROR_invalidAtomSpecification - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_invalidChainSpecification - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_invalidExpressionToken - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_invalidModelSpecification - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_invalidParameterOrder - Static variable in class org.jmol.script.ScriptError
- ERROR_keywordExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_missingEnd - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_moCoefficients - Static variable in class org.jmol.script.ScriptError
- ERROR_moIndex - Static variable in class org.jmol.script.ScriptError
- ERROR_moModelError - Static variable in class org.jmol.script.ScriptError
- ERROR_moOccupancy - Static variable in class org.jmol.script.ScriptError
- ERROR_moOnlyOne - Static variable in class org.jmol.script.ScriptError
- ERROR_multipleModelsDisplayedNotOK - Static variable in class org.jmol.script.ScriptError
- ERROR_multipleModelsNotOK - Static variable in class org.jmol.script.ScriptError
- ERROR_noData - Static variable in class org.jmol.script.ScriptError
- ERROR_noPartialCharges - Static variable in class org.jmol.script.ScriptError
- ERROR_noUnitCell - Static variable in class org.jmol.script.ScriptError
- ERROR_numberExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_numberExpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_numberMustBe - Static variable in class org.jmol.script.ScriptError
- ERROR_numberOrVariableNameExpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_numberOutOfRange - Static variable in class org.jmol.script.ScriptError
- ERROR_objectNameExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_planeExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_propertyNameExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_residueSpecificationExpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_spaceGroupNotFound - Static variable in class org.jmol.script.ScriptError
- ERROR_stringExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_stringOrIdentifierExpected - Static variable in class org.jmol.script.ScriptError
- ERROR_tokenExpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_tokenUnexpected - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_TOLERANCE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- ERROR_tooManyPoints - Static variable in class org.jmol.script.ScriptError
- ERROR_tooManyScriptLevels - Static variable in class org.jmol.script.ScriptError
- ERROR_unrecognizedAtomProperty - Static variable in class org.jmol.script.ScriptError
- ERROR_unrecognizedBondProperty - Static variable in class org.jmol.script.ScriptError
- ERROR_unrecognizedCommand - Static variable in class org.jmol.script.ScriptError
- ERROR_unrecognizedExpression - Static variable in class org.jmol.script.ScriptError
- ERROR_unrecognizedExpressionToken - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_unrecognizedObject - Static variable in class org.jmol.script.ScriptError
- ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptError
- ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_unrecognizedParameterWarning - Static variable in class org.jmol.script.ScriptError
- ERROR_unrecognizedShowParameter - Static variable in class org.jmol.script.ScriptError
- ERROR_unrecognizedToken - Static variable in class org.jmol.script.ScriptTokenParser
- ERROR_what - Static variable in class org.jmol.script.ScriptError
- ERROR_writeWhat - Static variable in class org.jmol.script.ScriptError
- errorEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
- errorEx(String, Throwable) - Static method in class org.jmol.util.Logger
-
Writes a log at ERROR level with detail on exception.
- errorEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at ERROR level with detail on exception.
- errorIntStr2(int, String, String) - Method in class org.jmol.script.ScriptTokenParser
- errorLine - Variable in class org.jmol.script.ScriptTokenParser
- errorMessage - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- errorMessage - Variable in class org.jmol.script.ScriptContext
- errorMessage - Variable in class org.jmol.script.ScriptError
- errorMessage - Variable in class org.jmol.script.ScriptTokenParser
- errorMessage - Variable in class org.jmol.viewer.Viewer
- errorMessageUntranslated - Variable in class org.jmol.script.ScriptContext
- errorMessageUntranslated - Variable in class org.jmol.script.ScriptError
- errorMessageUntranslated - Variable in class org.jmol.script.ScriptTokenParser
- errorMessageUntranslated - Variable in class org.jmol.viewer.Viewer
- errorMore(int, String, String, String) - Method in class org.jmol.script.ScriptError
- errorMsg - Variable in class org.jmol.image.AviCreator
- errorOrWarn(int, String, String, String, boolean) - Method in class org.jmol.script.ScriptError
- errorStr(int, String) - Method in class org.jmol.script.ScriptError
- errorStr(int, String) - Method in class org.jmol.script.ScriptTokenParser
- errorStr2(int, String, String) - Method in class org.jmol.script.ScriptError
- errorStr2(String, String) - Method in class org.jmol.script.ScriptTokenParser
- errorString(int, String, String, boolean) - Static method in class org.jmol.script.ScriptTokenParser
- errorString(int, String, String, String, boolean) - Static method in class org.jmol.script.ScriptError
- errorType - Variable in class org.jmol.script.ScriptContext
- errorType - Variable in class org.jmol.script.ScriptError
- errorType - Variable in class org.jmol.script.ScriptTokenParser
- esCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- escape() - Method in class org.jmol.script.SV
- Escape - Class in org.jmol.util
- Escape() - Constructor for class org.jmol.util.Escape
- escapeColor(int) - Static method in class org.jmol.util.Escape
- escapeFloatA(float[], boolean) - Static method in class org.jmol.util.Escape
- escapeFloatAA(float[][], boolean) - Static method in class org.jmol.util.Escape
- escapeFloatAAA(float[][][], boolean) - Static method in class org.jmol.util.Escape
- escapeHelical(String, int, P3, P3, T3[]) - Static method in class org.jmol.util.Escape
-
Jmol-specific post-processing of the array data returned by Measure.computeHelicalAxis
- escapeHTML(String) - Static method in class org.jmol.i18n.GT
- escapeMap(Map<String, Object>) - Static method in class org.jmol.util.Escape
- escapeModelFileNumber(int) - Static method in class org.jmol.util.Escape
- escapeMultiplier(T3) - Static method in class org.jmol.util.SimpleUnitCell
-
Generally the multiplier is just {ijk ijk scale}, but when we have 1iiijjjkkk 1iiijjjkkk scale, floats lose kkk due to Java float precision issues so we use P4 {1iiijjjkkk 1iiijjjkkk scale, 1kkkkkk}
- escapeNice(String) - Static method in class org.jmol.util.Escape
- espCharges - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- espressoContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- EspressoReader - Class in org.jmol.adapter.readers.xtal
- EspressoReader() - Constructor for class org.jmol.adapter.readers.xtal.EspressoReader
- ESTRBND - Static variable in class org.jmol.minimize.forcefield.ForceField
- eta - Static variable in class org.jmol.script.T
- ETORSION - Static variable in class org.jmol.minimize.forcefield.ForceField
- eV(Lst<SV>) - Static method in class org.jmol.util.Escape
- eval - Variable in exception org.jmol.script.ScriptException
- eval - Variable in class org.jmol.script.ScriptManager
- eval - Variable in class org.jmol.script.ScriptMathProcessor
- eval - Static variable in class org.jmol.script.T
- eval - Variable in class org.jmol.thread.JmolThread
- eval - Variable in class org.jmol.util.BZone
- eval - Variable in class org.jmol.viewer.Viewer
- eval(String) - Method in interface org.jmol.api.JmolStatusListener
- eval(String) - Method in class org.jmol.util.GenericApplet
- eval(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- eval(ScriptContext, ShapeManager) - Method in class org.jmol.script.ScriptParallelProcessor
- EVAL - Enum constant in enum org.jmol.c.CBK
- evalError(String, String) - Method in class org.jmol.script.ScriptError
- evalFile(String) - Method in interface org.jmol.api.JmolScriptManager
- evalFile(String) - Method in class org.jmol.api.JmolViewer
- evalFile(String) - Method in class org.jmol.script.ScriptManager
- evalFile(String) - Method in class org.jmol.viewer.Viewer
- evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.api.JmolScriptEvaluator
- evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.atomdata.AtomDataServer
- evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.script.ScriptEval
- evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.viewer.Viewer
- evalParallel(ScriptContext, ShapeManager) - Method in interface org.jmol.api.JmolScriptEvaluator
- evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.script.ScriptEval
- evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.scriptext.CmdExt
-
used for TRY command
- evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.viewer.Viewer
- evalString(String) - Method in class org.jmol.api.JmolViewer
- evalString(String) - Method in class org.jmol.viewer.Viewer
- evalStringGUI(String) - Method in class org.jmol.viewer.Viewer
-
Run a script asynchronously, adding the GUI flag to indicate that we should fire the SELECT callback at the end if there is one.
- evalStringQuiet(String) - Method in class org.jmol.api.JmolViewer
- evalStringQuiet(String) - Method in class org.jmol.viewer.Viewer
- evalStringQuietSync(String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
- evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
- evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
- evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
- evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- evalTemp - Variable in class org.jmol.script.ScriptManager
- evaluate(Object, boolean, boolean) - Method in class org.jmol.script.ScriptEval
- evaluate(ScriptMathProcessor, T, SV[], int) - Method in class org.jmol.scriptext.MathExt
- evaluateArray(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
- evaluateBin(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateCache(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateColor(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateCompare(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateCompiledScript(boolean, boolean, boolean, boolean, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- evaluateCompiledScript(boolean, boolean, boolean, boolean, SB, boolean) - Method in class org.jmol.script.ScriptEval
- evaluateConnected(ScriptMathProcessor, SV[], int, int) - Method in class org.jmol.scriptext.MathExt
- evaluateContact(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateData(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateDotDist(ScriptMathProcessor, SV[], int, int) - Method in class org.jmol.scriptext.MathExt
-
x = y.distance({atoms}) the average distance from elements of y to the CENTER of {atoms} x = {atomset1}.distance.min({atomset2}, asAtomSet) If asAtomSet is true, returns the closest atom in atomset1 to any atom of atomset2; if false or omitted, returns an array listing the distance of each atom in atomset1 to the closest atom in atomset2.
- evaluateExpression(Object) - Method in class org.jmol.api.JmolViewer
- evaluateExpression(Object) - Method in class org.jmol.viewer.Viewer
-
synchronized here trapped the eventQueue; see also evaluateExpressionAsVariable
- evaluateExpression(Object, boolean, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- evaluateExpression(Object, boolean, boolean) - Method in class org.jmol.script.ScriptEval
-
a general-use method to evaluate a "SET" type expression.
- evaluateExpressionAsVariable(Object) - Method in class org.jmol.api.JmolViewer
- evaluateExpressionAsVariable(Object) - Method in class org.jmol.viewer.Viewer
- evaluateFind(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateFormat(ScriptMathProcessor, int, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
- evaluateFunction(int) - Method in class org.jmol.script.ScriptMathProcessor
- evaluateGetProperty(ScriptMathProcessor, SV[], int, boolean) - Method in class org.jmol.scriptext.MathExt
-
_ by itself, not as a function, is shorthand for getProperty("auxiliaryInfo") $ print _.keys boundbox group3Counts group3Lists modelLoadNote models properties someModelsHaveFractionalCoordinates someModelsHaveSymmetry someModelsHaveUnitcells symmetryRange _m by itself, not as a function, is shorthand for getProperty("auxiliaryInfo.models")[_currentFrame] $ print format("json",_m.unitCellParams) [ 0.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.1660376,-2.1660376,0.0,-2.1660376, 2.1660376,-4.10273,0.0,0.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN ] {atomset}._ by itself delivers a subset array of auxiliaryInfo.models for all models in {atomset} $ print {*}._..1..aflowInfo (first model's aflowInfo) _(key) prepends "auxiliaryInfo.models", delivering a modelCount-length array of information $ print _("aflowInfo[SELECT auid WHERE H__eV___VASP_ < 0]") {atomset}._(key) selects for model Auxiliary info related to models of the specified atoms {atomset}.getProperty(key) defaults to atomInfo, but also allows key to start with "bondInfo" Examples: print _("aflowInfo[select sg where volume_cell > 70]") print {model>10}._("aflowInfo[select sg where volume_cell > 70]")
- evaluateHelix(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateIn(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateInChI(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateList(ScriptMathProcessor, int, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateLoad(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
- evaluateMath(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
- evaluateMeasure(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
- evaluateModulation(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluatePlane(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
-
plane() or intersection()
- evaluatePoint(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluatePointGroup(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
- evaluatePrompt(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateQuaternion(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
- evaluateRandom(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateReplace(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateRowCol(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
- evaluateScript(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
- evaluateSort(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
-
sort() or sort(n) or count() or count("xxxx")
- evaluateSpacegroup(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateString(ScriptMathProcessor, int, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateSubstructure(ScriptMathProcessor, SV[], int, boolean) - Method in class org.jmol.scriptext.MathExt
- evaluateSymop(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
- evaluateTensor(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evaluateUnitCell(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
- evaluateUserFunction(ScriptMathProcessor, String, SV[], int, boolean) - Method in class org.jmol.scriptext.MathExt
- evaluateValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- evaluateWithin(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
- evaluateWrite(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
- evalWait(String, String, String) - Method in class org.jmol.viewer.Viewer
- EVDW - Static variable in class org.jmol.minimize.forcefield.ForceField
- Event - Class in org.jmol.awtjs
- Event() - Constructor for class org.jmol.awtjs.Event
- EventManager - Interface in org.jmol.api
- eventNames - Static variable in class org.jmol.multitouch.ActionManagerMT
- EX - Variable in class org.jmol.quantum.MOCalculation
- excl_display_lists_shaders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- excludeAtoms(BS, boolean) - Method in class org.jmol.viewer.SelectionManager
- excludedTriangleCount - Variable in class org.jmol.jvxl.data.JvxlData
- excludedTriangleCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- excludedVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
- excludedVertexCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- excludeMaximumSet() - Method in class org.jmol.jvxl.readers.SurfaceReader
- excludeMinimumSet() - Method in class org.jmol.jvxl.readers.SurfaceReader
- excludePartialCubes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- excludeSelectionSet(BS) - Method in class org.jmol.viewer.SelectionManager
- EXEC_ASYNC - Static variable in class org.jmol.script.ScriptEval
- EXEC_ERR - Static variable in class org.jmol.script.ScriptEval
- EXEC_OK - Static variable in class org.jmol.script.ScriptEval
- execThread - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- execute(String) - Method in class org.jmol.console.AppletConsole
- execute(String) - Method in class org.jmol.console.GenericConsole
- execute(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- executeCommand(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- executeCommandAsThread(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- executeCommands(boolean, boolean) - Method in class org.jmol.script.ScriptEval
- ExecuteCommandThread(String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole.ExecuteCommandThread
- executeScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ExecuteScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
- executing - Variable in class org.jmol.script.ScriptEval
- executionPaused - Variable in class org.jmol.script.ScriptContext
- executionPaused - Variable in class org.jmol.script.ScriptEval
- executionStepping - Variable in class org.jmol.script.ScriptContext
- executionStepping - Variable in class org.jmol.script.ScriptEval
- executionStopped - Variable in class org.jmol.script.ScriptEval
- executor - Variable in class org.jmol.viewer.Viewer
- exit - Static variable in class org.jmol.script.T
- exitAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ExitAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
- exitBondRotation() - Method in class org.jmol.awt.AwtModelKitPopup
- exitBondRotation() - Method in class org.jmol.modelkit.ModelKitPopup
- exitBondRotation(String) - Method in class org.jmol.modelkit.ModelKit
- exitFirstMatch - Variable in class org.jmol.smiles.SmilesSearch
- exitjmol - Static variable in class org.jmol.script.T
- exitJmol() - Method in class org.jmol.viewer.Viewer
- exitJSpecView(boolean, Object) - Method in interface org.jmol.api.JSVInterface
- exitJSpecView(boolean, Object) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- exitMeasurementMode(String) - Method in class org.jmol.viewer.ActionManager
- expandFloatArray(float[], int, boolean) - Method in class org.jmol.script.ScriptEval
-
Accepts a float array and expands [1 -3] to [1 2 3], for example.
- expandMinMax(P3, SymmetryInterface, P3, P3) - Method in class org.jmol.adapter.readers.cif.MSRdr
- expCouples - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- expDists - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- expdta() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- expFor(int, BS) - Method in class org.jmol.scriptext.CmdExt
- explicitContours - Variable in class org.jmol.shapesurface.Isosurface
- explicitFaces - Variable in class org.jmol.shapespecial.Polyhedra
- explicitHydrogen - Variable in class org.jmol.smiles.SmilesGenerator
-
0 H all implicit 0x1000 CH2 explicit 0x2000 CH2 and CH3 explicit
- explicitHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
- explicitID - Variable in class org.jmol.shape.MeshCollection
- expNoes - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- expOrDistButton - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- EXPORT_CARTESIAN - Static variable in class org.jmol.util.GData
- EXPORT_DRIVER_LIST - Static variable in class org.jmol.viewer.JC
- EXPORT_NOT - Static variable in class org.jmol.util.GData
- EXPORT_RAYTRACER - Static variable in class org.jmol.util.GData
- export3D - Variable in class org.jmol.export.___Exporter
- Export3D - Class in org.jmol.export
- Export3D() - Constructor for class org.jmol.export.Export3D
- exportAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ExportAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
- exportActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ExportChoiceListener() - Constructor for class org.jmol.dialog.Dialog.ExportChoiceListener
- exportChooser - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- exportDone(JComponent, Transferable, int) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- exporter - Variable in class org.jmol.export.Export3D
- exportName - Variable in class org.jmol.export.Export3D
- exportPass - Variable in class org.jmol.render.MeshRenderer
- exportscale - Static variable in class org.jmol.script.T
- exportScale - Variable in class org.jmol.export.___Exporter
- exportScale - Variable in class org.jmol.viewer.GlobalSettings
- exportSurface(short) - Method in class org.jmol.render.MeshRenderer
- exportType - Variable in class org.jmol.export.___Exporter
- exportType - Variable in class org.jmol.render.ShapeRenderer
- expressionBegin - Static variable in class org.jmol.script.T
- expressionEnd - Static variable in class org.jmol.script.T
- expValue - Variable in class org.openscience.jmol.app.janocchio.Measure
- ext - Variable in class org.jmol.modelsetbio.BioModelSet
- extendGrid - Variable in class org.jmol.jvxl.readers.Parameters
- extendLadder(int, int) - Method in class org.jmol.dssx.Bridge
- extendRuns(STR[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
- extension - Variable in class org.jmol.dialog.Dialog
- extensions - Variable in class org.jmol.dialog.Dialog
- extensions - Variable in class org.openscience.jmol.app.janocchio.MyFileFilter
- extents - Variable in class org.jmol.jvxl.readers.JaguarReader
- externalContainer - Variable in class org.jmol.console.JmolConsole
- extractFlags(String, int[]) - Static method in class org.jmol.smiles.SmilesParser
- extractLatticeInfo(String) - Method in class org.jmol.symmetry.HallInfo
- extractMolData(String) - Method in class org.jmol.api.JmolViewer
- extractMolData(String) - Method in class org.jmol.viewer.Viewer
- extractProperty(Object, Object, int) - Method in class org.jmol.viewer.Viewer
- extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in class org.jmol.viewer.PropertyManager
- extractRotationInfo(String, int, char) - Method in class org.jmol.symmetry.HallInfo
- extractTag(String, String, String, boolean) - Static method in class org.jmol.jvxl.readers.XmlReader
- extractTagOnly(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
- extractVectorInfo(String) - Method in class org.jmol.symmetry.HallInfo
- EY - Variable in class org.jmol.quantum.MOCalculation
- EZ - Variable in class org.jmol.quantum.MOCalculation
F
- f14 - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- f16 - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- Face(int, int, int, P3) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Face
- FACE_COUNT_MAX - Static variable in class org.jmol.shapespecial.Polyhedra
- facecenteroffset - Static variable in class org.jmol.script.T
- faceCenterOffset - Variable in class org.jmol.shapespecial.Polyhedra
- faceCenters - Variable in class org.jmol.util.BZone
- faceIndices - Variable in class org.jmol.util.BZone
- faceIndices(P3[], P3[]) - Method in class org.jmol.util.BZone
- faceMap - Variable in class org.jmol.renderspecial.DotsRenderer
- facePoints - Static variable in class org.jmol.util.BoxInfo
- facePt1 - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
- facePt2 - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
- facePt3 - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
- faces - Variable in class org.jmol.shapespecial.Polyhedron
- faces - Variable in class org.jmol.util.BZone
- faceTriangles - Variable in class org.jmol.shapespecial.Polyhedron
- faceVertexesArrays - Static variable in class org.jmol.util.Geodesic
- faceVertexesIcosahedron - Static variable in class org.jmol.util.Geodesic
- fact - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
- fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
-
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
- fact1 - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
- factor - Variable in class org.jmol.adapter.readers.simple.FAHReader
- FACTOR - Enum constant in enum org.jmol.atomdata.RadiusData.EnumType
- factoredLengths - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- factors - Variable in class org.jmol.jvxl.readers.IsoIntersectGridReader
- factorType - Variable in class org.jmol.atomdata.RadiusData
- FAHReader - Class in org.jmol.adapter.readers.simple
-
FoldingAtHome json reader.
- FAHReader() - Constructor for class org.jmol.adapter.readers.simple.FAHReader
- failed - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
and indictor that we should abort, and why
- FALSE - Static variable in class org.jmol.viewer.SelectionManager
- falsifyMesh() - Method in class org.jmol.shapebio.BioShape
- falsifyNearbyMesh(int) - Method in class org.jmol.shapebio.BioShape
- FAMILY_ASSEM_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_ATOM - Static variable in class org.jmol.adapter.readers.cif.CifReader
- FAMILY_CHEMCOMP_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_COMPBOND - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_COMPBOND_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_NCS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_NCS_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_OPER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_OPER_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_SEQUENCEDIF_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_SGOP - Static variable in class org.jmol.adapter.readers.cif.CifReader
- FAMILY_SHEET - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_SHEET_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_STRUCSITE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_STRUCSITE_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_STRUCTCONF - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_STRUCTCONF_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_STRUCTCONN - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- FAMILY_STRUCTCONN_CAT - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- fast_idle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- fatal(String) - Method in class org.jmol.util.DefaultLogger
- fatal(String) - Static method in class org.jmol.util.Logger
-
Writes a log at FATAL level.
- fatal(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at FATAL level.
- fatalError(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- fatalEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
- fatalEx(String, Throwable) - Static method in class org.jmol.util.Logger
-
Writes a log at FATAL level with detail on exception.
- fatalEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at ERROR level with detail on exception.
- fc - Variable in class org.openscience.jmol.app.webexport.Test
- fc - Variable in class org.openscience.jmol.app.webexport.WebPanel
- fc(float) - Static method in class org.jmol.symmetry.SymmetryOperation
- FC - Static variable in class org.jmol.quantum.QS
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
- FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
- fc2(float) - Method in class org.jmol.symmetry.SymmetryOperation
-
Get string version of fraction when divisor == 0
- fcadj - Variable in class org.jmol.minimize.forcefield.AtomType
- fclist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- fcoord(T3) - Method in interface org.jmol.api.SymmetryInterface
- fcoord(T3) - Method in class org.jmol.symmetry.Symmetry
- fcoord(T3) - Static method in class org.jmol.symmetry.SymmetryOperation
-
Get string version of fraction
- fcoord2(T3) - Method in class org.jmol.symmetry.SymmetryOperation
- FD_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- fd_oldFileName - Variable in class org.jmol.awt.FileDropper
- fd_propSupport - Variable in class org.jmol.awt.FileDropper
- FDPARAM_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- fetch_host - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- fetch_path - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ff - Variable in class org.jmol.minimize.forcefield.Calculations
- ff - Variable in class org.jmol.minimize.Minimizer
- FF - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- ffAtomType - Variable in class org.jmol.minimize.MinAtom
- fFixed - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- fflistValue(T, int) - Static method in class org.jmol.script.SV
- FFParam - Class in org.jmol.minimize.forcefield
- FFParam() - Constructor for class org.jmol.minimize.forcefield.FFParam
- ffParams - Variable in class org.jmol.minimize.forcefield.Calculations
- ffParams - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- ffParams - Variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- ffType - Variable in class org.jmol.minimize.MinAtom
- ffTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
- fid - Variable in class org.jmol.modelset.Text
- fid - Variable in class org.jmol.render.LabelsRenderer
- fid - Variable in class org.jmol.util.Font
- fidPrevious - Variable in class org.jmol.render.LabelsRenderer
- fids - Variable in class org.jmol.shape.Labels
- field - Variable in class org.jmol.adapter.readers.cif.CifReader
- field - Variable in class org.jmol.adapter.readers.cif.MSCifParser
- field - Variable in class org.openscience.jmol.app.janocchio.FrameCounter
- field - Variable in class org.openscience.jmol.app.janocchio.LabelSetter
- field - Variable in class org.openscience.jmol.app.janocchio.PopulationDisplay
- field_of_view - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- fieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- fieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- fieldCount - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- fieldProperty(int) - Method in class org.jmol.adapter.readers.cif.CifReader
- fieldProperty(CifReader, int) - Method in class org.jmol.adapter.readers.cif.MSCifParser
- fieldTypes - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- FIL - Enum in org.jmol.c
- FIL(int) - Constructor for enum org.jmol.c.FIL
- file - Static variable in class org.jmol.script.T
- file - Variable in class org.openscience.jmol.app.HistoryFile
-
The location of the history file.
- file - Variable in class org.openscience.jmol.app.janocchio.NmrReaderThread
- file - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- FILE_DROPPED - Static variable in interface org.jmol.api.JmolScriptManager
- FILE_OPEN_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- fileAtomCount - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- fileAtomIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- fileButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- FileButton - Variable in class org.openscience.jmol.app.webexport.Test
- filecachedirectory - Static variable in class org.jmol.script.T
- filecaching - Static variable in class org.jmol.script.T
- FileChecker(String) - Constructor for class org.jmol.console.JmolConsole.FileChecker
- fileChooser - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- FileChooser - Class in org.jmol.dialog
-
JFileChooser with possibility to fix size and location
- FileChooser() - Constructor for class org.jmol.dialog.FileChooser
- fileCoordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fileData - Variable in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- fileDotModel - Variable in class org.jmol.jvxl.readers.AtomDataReader
- FileDropper - Class in org.jmol.awt
-
A simple Dropping class to allow files to be dragged onto a target.
- FileDropper(JmolStatusListener, Viewer, JmolDropEditor) - Constructor for class org.jmol.awt.FileDropper
- fileField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- fileHasUnitCell - Variable in class org.jmol.popup.JmolPopup
- fileHeader - Variable in class org.jmol.modelset.ModelLoader
- fileIndex - Variable in class org.jmol.jvxl.readers.Parameters
- fileIndex - Variable in class org.jmol.modelset.Model
- fileList - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- fileLoadThread - Variable in class org.jmol.script.ScriptEval
- FileLoadThread - Class in org.jmol.script
- FileLoadThread(JmolScriptEvaluator, Viewer, String, String, String) - Constructor for class org.jmol.script.FileLoadThread
-
JavaScript only
- FileManager - Class in org.jmol.viewer
- FileManager(Viewer) - Constructor for class org.jmol.viewer.FileManager
- fileModelNumber - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- FileMolOnly - Variable in class org.jmol.popup.JmolPopup
- filename - Variable in class org.jmol.console.ScriptEditor
- filename - Variable in class org.jmol.script.ScriptCompiler
- fileName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fileName - Variable in class org.jmol.atomdata.AtomData
- fileName - Variable in class org.jmol.export.___Exporter
- fileName - Variable in class org.jmol.jvxl.readers.AtomDataReader
- fileName - Variable in class org.jmol.jvxl.readers.MsmsReader
- fileName - Variable in class org.jmol.jvxl.readers.Parameters
- fileName - Variable in class org.jmol.script.FileLoadThread
- fileName - Variable in class org.jmol.util.JmolAudio
- fileName - Variable in class org.jmol.viewer.FileManager
- fileName - Variable in exception org.jmol.viewer.JmolAsyncException
- fileName - Variable in class org.jmol.viewer.ModelManager
- fileNameIn - Variable in class org.jmol.io.FileReader
- fileOcc - Variable in class org.jmol.util.ModulationSet
- fileOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fileOffsetFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filePath - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- FilePreview - Class in org.jmol.dialog
-
File previsualisation before opening
- FilePreview(Viewer, JFileChooser, boolean, Map<String, Object>) - Constructor for class org.jmol.dialog.FilePreview
-
Constructor
- FilePreview.FPPanel - Class in org.jmol.dialog
- filePt - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- FileReader - Class in org.jmol.io
- FileReader - Class in org.openscience.jvxl
- FileReader() - Constructor for class org.openscience.jvxl.FileReader
- FileReader(Viewer, String, String, String, String, Object, Map<String, Object>, boolean) - Constructor for class org.jmol.io.FileReader
- files - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- fileScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filesData - Variable in class org.jmol.jvxl.readers.Parameters
- fileSgName - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- FilesReader - Class in org.jmol.io
-
open a set of models residing in different files
- FilesReader() - Constructor for class org.jmol.io.FilesReader
- fileStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- fileType - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- fileTypeIn - Variable in class org.jmol.io.FileReader
- fileTypeName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- fileTypesIn - Variable in class org.jmol.io.FilesReader
- FileUnitOnly - Variable in class org.jmol.popup.JmolPopup
- fileWriter(File, JList<JmolInstance>) - Method in class org.openscience.jmol.app.webexport.WebPanel
- fill - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- fill - Static variable in class org.jmol.script.T
- fill3x3(String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
fills a double[3][3]
- fillADa(AtomData, int) - Method in class org.jmol.modelset.AtomCollection
- fillArc - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- fillAtomData(AtomData, int) - Method in interface org.jmol.atomdata.AtomDataServer
- fillAtomData(AtomData, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- fillAtomData(AtomData, int) - Method in class org.jmol.modelset.ModelSet
- fillAtomData(AtomData, int) - Method in class org.jmol.viewer.Viewer
- fillBackground(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
- fillBackground(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
- fillBackground(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
- fillCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- fillCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
- fillCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- fillConeScreen(short, byte, int, P3, P3, boolean) - Method in class org.jmol.export.___Exporter
- fillConeScreen(short, byte, int, P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
- fillConeScreen(short, byte, int, P3, P3, boolean) - Method in class org.jmol.export.__RayTracerExporter
- fillConeScreen(P3, P3, boolean) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- fillConeScreen3f(byte, int, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.export.Export3D
- fillConeScreen3f(byte, int, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export.__RayTracerExporter
- fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export._TachyonExporter
- fillCsfArray(String, String[], int, Object, boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- fillCylinder(byte, int, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.export.Export3D
- fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
- fillCylinder(JmolRendererInterface, short, short, byte, int, int, int, int, int, int, int, boolean) - Static method in class org.jmol.render.FontLineShapeRenderer
- fillCylinderBits(byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.export.Export3D
- fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- fillCylinderBits2(short, short, byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.export.Export3D
- fillCylinderBits2(short, short, byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- fillCylinderScreen(short, byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.___Exporter
- fillCylinderScreen(short, byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.__CartesianExporter
- fillCylinderScreen(short, byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.__RayTracerExporter
- fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.Export3D
- fillCylinderScreen3I(byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.g3d.Graphics3D
- fillCylinderScreenMad(short, byte, int, P3, P3) - Method in class org.jmol.export.___Exporter
- fillCylinderScreenMad(short, byte, int, P3, P3) - Method in class org.jmol.export.__CartesianExporter
- fillCylinderScreenMad(short, byte, int, P3, P3) - Method in class org.jmol.export.__RayTracerExporter
- fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
- fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- fillDataBlock(String[][], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
fills an array with a pre-defined number of lines of token data, skipping blank lines in the process
- fillDataBlockFixed(String[][], int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
Fills an array with a predefined number of lines of data that is arranged in fixed FORTRAN-like column format.
- fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in interface org.jmol.api.JmolRendererInterface
- fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.export.Export3D
- fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.g3d.Graphics3D
- fillEllipsoid(P3, P3[], short, int, int, int, int, M3, double[], M4, P3[]) - Method in class org.jmol.export.___Exporter
- fillEllipsoid(P3, P3[], short, int, int, int, int, M3, double[], M4, P3[]) - Method in class org.jmol.export.__CartesianExporter
- fillEllipsoid(P3, P3[], short, int, int, int, int, M3, double[], M4, P3[]) - Method in class org.jmol.export.__RayTracerExporter
- fillFloat(float[], int, int) - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- fillFloatArray(String, int, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
fills a float array with string data from a file
- fillFloatArrayFromBytes(byte[], float[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- fillFrequencyData(int, int, int, boolean[], boolean, int, int, int[], int, String[][]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
Extracts a block of frequency data from a file.
- fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
- fillHermite(int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- fillIntArrayFromBytes(byte[], int[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- fillMeshData(MeshData, int, IsosurfaceMesh) - Method in interface org.jmol.jvxl.api.MeshDataServer
- fillMeshData(MeshData, int, IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
- fillOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- fillPointsForMove(SymmetryInterface, BS, int, P3, P3, P3[]) - Method in class org.jmol.modelkit.ModelKit
-
Find the operator that transforms fractional point fa to one of its symmetry-equivalent points, and then also transform pt by that same matrix.
- fillPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
- fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
- fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
- fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
- fillQuadrilateral(P3, P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fillRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- fillRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- fillRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- fillSlater(int[], int, int, int) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- fillSparseArray(float[], BS, float[]) - Method in class org.jmol.viewer.DataManager
- fillSphere(short, int, P3) - Method in class org.jmol.export.___Exporter
- fillSphere(short, int, P3) - Method in class org.jmol.export.__CartesianExporter
- fillSphere(short, int, P3) - Method in class org.jmol.export.__RayTracerExporter
- fillSphereBits(int, P3) - Method in interface org.jmol.api.JmolRendererInterface
-
fills a solid sphere
- fillSphereBits(int, P3) - Method in class org.jmol.export.Export3D
-
fills a solid sphere
- fillSphereBits(int, P3) - Method in class org.jmol.g3d.Graphics3D
-
fills a solid sphere
- fillSphereI(int, P3i) - Method in interface org.jmol.api.JmolRendererInterface
-
fills a solid sphere
- fillSphereI(int, P3i) - Method in class org.jmol.export.Export3D
-
fills a solid sphere
- fillSphereI(int, P3i) - Method in class org.jmol.g3d.Graphics3D
-
fills a solid sphere
- fillSphereXYZ(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
fills a solid sphere
- fillSphereXYZ(int, int, int, int) - Method in class org.jmol.export.Export3D
-
fills a solid sphere
- fillSphereXYZ(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
fills a solid sphere
- fillTextRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
-
fills background rectangle for label
- fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
-
fills background rectangle for label
- fillTextRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
fills background rectangle for label
- fillTriangle() - Method in class org.jmol.rendercgo.CGORenderer
- fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.___Exporter
- fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.__CartesianExporter
- fillTriangle(short, T3, T3, T3, boolean) - Method in class org.jmol.export.__RayTracerExporter
- fillTriangle(P3i, P3i, P3i, boolean) - Method in class org.jmol.g3d.TriangleRenderer
- fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.export.Export3D
- fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.g3d.Graphics3D
- fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.export.Export3D
- fillTriangle3CNBits(P3, short, short, P3, short, short, P3, short, short, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillTriangle3f(P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
- fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.export.Export3D
- fillTriangle3i(P3, P3, P3, T3, T3, T3, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillTriangleP3f(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
- fillTriangles - Variable in class org.jmol.shape.Mesh
- fillTriangleTwoSided(short, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
- fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.export.Export3D
- fillTriangleTwoSided(short, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
- filter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filter - Static variable in class org.jmol.script.T
- filter1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filter1Cased - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filter2 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filter2Cased - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterAllHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterAltLoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterAssembly - Variable in class org.jmol.adapter.readers.cif.CifReader
- filterAtom(Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterAtomName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterAtomNameTerminator - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterAtomType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterAtomTypeStr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterCased - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterChain - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterCIFAtom(Atom, String) - Method in class org.jmol.adapter.readers.cif.CifReader
- filterData(boolean, float) - Method in class org.jmol.jvxl.data.VolumeData
- filterElement - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterEveryNth - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterGroup3 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterGroups(BS, float[]) - Method in class org.jmol.symmetry.SpaceGroupFinder
-
Remove possibilities based on unit cells.
- filterHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterIsNot - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- filterMO() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
check line for filter options
- filterMOs - Variable in class org.jmol.adapter.writers.QCJSONWriter
- filterN - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterPDBAtom(Atom, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- filterReject(String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterShow(String, String) - Method in class org.jmol.scriptext.CmdExt
- filterSymop - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- filterSymop - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- filterTokens - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- finalize() - Method in class org.jmol.viewer.Viewer
- finalizeAromatic(Node[], BS, Lst<BS>, Lst<SmilesRing>, int[], boolean, boolean) - Static method in class org.jmol.smiles.SmilesAromatic
-
Iteratively trims a set of aromatic atoms that may be initially assigned to be aromatic but because their double bonds extend to non-aromatic atoms must be removed.
- finalizeAtom() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- finalizeAtoms(BS, boolean) - Method in class org.jmol.viewer.ShapeManager
- finalized - Variable in class org.jmol.adapter.readers.cif.MSRdr
- finalized - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- finalizeD(double, int) - Static method in class org.jmol.symmetry.SymmetryOperation
- finalizeEdges() - Method in class org.jmol.adapter.readers.xtal.CgdReader
-
Now that we have all the edge data we can add edges to atoms
- finalizeF(float, int) - Static method in class org.jmol.symmetry.SymmetryOperation
- finalizeGroupBuild() - Method in class org.jmol.modelset.ModelLoader
- finalizeHydrogens() - Method in class org.jmol.modelsetbio.BioResolver
- finalizeLink() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
-
Take all actions prior to applying symmetry.
- finalizeLinkNode(int) - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- finalizeLoad(boolean, boolean, boolean, boolean, int, int, int, boolean) - Method in class org.jmol.script.ScriptEval
- finalizeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
- finalizeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
- finalizeMOData(Map<String, Object>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finalizeModel() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- finalizeModels(int) - Method in class org.jmol.modelset.ModelLoader
-
Model numbers are considerably more complicated in Jmol 11.
- finalizeModelSet() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
At the end of the day, we need to finalize all the JmolObjects, set the trajectories, and, if filtered with DOCACHE, cache a streamlined binary file for inclusion in the PNGJ file.
- finalizeModelSet() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finalizeModulation() - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Create a script that will run to turn modulation on and to display only atoms with modulated occupancy >= 0.5.
- finalizeModulation() - Method in interface org.jmol.adapter.smarter.MSInterface
- finalizeNet() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- finalizeNet() - Method in class org.jmol.adapter.readers.xtal.CgdReader
-
Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdges
- finalizeNode(M4[]) - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- finalizeObject(int, int, float, int, boolean, Object, int, BS) - Method in class org.jmol.scriptext.ScriptExt
- finalizeObject(PyMOLScene, ModelSet, String, boolean) - Method in class org.jmol.adapter.readers.pymol.JmolObject
- finalizeObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Finally, we turn each JmolObject into its Jmol equivalent.
- finalizeOutput() - Method in interface org.jmol.api.JmolRendererInterface
- finalizeOutput() - Method in class org.jmol.export.___Exporter
- finalizeOutput() - Method in class org.jmol.export._IdtfExporter
- finalizeOutput() - Method in class org.jmol.export._ObjExporter
- finalizeOutput() - Method in class org.jmol.export._PovrayExporter
- finalizeOutput() - Method in class org.jmol.export._StlExporter
- finalizeOutput() - Method in class org.jmol.export.Export3D
- finalizeOutput() - Method in class org.jmol.g3d.Graphics3D
- finalizeOutput2() - Method in class org.jmol.export.___Exporter
- finalizeOutput2() - Method in class org.jmol.export.__RayTracerExporter
- finalizePdbCharges() - Method in class org.jmol.modelsetbio.BioResolver
- finalizePdbMultipleBonds() - Method in class org.jmol.modelsetbio.BioResolver
- finalizeReader() - Method in interface org.jmol.adapter.readers.cif.CifReader.Parser
- finalizeReader() - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
PRIOR to symmetry application, process all internal symop/translation aspects.
- finalizeReaderASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finalizeReaderMR() - Method in class org.jmol.adapter.readers.molxyz.MolReader
- finalizeReaderPDB() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- finalizeRna3d(Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
- finalizeSceneData() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Make sure atom uniqueID (vectorX) and cartoonType (vectorY) are made permanent
- finalizeShapes() - Method in class org.jmol.modelset.ModelLoader
- finalizeStructures() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
- finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.cif.CifReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.P2nReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FAHReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.InputReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
Set final auxiliary info and symmetry, including "fileHeader", "magresUnits", and "interactionTensors"; note that print getProperty("auxiliaryInfo.models[1].magresUnits") should return a catalog of tensor types.
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- finalizeSubclassReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
optional reader-specific method run first.
- finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
- finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
- finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
- finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finalizeSymmetry(boolean) - Method in interface org.jmol.adapter.readers.cif.CifReader.Parser
- finalizeSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Symmetry has been applied.
- finalizeSymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- finalizeTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- finalizeTrajectoryAs(Lst<P3[]>, Lst<V3[]>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- finalizeTransformParameters() - Method in class org.jmol.viewer.TransformManager
- finalizeTransformParameters() - Method in class org.jmol.viewer.Viewer
- finalizeUniqueBonds() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- finalizeUnitCell(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
-
Ensure that ModelLoader sets up the supercell unit cell.
- finalizeValidations(Viewer, Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
-
Create property_xxxx for each validation category.
- finalizeVisibility() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Create group JmolObjects, and set hierarchical visibilities
- finalizeZone(BZone) - Method in class org.jmol.util.BZone
-
Finalize a Brillouin zone.
- finalOperations - Variable in class org.jmol.symmetry.SpaceGroup
- find - Static variable in class org.jmol.script.T
- find(String, int) - Method in class org.jmol.util.CommandHistory
- find(String, String, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- find(String, String, int) - Method in class org.jmol.smiles.SmilesMatcher
-
Searches for all matches of a pattern within a SMILES string.
- find(Lst<Measurement>, Measurement) - Static method in class org.jmol.modelset.Measurement
- find(Measurement) - Method in class org.jmol.shape.Measures
- findAdditionalAxes(int) - Method in class org.jmol.symmetry.PointGroup
- findAnnotationAtoms(Viewer, String, Lst<SV>, String, BS) - Method in class org.jmol.dssx.AnnotationParser
-
find annotations; allows for wild cards InterPro.* where .....
- findApplets(String, String, String, Lst<String>) - Static method in class org.jmol.util.GenericApplet
- findAromaticNeighbor(int) - Method in class org.jmol.modelset.Atom
- findAtom(int, int, int, int, boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- findAtom(P3) - Method in class org.jmol.adapter.readers.xtal.CgdReader
- findAtomDipole(Atom, Atom, boolean) - Method in class org.jmol.shapespecial.Dipoles
- findAtomForRange(int, int, int, int, boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- findAtomsInRectangle(Rectangle) - Method in class org.jmol.modelset.ModelSet
- findAtomsLike(String) - Method in class org.jmol.modelset.Atom
- findAtomsLike(String) - Method in class org.jmol.smiles.SmilesAtom
- findAtomsLike(String) - Method in interface org.jmol.util.Node
- findBestFit(int, int[]) - Static method in class org.jmol.util.TempArray
- findBondDipole(Bond) - Method in class org.jmol.shapespecial.Dipoles
- findCAxes() - Method in class org.jmol.symmetry.PointGroup
- findCumulativeCenter(CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPDataSmiles
- findDipole(String) - Method in class org.jmol.shapespecial.Dipoles
- findDipoleFor(String, String) - Method in class org.jmol.shapespecial.Dipoles
- findEdge(int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- findElementsPresent() - Method in class org.jmol.modelset.ModelLoader
- findEquiv(int, SymmetryOperation, int, BS, P3, boolean) - Method in class org.jmol.symmetry.SpaceGroupFinder
- findFrequency(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Have the vwr show a particular frame with frequencies if it can be found.
- findHelixes(int, int[][][]) - Method in class org.jmol.dssx.DSSP
-
(p.
- findHelixes2(int, int, int, int[][][], STR, int, BS, boolean) - Method in class org.jmol.dssx.DSSP
- findImplicitHydrogen(Node) - Method in class org.jmol.smiles.SmilesSearch
- findInversionCenter() - Method in class org.jmol.symmetry.PointGroup
- findLeftLeaf() - Method in class org.jmol.bspt.CubeIterator
-
does the work
- findMaxRadii() - Method in class org.jmol.modelset.AtomCollection
- findModelById(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- findMonomer(BS, boolean) - Method in class org.jmol.modelsetbio.ProteinStructure
- findNearest2(int, int, Atom[], BS, int) - Method in class org.jmol.modelset.AtomCollection
- findNearestAtom(int, int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
- findNearestAtomIndex(int, int) - Method in class org.jmol.api.JmolViewer
- findNearestAtomIndex(int, int) - Method in class org.jmol.viewer.Viewer
- findNearestAtomIndex(int, int, BS, int) - Method in class org.jmol.modelset.ModelSet
- findNearestAtomIndex(int, int, Atom[], short[], int, BS) - Method in class org.jmol.modelsetbio.BioPolymer
- findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.AminoMonomer
- findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
- findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.Monomer
-
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
- findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.NucleicMonomer
- findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shape.Shape
- findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShape
- findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShapeCollection
- findNearestAtomIndexMovable(int, int, boolean) - Method in class org.jmol.viewer.Viewer
- findNearestLabel(int, int) - Method in class org.jmol.shape.Labels
- findNearestShapeAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.viewer.ShapeManager
- findNearestThreePoints(float, float, float[][], int[]) - Static method in class org.jmol.jvxl.readers.SurfaceGenerator
- findNearestVertex(Lst<MeshCapper.CapVertex>, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
-
Find the nearest vertex to v0 in the list v1s.
- findNode(String, int, P3) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Called from TLink and TAtom to find a node with the given symmetry.
- findNotAttached(int, int[][], int[], int) - Method in class org.jmol.modelset.AtomCollection
- findPickedBond(int, int, BS, P3, int[]) - Method in class org.jmol.shape.Sticks
- findPickedObject(int, int, boolean, BS) - Method in class org.jmol.shapespecial.Draw
- findPickedObject(int, int, boolean, BS) - Method in class org.jmol.shapespecial.Ellipsoids
- findPlanes() - Method in class org.jmol.symmetry.PointGroup
- findPoly(String, int, boolean) - Method in class org.jmol.shapespecial.Polyhedra
- findPolyBS(BS) - Method in class org.jmol.shapespecial.Polyhedra
- findRecord(String) - Method in class org.jmol.jsv.JDXMOLParser
- findSet(int) - Method in class org.jmol.jvxl.data.MeshData
- findShorter(int, int[]) - Static method in class org.jmol.util.TempArray
- findSpaceGroup(int, String) - Static method in class org.jmol.symmetry.SpaceGroup
- findSpaceGroup(BS, String, float[], boolean, boolean) - Method in class org.jmol.viewer.Viewer
- findSpaceGroup(Viewer, BS, String, float[], boolean, boolean) - Method in interface org.jmol.api.SymmetryInterface
- findSpaceGroup(Viewer, BS, String, float[], boolean, boolean) - Method in class org.jmol.symmetry.Symmetry
- findSpaceGroup(Viewer, BS, String, float[], SymmetryInterface, boolean, boolean) - Method in class org.jmol.symmetry.SpaceGroupFinder
- findString - Variable in class org.jmol.jvxl.readers.KinemageReader
- findValue(int, int, boolean, BS) - Method in class org.jmol.shapesurface.Isosurface
- finish() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- finish() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- finish(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- finish(Object) - Method in class org.jmol.api.JmolAdapter
- FINISH - Static variable in class org.jmol.thread.JmolThread
- fireJmolScriptCallback(boolean, CBK, Object[]) - Method in class org.jmol.viewer.StatusManager
- first - Variable in class org.jmol.modelset.TickInfo
- first - Static variable in class org.jmol.script.T
- firstAtom - Variable in class org.jmol.adapter.readers.cif.CifReader
- firstAtom - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- firstAtom - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- firstAtomIndex - Variable in class org.jmol.atomdata.AtomData
- firstAtomIndex - Variable in class org.jmol.modelset.Group
- firstAtomIndex - Variable in class org.jmol.modelset.Model
- firstAtomIndex - Variable in class org.jmol.util.JmolMolecule
- firstAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
- firstAtomOffset - Variable in class org.jmol.quantum.QuantumCalculation
- firstAtomToBond - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- firstChar - Variable in class org.jmol.adapter.readers.cif.CifReader
- firstFrameDelay - Variable in class org.jmol.viewer.AnimationManager
- firstFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
- firstFrameIndex - Variable in class org.jmol.viewer.AnimationManager
- firstIsotope - Static variable in class org.jmol.util.Elements
-
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
- firstLastStep - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- firstLine - Variable in class org.jmol.adapter.readers.simple.InputReader
- firstLine - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- firstLineOf(String) - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- firstModelIndex - Variable in class org.jmol.atomdata.AtomData
- firstMoleculeIndex - Variable in class org.jmol.modelset.Model
- firstNearbyAtom - Variable in class org.jmol.jvxl.readers.AtomDataReader
- firstPosition - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- firstProper - Static variable in class org.jmol.symmetry.PointGroup
- firstRealVertex - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- fit_iterations - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- fit_kabsch - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- fit_tolerance - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- fix(float) - Method in class org.jmol.symmetry.UnitCell
- fix(String) - Static method in class org.jmol.i18n.Resource
- fixACDAtomList(String, Map<String, String>, int) - Method in class org.jmol.jsv.JDXMOLParser
- fixAnnotations(int, String, int) - Method in class org.jmol.modelsetbio.BioResolver
- fixAtom(Atom) - Method in class org.jmol.modelset.Trajectory
- fixAtomForBonding(P3, int) - Method in class org.jmol.adapter.readers.cif.CifReader
- fixAtomName(String) - Static method in class org.jmol.adapter.readers.xtal.CrystalReader
-
MN33 becomes Mn33
- fixAtoms(int, SV, BS, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
- fixAtoms(int, SV, BS, int, int) - Method in class org.jmol.dssx.AnnotationParser
-
Adjusts _atoms bitset to account for added hydrogen atoms.
- fixBaseIndices() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fixBasisLine(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
- fixChirality(SmilesSearch) - Method in class org.jmol.smiles.SmilesParser
- fixCoefficients(double[]) - Method in class org.jmol.adapter.writers.QCJSONWriter
-
Jmol allows for a set of arrays that map coefficient indicies with nonstandard order to Gaussian/Molden order.
- fixConnections() - Method in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- fixD(float, boolean) - Method in class org.jmol.modelset.BondCollection
- fixDataString(String) - Static method in class org.jmol.util.Parser
- fixDOSName(String) - Static method in class org.jmol.viewer.FileManager
-
Switch \ for / only for DOS names such as C:\temp\t.xyz, not names like http://cactus.nci.nih.gov/chemical/structure/CC/C=C\CC
- fixDouble(double) - Method in class org.jmol.adapter.readers.cif.MSCifParser
- fixDoubleA(double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
- fixDSSRJSONMap(Map<String, Object>) - Method in interface org.jmol.api.JmolAnnotationParser
- fixDSSRJSONMap(Map<String, Object>) - Method in class org.jmol.dssx.AnnotationParser
- fixDSSRJSONMap(Map<String, Object>) - Method in class org.jmol.dssx.DSSR1
-
kissingLoops and coaxStacks use index arrays instead of duplication;
- fixed - Static variable in class org.jmol.script.T
- fixedCount - Variable in class org.jmol.jvxl.readers.PmeshReader
- fixedLattice - Variable in class org.jmol.jvxl.data.JvxlData
- fixedOrigin - Variable in class org.jmol.shape.Axes
- fixedOriginUC - Variable in class org.jmol.shape.Axes
- fixedRotationAxis - Variable in class org.jmol.viewer.TransformManager
- fixedRotationCenter - Variable in class org.jmol.export.___Exporter
- fixedRotationCenter - Variable in class org.jmol.viewer.TransformManager
- fixedRotationOffset - Variable in class org.jmol.viewer.TransformManager
- fixedSite - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- fixedtemp - Static variable in class org.jmol.script.T
- FIXEDTEMP - Enum constant in enum org.jmol.c.PAL
- fixedTranslation - Variable in class org.jmol.viewer.TransformManager
- fixedValue - Variable in class org.jmol.modelset.Measurement
- fixedValue - Variable in class org.jmol.modelset.MeasurementData
- fixEndsAndSortVertices(MeshCapper.CapVertex[]) - Method in class org.jmol.util.MeshCapper
-
Generate yxNext links based on scanning Y large to small and if Y1==Y2, then X small to large
- fixExplicitFaceWinding(int[], int, P3[], V3[]) - Method in class org.jmol.shapespecial.Polyhedra
-
Check to see that the winding of the explicit face is correct.
- fixFlowAddLine(ScriptFlowContext) - Method in class org.jmol.script.ScriptCompiler
- fixFormalCharges(BS) - Method in class org.jmol.modelset.AtomCollection
- fixHtml(String) - Method in class org.openscience.jmol.app.webexport.PopInJmol
- fixHtml(String) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
- fixHtml(String) - Method in class org.openscience.jmol.app.webexport.WebPanel
- fixHydrogens(Viewer, AminoMonomer) - Static method in class org.jmol.modelsetbio.BioExt
- fixIndices(int, int, BS) - Method in class org.jmol.modelset.Model
- fixIndices(int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
- fixIndices(int, BS) - Method in class org.jmol.modelset.Chain
- fixIndices(int, BS) - Method in class org.jmol.modelset.Group
- fixIndices(Map<String, Object>, String, String) - Method in class org.jmol.dssx.DSSR1
-
create a key/value pair root+"s" for all indices of root+"_indices"
- fixIndicesM(int, int, BS) - Method in class org.jmol.modelset.Model
- fixInlineString(String, char) - Static method in class org.jmol.viewer.Viewer
- fixIntegration() - Static method in class org.jmol.adapter.writers.QCJSONWriter
-
When an MO is calculated in Jmol, Jmol will check the integration so that it can be checked to be close to 1.0000.
- fixJavaFloat - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fixJMEFormalCharges(BS, String) - Method in interface org.jmol.api.JmolPropertyManager
- fixJMEFormalCharges(BS, String) - Method in class org.jmol.viewer.PropertyManager
-
Fix a JME string returned from NCI CIR to have the proper formal charges.
- fixLabel(Atom, String) - Method in class org.jmol.render.HoverRenderer
- fixLattice() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- fixLegendre() - Method in class org.jmol.adapter.readers.cif.MSRdr
- fixLineFolding(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
allow white space between \ and \n
- fixLocal(String) - Method in class org.jmol.adapter.readers.xml.XmlReader
- fixMagneticXYZ(M4, String, boolean) - Method in class org.jmol.symmetry.SymmetryOperation
- fixMinus(String) - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- fixModelSpec(T) - Method in class org.jmol.script.ScriptTokenParser
- fixMovieCommands(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Could possibly implement something here that interprets PyMOL script commands.
- fixMovieViews(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Could implement something here that creates a Jmol view.
- fixN - Variable in class org.jmol.adapter.readers.molxyz.MolReader
-
fix charges for RN(=O)(O), =N(O)*, =N
- fixName(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- fixName(String) - Static method in class org.jmol.util.ColorEncoder
- fixOptimadeCall(String) - Static method in class org.jmol.viewer.JC
-
Get all necessary response fields if an optimade call.
- fixOrbitalType() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- fixOrder(int[], int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- fixOrder(int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- fixPath(String) - Static method in class org.jmol.viewer.FileManager
- fixPDBFormat(Lst<String>, Map<String, Integer>, OC, int[], int) - Method in class org.jmol.adapter.writers.PDBWriter
-
must re-order by resno and then renumber atoms and add TER records based on BioPolymers note: 3hbt has a break between residues 39 and 51 with no TER record, but Jmol will put that in.
- fixPeriodic(P3, P3) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
- fixPoint(float, float) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
- fixPropertyValue(BS, Object, boolean) - Method in class org.jmol.modelsetbio.BioResolver
- fixProtocol(String) - Static method in class org.jmol.viewer.JC
-
Check for databases that have changed from http:// to https:// over time.
- fixRadius(float) - Static method in class org.jmol.adapter.readers.pdb.PdbReader
- fixReps(BS[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- fixScreenZ(int) - Method in class org.jmol.export.___Exporter
- fixScriptPath(String, String) - Method in class org.jmol.script.ScriptEval
- fixSelectQuotes(String) - Method in class org.jmol.viewer.PropertyManager
- fixSerialName(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- fixSettings(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Recent PyMOL files may not have all settings.
- fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- fixSlaterTypes(int, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- fixStereo(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
-
Check number of connections and permute them to match a canonical version
- fixTag(String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Returns a modified identifier for a tag, so that the element can be determined from it in the
Atom
. - fixTextImageRGB(int) - Static method in class org.jmol.g3d.Graphics3D
- fixTitleLine(int, Map<String, Object>) - Method in class org.jmol.jvxl.readers.IsoMOReader
- fixToken(int) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- fixTrajectory(Atom) - Method in class org.jmol.modelset.AtomCollection
- fixTypeOrder(int[], int, int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- fixTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- fixUnits(String) - Static method in class org.jmol.modelset.Measurement
- fixValue(String, boolean) - Method in class org.jmol.modelset.Measurement
- fixXY(float, float, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- FLAG_exfoliate - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- FLAG_ignore - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- FLAG_inorganic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- FLAG_MASK - Static variable in class org.jmol.modelset.Atom
- FLAG_no_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- FLAG_NOSURFACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- FLAG_organic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- FLAG_polymer - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- FLAG_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- flags - Variable in class org.jmol.smiles.SmilesGenerator
- flags - Variable in class org.jmol.smiles.SmilesParser
- flags - Variable in class org.jmol.smiles.SmilesSearch
- FLAGS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- flat - Static variable in class org.jmol.script.T
- FLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- FLICK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- flipLighting(int) - Method in class org.jmol.shape.Mesh
- fList - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- flistValue(T, int) - Static method in class org.jmol.script.SV
- float_labels - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- floatArraySet(int, int, int) - Method in class org.jmol.scriptext.IsoExt
- floatArraySetXYZ(int, int, int, int) - Method in class org.jmol.scriptext.IsoExt
- floatAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- floatparam - Static variable in class org.jmol.script.T
- floatParameter(int) - Method in class org.jmol.script.ScriptParam
- floatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- floatParameterRange(int, float, float) - Method in class org.jmol.script.ScriptParam
- floatParameterSet(int, int, int) - Method in class org.jmol.script.ScriptParam
-
process a general string or set of parameters as an array of floats, allowing for relatively free form input
- floatproperty - Static variable in class org.jmol.script.T
- floatRange - Variable in class org.jmol.shapebio.BioShape
- floats - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- floatsAt(Lst<Object>, int, float[], int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- floatSecondsTotal - Variable in class org.jmol.navigate.Navigator
- floatSecondsTotal - Variable in class org.jmol.thread.MoveToThread
- floatSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- floatValue() - Method in class org.jmol.script.ScriptTokenParser
- flowCommand - Static variable in class org.jmol.script.T
- flowContext - Variable in class org.jmol.script.ScriptCompiler
- FlowLayout - Class in org.jmol.awtjs.swing
- FlowLayout() - Constructor for class org.jmol.awtjs.swing.FlowLayout
- flowStart(T) - Method in class org.jmol.script.ScriptCompiler
- flush(Object) - Static method in class org.jmol.awt.Image
- flushCaches() - Method in class org.jmol.util.Shader
- flushImage(Object) - Method in interface org.jmol.api.GenericPlatform
- flushImage(Object) - Method in class org.jmol.awt.Platform
- flushImage(Object) - Method in class org.jmol.awtjs2d.Platform
- flushQueue(String) - Method in class org.jmol.script.ScriptManager
- fm - Variable in class org.jmol.adapter.readers.spartan.SpartanUtil
- fm - Variable in class org.jmol.io.DOMReader
- fm - Variable in class org.jmol.io.FilesReader
- fm - Variable in class org.jmol.viewer.Viewer
- fmt(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- FO_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- foccupancy - Variable in class org.jmol.adapter.smarter.Atom
- fog - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- fog_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- FoldingXyzReader - Class in org.jmol.adapter.readers.simple
-
This reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.
- FoldingXyzReader() - Constructor for class org.jmol.adapter.readers.simple.FoldingXyzReader
- font - Variable in class org.jmol.g3d.TextString
- font - Variable in class org.jmol.modelset.Text
- font - Static variable in class org.jmol.script.T
- font - Variable in class org.jmol.util.Font
- Font - Class in org.jmol.util
-
Provides font support using a int fid (Font ID) as an index into font table.
- Font(FontManager, int, int, int, float, float, Object) - Constructor for class org.jmol.util.Font
- FONT - Static variable in class org.jmol.shapecgo.CGOMesh
- FONT_ALLOCATION_UNIT - Static variable in class org.jmol.util.Font
- FONT_AXES - Static variable in class org.jmol.shapecgo.CGOMesh
- FONT_FACE_MONO - Static variable in class org.jmol.util.Font
- FONT_FACE_SANS - Static variable in class org.jmol.util.Font
- FONT_FACE_SERIF - Static variable in class org.jmol.util.Font
- FONT_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
- FONT_STYLE_BOLD - Static variable in class org.jmol.util.Font
- FONT_STYLE_BOLDITALIC - Static variable in class org.jmol.util.Font
- FONT_STYLE_ITALIC - Static variable in class org.jmol.util.Font
- FONT_STYLE_PLAIN - Static variable in class org.jmol.util.Font
- FONT_VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
- font3d - Variable in class org.jmol.render.FontLineShapeRenderer
- font3d - Variable in class org.jmol.shape.FontLineShape
- font3d - Variable in class org.jmol.shape.Frank
- font3d - Variable in class org.jmol.shape.Measures
- font3ds - Static variable in class org.jmol.util.Font
- fontButton - Variable in class org.jmol.console.ScriptEditor
- fontButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- fontcaching - Static variable in class org.jmol.script.T
- fontCaching - Variable in class org.jmol.viewer.GlobalSettings
- fontChild - Variable in class org.jmol.export._VrmlExporter
- fontFace - Variable in class org.jmol.export._VrmlExporter
- fontFace - Variable in class org.jmol.util.Font
- FONTFACE - Static variable in class org.jmol.shape.Echo
- FONTFACE - Static variable in class org.jmol.shape.Hover
- fontFaces - Static variable in class org.jmol.util.Font
- fontID - Variable in class org.jmol.shapespecial.DrawMesh
- fontkeyCount - Static variable in class org.jmol.util.Font
- fontkeys - Static variable in class org.jmol.util.Font
- FontLineShape - Class in org.jmol.shape
- FontLineShape() - Constructor for class org.jmol.shape.FontLineShape
- FontLineShapeRenderer - Class in org.jmol.render
- FontLineShapeRenderer() - Constructor for class org.jmol.render.FontLineShapeRenderer
- FontManager - Interface in org.jmol.api
-
A generic interface for font queries.
- fontMetrics - Variable in class org.jmol.util.Font
- fontScale - Variable in class org.jmol.modelset.Text
- fontScale - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- fontscaling - Static variable in class org.jmol.script.T
- fontScaling - Variable in class org.jmol.viewer.GlobalSettings
- fontsize - Static variable in class org.jmol.script.T
- fontSize - Variable in class org.jmol.console.ScriptEditor
- fontSize - Variable in class org.jmol.export._VrmlExporter
- fontSize - Variable in class org.jmol.util.Font
- fontSize - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- FONTSIZE - Static variable in class org.jmol.shape.Echo
- FONTSIZE - Static variable in class org.jmol.shape.Hover
- fontSizeNominal - Variable in class org.jmol.util.Font
- fontStringWidth(Font, String) - Method in interface org.jmol.api.FontManager
- fontStringWidth(Font, String) - Method in class org.jmol.awt.Platform
- fontStringWidth(Font, String) - Method in class org.jmol.awtjs2d.Platform
- fontStyle - Variable in class org.jmol.export._VrmlExporter
- fontStyle - Variable in class org.jmol.util.Font
- FONTSTYLE - Static variable in class org.jmol.shape.Hover
- fontStyles - Static variable in class org.jmol.util.Font
- FOOP - Static variable in class org.jmol.minimize.forcefield.MMFFOOPCalc
- FOOPD - Static variable in class org.jmol.minimize.forcefield.MMFFOOPCalc
- FOPARAM_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- force - Variable in class org.jmol.minimize.MinAtom
- forceAsyncLoad(String) - Method in interface org.jmol.api.GenericPlatform
- forceAsyncLoad(String) - Method in class org.jmol.awt.Platform
- forceAsyncLoad(String) - Method in class org.jmol.awtjs2d.Platform
- forceautobond - Static variable in class org.jmol.script.T
- forceAutoBond - Variable in class org.jmol.viewer.GlobalSettings
- forceEndIf - Variable in class org.jmol.script.ScriptFlowContext
- forcefield - Static variable in class org.jmol.script.T
- forceField - Variable in class org.jmol.viewer.GlobalSettings
- ForceField - Class in org.jmol.minimize.forcefield
- ForceField() - Constructor for class org.jmol.minimize.forcefield.ForceField
- ForceFieldMMFF - Class in org.jmol.minimize.forcefield
-
MMFF94 implementation 5/14/2012 - fully validated for atom types and charges - reasonably well validated for energies (see below) - TODO: add UFF for preliminary/backup calculation
- ForceFieldMMFF(Minimizer, boolean) - Constructor for class org.jmol.minimize.forcefield.ForceFieldMMFF
- ForceFieldReader - Class in org.jmol.adapter.readers.more
- ForceFieldReader() - Constructor for class org.jmol.adapter.readers.more.ForceFieldReader
- ForceFieldUFF - Class in org.jmol.minimize.forcefield
- ForceFieldUFF(Minimizer, boolean) - Constructor for class org.jmol.minimize.forcefield.ForceFieldUFF
- forceFlowContext - Variable in class org.jmol.script.ScriptCompiler
- forceFlowEnd(T) - Method in class org.jmol.script.ScriptCompiler
- forceMOPAC - Variable in class org.jmol.adapter.readers.quantum.MOReader
- forceNoAddHydrogens - Variable in class org.jmol.script.ScriptEval
- forcePacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- forceShowTriangles - Variable in class org.jmol.render.MeshRenderer
- forceSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- forcmd - Static variable in class org.jmol.script.T
- FORMAL_CHARGE - Enum constant in enum org.jmol.c.PAL
- FORMAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
- FORMAL_CHARGE_MAX - Static variable in class org.jmol.util.Elements
- FORMAL_CHARGE_MIN - Static variable in class org.jmol.util.Elements
-
ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
- formalcharge - Static variable in class org.jmol.script.T
- formalCharge - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
- formalCharge - Variable in class org.jmol.adapter.smarter.Atom
- formalCharge - Variable in class org.jmol.minimize.forcefield.AtomType
- FORMALCHARGE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- formalChargeAndFlags - Variable in class org.jmol.modelset.Atom
- format - Static variable in class org.jmol.script.T
- format(float, String, T3) - Method in class org.jmol.modelset.LabelToken
- format(SV[], int) - Static method in class org.jmol.script.SV
-
Accepts arguments from the format() function First argument is a format string.
- formatAngle(float) - Method in class org.jmol.modelset.Measurement
- formatDistance(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
- formatDistance(String) - Method in class org.jmol.modelset.Measurement
- formatExpNOE(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
- formatJ(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
- formatLabel(Viewer, Atom, String, P3) - Method in class org.jmol.modelset.LabelToken
- formatLabelAtomArray(Viewer, Atom, LabelToken[], char, int[], P3) - Static method in class org.jmol.modelset.LabelToken
-
returns a formatted string based on the precompiled label tokens
- formatLabelBond(Viewer, Bond, LabelToken[], Map<String, Object>, int[], P3) - Static method in class org.jmol.modelset.LabelToken
- formatLabelMeasure(Viewer, Measurement, String, float, String) - Static method in class org.jmol.modelset.LabelToken
- formatMeasurement(String) - Method in class org.jmol.modelset.Measurement
- formatMeasurementAs(String, String, boolean) - Method in class org.jmol.modelset.Measurement
- formatNOE(double) - Static method in class org.openscience.jmol.app.janocchio.Measure
- formatNumber(float) - Method in class org.jmol.adapter.writers.QCJSONWriter
- formats - Variable in class org.jmol.shape.Labels
- formatString(float, String, String) - Method in class org.jmol.modelset.Measurement
- formatText(String) - Method in class org.jmol.viewer.Viewer
- formul() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- formula - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
- forPoint3 - Variable in class org.jmol.script.ScriptCompiler
- forThermalEllipsoid - Variable in class org.jmol.util.Tensor
- forVars - Variable in class org.jmol.script.ContextToken
- forVars - Variable in class org.jmol.script.ScriptContext
- foundDistance2() - Method in interface org.jmol.api.AtomIndexIterator
- foundDistance2() - Method in class org.jmol.bspt.CubeIterator
-
After calling nextElement(), allows one to find out the value of the distance squared.
- foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- foundDistance2() - Method in class org.jmol.symmetry.UnitCellIterator
- foundDuringLastSync - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- fourdots - Static variable in class org.jmol.render.FontLineShapeRenderer
- FPAR - Static variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- FPARAM_DISP_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_DISP_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_DISP_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_DISP_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_OCC_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_OCC_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_OCC_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_OCC_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_SPIN_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_SPIN_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_SPIN_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_SPIN_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_U_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_U_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_U_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPARAM_U_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FPPanel(Map<String, Object>) - Constructor for class org.jmol.dialog.FilePreview.FPPanel
- fps - Static variable in class org.jmol.script.T
- fps - Variable in class org.jmol.thread.MoveToThread
- FPS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Maximum value for the fps slider.
- fpsSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- fracB - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- fracs - Variable in class org.jmol.util.MeshSlicer
- FRACT_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
- FRACT_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
- FRACT_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
- fractionalizeCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- fractionalOffset - Variable in class org.jmol.symmetry.UnitCell
- fractionalOrigin - Variable in class org.jmol.util.SimpleUnitCell
- fractionalPoint - Variable in class org.jmol.script.ScriptParam
-
set in getPointOrPlane
- fractionalrelative - Static variable in class org.jmol.script.T
- fractionalRelative - Variable in class org.jmol.viewer.GlobalSettings
- fractionData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- fractionPtr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- fracx - Static variable in class org.jmol.script.T
- fracxyz - Static variable in class org.jmol.script.T
- fracy - Static variable in class org.jmol.script.T
- fracz - Static variable in class org.jmol.script.T
- frame - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- frame - Static variable in class org.jmol.script.T
- frame - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- frame - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- FRAME_FIRST - Static variable in class org.jmol.viewer.AnimationManager
- FRAME_LAST - Static variable in class org.jmol.viewer.AnimationManager
- frameControl(int) - Method in class org.jmol.script.ScriptEval
- frameCount - Variable in class org.openscience.jmol.app.janocchio.FrameCounter
- frameCounter - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- FrameCounter - Class in org.openscience.jmol.app.janocchio
- FrameCounter(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.FrameCounter
-
Constructor
- frameDelay - Variable in class org.jmol.modelset.Model
- frameDeltaCouple - Variable in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- frameDeltaDisplay - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- frameDeltaDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- frameDeltaDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- frameDeltaDisplay - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- FrameDeltaDisplay - Class in org.openscience.jmol.app.janocchio
- FrameDeltaDisplay(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
-
Constructor
- FrameDeltaDisplayAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.FrameDeltaDisplayAction
- frameDeltaNoe - Variable in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- frameNumber - Variable in class org.openscience.jmol.app.janocchio.FrameCounter
- frameNumber - Variable in class org.openscience.jmol.app.janocchio.PopulationDisplay
- frameObj - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- frameOffset - Variable in class org.jmol.viewer.TransformManager
- frameOffsets - Variable in class org.jmol.viewer.TransformManager
- framePointer1 - Variable in class org.jmol.thread.AnimationThread
- framePointer2 - Variable in class org.jmol.thread.AnimationThread
- frames - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- FramesOnly - Variable in class org.jmol.popup.JmolPopup
- frameStep - Variable in class org.jmol.viewer.AnimationManager
- frameTimeMillis - Variable in class org.jmol.navigate.Navigator
- frameTimeMillis - Variable in class org.jmol.thread.MoveToThread
- frameTitles - Variable in class org.jmol.modelset.ModelSet
- frank - Static variable in class org.jmol.script.T
- Frank - Class in org.jmol.shape
- Frank() - Constructor for class org.jmol.shape.Frank
- frankAscent - Variable in class org.jmol.shape.Frank
- frankClicked(int, int) - Method in class org.jmol.viewer.Viewer
- frankClickedModelKit(int, int) - Method in class org.jmol.viewer.Viewer
- frankDescent - Variable in class org.jmol.shape.Frank
- frankList - Variable in class org.jmol.popup.JmolPopup
- frankMargin - Static variable in class org.jmol.shape.Frank
- frankOn - Variable in class org.jmol.viewer.Viewer
- frankPopup - Variable in class org.jmol.popup.JmolGenericPopup
- FrankRenderer - Class in org.jmol.render
- FrankRenderer() - Constructor for class org.jmol.render.FrankRenderer
- frankString - Variable in class org.jmol.shape.Frank
- frankWidth - Variable in class org.jmol.shape.Frank
- freeBonds - Variable in class org.jmol.modelset.BondCollection
- freeEnum - Variable in class org.jmol.util.TempArray
- freeEnumSize - Static variable in class org.jmol.util.TempArray
- freePoints - Variable in class org.jmol.util.TempArray
- freePointsSize - Static variable in class org.jmol.util.TempArray
- freeScreens - Variable in class org.jmol.util.TempArray
- freeScreensSize - Static variable in class org.jmol.util.TempArray
- freeTempArrays() - Method in class org.jmol.renderbio.BioShapeRenderer
- freeTempEnum(STR[]) - Method in class org.jmol.util.TempArray
- freeTempEnum(STR[]) - Method in class org.jmol.viewer.Viewer
- freeTempPoints(P3[]) - Method in class org.jmol.util.TempArray
- freeTempPoints(P3[]) - Method in class org.jmol.viewer.Viewer
- freeTempScreens(P3i[]) - Method in class org.jmol.util.TempArray
- freeTempScreens(P3i[]) - Method in class org.jmol.viewer.Viewer
- freeze() - Method in class org.jmol.modelset.Model
- freeze() - Method in class org.jmol.modelset.ModelLoader
- freeze() - Method in class org.jmol.modelsetbio.BioModel
- freeze(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- freezeM() - Method in class org.jmol.modelset.Model
- freezeModels() - Method in class org.jmol.modelset.ModelSet
- freq - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- freq - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- freqAtom0 - Variable in class org.jmol.adapter.readers.simple.AmpacReader
- freqField - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- freqFieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- freqLabel - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- fReturn - Variable in class org.jmol.jvxl.calc.MarchingCubes
- FRIENDLY - Static variable in class org.jmol.util.ColorEncoder
- from - Static variable in class org.jmol.script.T
- fromOABC(T3[], boolean) - Static method in class org.jmol.symmetry.UnitCell
-
A special constructor for spacially defined unit cells.
- fromParams(float[], boolean) - Static method in class org.jmol.symmetry.UnitCell
- fromUnits(float, String) - Static method in class org.jmol.modelset.Measurement
- front - Static variable in class org.jmol.script.T
- frontAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- frontedges - Static variable in class org.jmol.script.T
- frontlit - Static variable in class org.jmol.script.T
- frontonly - Static variable in class org.jmol.script.T
- frontonly - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- frontOnly - Variable in class org.jmol.render.MeshRenderer
- frontOnly - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- frontOnly - Variable in class org.jmol.shape.Mesh
- FS - Static variable in class org.jmol.quantum.QS
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
- FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
- fScrPt - Variable in class org.jmol.viewer.TransformManager
- fset0 - Static variable in class org.jmol.adapter.writers.CIFWriter
- fset0 - Variable in class org.jmol.render.UccageRenderer
- fslist - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- fSpherical - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- fStep - Variable in class org.jmol.thread.MoveToThread
- FSTRETCH - Static variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
- FU_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- full - Static variable in class org.jmol.script.T
- full_screen - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- fullCommand - Variable in class org.jmol.script.ScriptEval
- fullCommand - Variable in class org.jmol.shapesurface.LcaoCartoon
- fullCubeCorners - Static variable in class org.jmol.util.Triangulator
-
For each corner 0-7: {c c c t} where c c c are the connected corners, arranged clockwise and t is the bitset of triangles associated with faces intersecting at this corner.
- fullCubePolygon - Static variable in class org.jmol.util.Triangulator
- fullName - Variable in class org.jmol.awtjs2d.JSFile
- fullName - Variable in class org.jmol.util.GenericApplet
- fullName - Variable in class org.jmol.viewer.Viewer
- fullPathName - Variable in class org.jmol.viewer.FileManager
- fullPathNameIn - Variable in class org.jmol.io.FileReader
- fullPathNamesIn - Variable in class org.jmol.io.FilesReader
- fullplane - Static variable in class org.jmol.script.T
- fullSymmetry - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- fullylit - Static variable in class org.jmol.script.T
- fullyLit - Variable in class org.jmol.jvxl.readers.Parameters
- func - Variable in class org.jmol.jvxl.readers.IsoFxyReader
- func - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- func - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
- func - Variable in class org.jmol.jvxl.readers.Parameters
- function - Variable in class org.jmol.script.ScriptFlowContext
- function - Static variable in class org.jmol.script.T
- functionInfo - Variable in class org.jmol.jvxl.readers.Parameters
- functionName - Variable in class org.jmol.script.ScriptContext
- functionName - Variable in class org.jmol.script.ScriptEval
- functionxy - Static variable in class org.jmol.script.T
- functionXY(String, int, int) - Method in interface org.jmol.api.JmolStatusListener
-
for isosurface FUNCTIONXY
- functionXY(String, int, int) - Method in class org.jmol.util.GenericApplet
- functionXY(String, int, int) - Method in class org.jmol.viewer.StatusManager
- functionXY(String, int, int) - Method in class org.jmol.viewer.Viewer
-
fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.
- functionXY(String, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
this is just a test method for isosurface FUNCTIONXY
- functionxyz - Static variable in class org.jmol.script.T
- functionXYZ(String, int, int, int) - Method in interface org.jmol.api.JmolStatusListener
-
for isosurface FUNCTIONXYZ
- functionXYZ(String, int, int, int) - Method in class org.jmol.util.GenericApplet
- functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.StatusManager
- functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.Viewer
- functionXYZ(String, int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- funcType - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- funcType - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
- FUPARAM_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- fux - Static variable in class org.jmol.script.T
- fuxyz - Static variable in class org.jmol.script.T
- fuy - Static variable in class org.jmol.script.T
- fuz - Static variable in class org.jmol.script.T
- fval(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- fValue(T) - Static method in class org.jmol.script.SV
- FWV_DISP_AXIS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_DISP_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_DISP_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_OCC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_OCC_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_Q_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_SPIN_AXIS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_SPIN_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_SPIN_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_U_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_U_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_U_TENS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_X - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_Y - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- FWV_Z - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
G
- g - Variable in class org.jmol.g3d.Pixelator
- g - Variable in class org.jmol.util.Rgb16
- g - Variable in class org.jmol.viewer.Viewer
- g1 - Variable in class org.jmol.modelsetbio.BasePair
- g2 - Variable in class org.jmol.modelsetbio.BasePair
- g3d - Variable in class org.jmol.g3d.CircleRenderer
- g3d - Variable in class org.jmol.g3d.CylinderRenderer
- g3d - Variable in class org.jmol.g3d.HermiteRenderer
- g3d - Variable in class org.jmol.g3d.LineRenderer
- g3d - Variable in class org.jmol.g3d.SphereRenderer
- g3d - Variable in class org.jmol.g3d.TriangleRenderer
- g3d - Variable in class org.jmol.modelset.AtomCollection
- g3d - Variable in class org.jmol.render.ShapeRenderer
-
could be vwr.gdata or an exporter
- g3d - Variable in class org.jmol.renderbio.NucleicRenderer
- g3d - Variable in class org.jmol.renderbio.RocketRenderer
- g3d - Variable in class org.jmol.viewer.ColorManager
- G3DRenderer - Interface in org.jmol.g3d
- GamessReader - Class in org.jmol.adapter.readers.quantum
- GamessReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessReader
- gamessUKContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- GamessUKReader - Class in org.jmol.adapter.readers.quantum
- GamessUKReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUKReader
- gamessUSContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- GamessUSReader - Class in org.jmol.adapter.readers.quantum
- GamessUSReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUSReader
- gamma - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gamma - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- gamma - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- gamma - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- gamma - Variable in class org.jmol.jvxl.readers.MapFileReader
- gamma - Variable in class org.jmol.util.SimpleUnitCell
- gammaE - Variable in class org.jmol.adapter.readers.cif.MSRdr
- gammaE - Variable in class org.jmol.util.ModulationSet
- gammaIinv - Variable in class org.jmol.util.ModulationSet
- gaussian_b_adjust - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gaussian_b_floor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gaussian_resolution - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gaussianAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- GaussianAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
- gaussianContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- gaussianCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
- gaussianCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- gaussianCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- gaussianDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- GaussianDialog - Class in org.openscience.jmol.app.jmolpanel
- GaussianDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.GaussianDialog
- gaussianFchkContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- GaussianFchkReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data
- GaussianFchkReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianFchkReader
- gaussianPtr - Variable in class org.jmol.quantum.MOCalculation
- GaussianReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Gaussian 94/98/03/09 output files.
- GaussianReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianReader
- gaussians - Variable in class org.jmol.adapter.readers.quantum.MOReader
- gaussians - Variable in class org.jmol.quantum.MOCalculation
- GaussianWfnReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Gaussian Wfn files -- not implemented yet
- GaussianWfnReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianWfnReader
- GC - Static variable in class org.jmol.quantum.QS
- GC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- gdata - Variable in class org.jmol.export.___Exporter
- gdata - Variable in class org.jmol.export.Export3D
- gdata - Variable in class org.jmol.g3d.HermiteRenderer
- gdata - Variable in class org.jmol.viewer.Viewer
- GData - Class in org.jmol.util
- GData() - Constructor for class org.jmol.util.GData
-
It is possible to instantiate this class with no Graphics3D.
- generalResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- generateAllOperators(HallInfo) - Method in class org.jmol.symmetry.SpaceGroup
- generateBaseEllipsePrecisely(boolean) - Method in class org.jmol.g3d.CylinderRenderer
- generateColors(Object[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Set PyMOL "atom-wise" colors -- the colors that are defined initially as element colors but possibly set with the PyMOL 'color' command and are used when representation colors (cartoon, dots, etc.) are not defined (-1).
- generateContourData(boolean, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- generateCrystalClass(int, P3) - Method in class org.jmol.modelset.AtomCollection
- generateCrystalClass(P3) - Method in interface org.jmol.api.SymmetryInterface
- generateCrystalClass(P3) - Method in class org.jmol.symmetry.Symmetry
- generateCube() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
- generateCube() - Method in class org.jmol.jvxl.readers.IsoMepReader
- generateCube() - Method in class org.jmol.jvxl.readers.IsoMOReader
- generateCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
- generateCube() - Method in class org.jmol.jvxl.readers.VolumeDataReader
- generateOperatorsFromXyzInfo(String) - Method in class org.jmol.symmetry.SpaceGroup
- generateOutputForExport(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
-
for POV-Ray
- generateOutputForExport(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- generateRaster(int, int, int, int[], int[], int, Rgb16[]) - Method in class org.jmol.g3d.TriangleRenderer
- generateResidueSpecCode(T) - Method in class org.jmol.script.ScriptTokenParser
- generateRingData() - Method in class org.jmol.smiles.SmilesGenerator
-
get aromaticity, ringSets, and aromaticRings fields so that we can assign / and \ and also provide inter-aromatic single bond
- generateScene(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Generate the saved scene using file settings preserved here and scene-specific information including frame, view, colors, visibilities, .
- generateScene(Map<String, Object>) - Method in interface org.jmol.api.JmolSceneGenerator
- generateShapes(Object[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Create all Jmol shape objects.
- generateSolventCavity() - Method in class org.jmol.jvxl.readers.IsoSolventReader
- generateSolventCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
- generateSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- generateSurfaceData() - Method in class org.jmol.jvxl.readers.SurfaceReader
- generateVisibilities(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Hide everything, then just make visible the sets of atoms specified in the visibility (i.e.
- generic - Static variable in class org.jmol.adapter.readers.cif.MSRdr
- GenericApplet - Class in org.jmol.util
-
A collection of all methods necessary for initialization of and communication with the applet.
- GenericApplet() - Constructor for class org.jmol.util.GenericApplet
- GenericConsole - Class in org.jmol.console
- GenericConsole() - Constructor for class org.jmol.console.GenericConsole
- GenericConsoleTextArea - Interface in org.jmol.api.js
- GenericFileInterface - Interface in org.jmol.api
- GenericGraphics - Interface in org.jmol.api
- GenericImageDialog - Interface in org.jmol.api
- GenericMenuInterface - Interface in org.jmol.api
- GenericMouseInterface - Interface in org.jmol.api
- GenericPlatform - Interface in org.jmol.api
- GenericPopup - Class in org.jmol.popup
-
The overall parent of all popup classes in Jmol and JSmol.
- GenericPopup() - Constructor for class org.jmol.popup.GenericPopup
- GenericTextArea - Interface in org.jmol.console
- GenericTextPane() - Constructor for class org.jmol.console.AppletConsole.GenericTextPane
- GenNBOReader - Class in org.jmol.adapter.readers.quantum
-
NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold upgrade to NBO 6 allows reading of resonance structures, including base structure
- GenNBOReader() - Constructor for class org.jmol.adapter.readers.quantum.GenNBOReader
- Geodesic - Class in org.jmol.util
-
J2SRequireImport is needed because we use ArrayUtil in a static method
- Geodesic() - Constructor for class org.jmol.util.Geodesic
- geodesicCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
- geodesicMap - Variable in class org.jmol.geodesic.EnvelopeCalculation
- GEOM - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- GEOM_BOND_ATOM_SITE_LABEL_1 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- GEOM_BOND_ATOM_SITE_LABEL_2 - Static variable in class org.jmol.adapter.readers.cif.CifReader
- GEOM_BOND_DISTANCE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- geomBondFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
- geometry_export_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- geomOpt - Variable in class org.jmol.adapter.readers.xtal.DmolReader
- geosurface - Static variable in class org.jmol.script.T
- GeoSurface - Class in org.jmol.shapespecial
- GeoSurface() - Constructor for class org.jmol.shapespecial.GeoSurface
- GeoSurfaceRenderer - Class in org.jmol.renderspecial
- GeoSurfaceRenderer() - Constructor for class org.jmol.renderspecial.GeoSurfaceRenderer
- Gesture - Class in org.jmol.viewer
- Gesture(int, Viewer) - Constructor for class org.jmol.viewer.Gesture
- gestureServer - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- gestureswipefactor - Static variable in class org.jmol.script.T
- gestureSwipeFactor - Variable in class org.jmol.viewer.ActionManager
- get(int) - Method in class org.jmol.util.Int2IntHash
- get(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- GET - Static variable in class org.jmol.modelkit.ModelKit
- GET_CREATE - Static variable in class org.jmol.modelkit.ModelKit
- GET_DELETE - Static variable in class org.jmol.modelkit.ModelKit
- get1(int) - Static method in class org.jmol.awtjs.swing.Color
- get2SidedNormix(V3, BS) - Static method in class org.jmol.util.Normix
- get3(int, int, int) - Method in class org.jmol.awt.AwtColor
- get3(int, int, int) - Static method in class org.jmol.awtjs.swing.Color
- get3dContour(IsosurfaceMesh, Lst<Object>, float, short) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
- get3DStraightness(String, Quat, Quat) - Static method in class org.jmol.modelsetbio.BioExt
- get4(int, int, int, int) - Method in class org.jmol.awt.AwtColor
- get4(int, int, int, int) - Static method in class org.jmol.awtjs.swing.Color
- getACDPeakWidth(String) - Method in class org.jmol.jsv.JDXMOLParser
- getACFValue(float) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Fetch the action that was created for the given command.
- getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- getActionCommand() - Method in interface org.jmol.api.SC
- getActionCommand() - Method in class org.jmol.awt.AwtSwingComponent
- getActionCommand() - Method in class org.jmol.awtjs.swing.JComponent
- getActionFromName(String) - Static method in class org.jmol.viewer.ActionManager
- getActionName(int) - Static method in class org.jmol.viewer.ActionManager
- getActiveMenu() - Method in class org.jmol.modelkit.ModelKit
-
for the thin box on the top left of the window
- getAdditionalHydrogens(BS, Lst<Atom>, int) - Method in class org.jmol.viewer.Viewer
- getADPMinMax(boolean) - Method in class org.jmol.modelset.Atom
- getAlignment(int) - Static method in class org.jmol.viewer.JC
- getAllAtomInfo(BS) - Method in class org.jmol.viewer.PropertyManager
- getAllAtoms() - Method in class org.jmol.viewer.Viewer
- getAllAtomTensors(String) - Method in class org.jmol.modelset.AtomCollection
- getAllAxes(V3) - Method in class org.jmol.symmetry.PointGroup
- getAllBasePairBits(String) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllBondInfo(Object) - Method in class org.jmol.viewer.PropertyManager
- getAllChainInfo(BS) - Method in class org.jmol.viewer.PropertyManager
- getAllChimeInfo(SB) - Method in class org.jmol.viewer.ChimeMessenger
- getAllChimeInfo(SB) - Method in interface org.jmol.viewer.JmolChimeMessenger
- getAllDefaultStructures(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getAlleneAtoms(boolean, SmilesAtom, SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
- getAllHeteroList(int) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllInfo() - Method in class org.jmol.shape.Measures
- getAllInfoAsString() - Method in class org.jmol.shape.Measures
- getAllMolecularDipoles(BS) - Method in class org.jmol.shapespecial.Dipoles
- getAllMolecules() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getAllOperators() - Method in class org.jmol.modelkit.ModelKit
- getAllowedGestures(int) - Method in class org.jmol.multitouch.ActionManagerMT
- getAllowedGestures(int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
- getAllowedGestures(int) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- getAllowJSThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
- getAllowJSThreads() - Method in class org.jmol.script.ScriptEval
- getAllPoints(int, int) - Method in class org.jmol.scriptext.ScriptExt
- getAllPolymerInfo(BS) - Method in class org.jmol.viewer.PropertyManager
- getAllPolymerInfo(BS, Map<String, Lst<Map<String, Object>>>) - Method in class org.jmol.modelsetbio.BioExt
- getAllPolymerInfo(BS, Map<String, Lst<Map<String, Object>>>) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllProperties(SV, String) - Method in class org.jmol.script.ScriptMathProcessor
- getAllredRochowElectroNeg(int) - Static method in class org.jmol.util.Elements
- getAllRenderers() - Method in class org.jmol.render.RepaintManager
- getAllSequenceBits(String, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllSettings(String) - Method in class org.jmol.viewer.JmolStateCreator
- getAllSettings(String) - Method in class org.jmol.viewer.StateCreator
- getAllSettings(String) - Method in class org.jmol.viewer.Viewer
- getAllStructures(String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
- getAllUnitIds(String, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getAllVariables() - Method in class org.jmol.viewer.GlobalSettings
- getAllZipData(InputStream, String[], String, String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
-
reads a ZIP file and saves all data in a Hashtable so that the files may be organized later in a different order.
- getAlphasAndExponents() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- getAltLoc() - Method in class org.jmol.adapter.smarter.AtomIterator
- getAltLoc() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getAltLocCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getAltLocIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
- getAltLocListInModel(int) - Method in class org.jmol.modelset.ModelSet
- getAmbientPercent() - Method in class org.jmol.util.GData
- getAmino() - Method in class org.jmol.util.ColorEncoder
- getAminoAcidValenceAndCharge(String, String, int[]) - Method in class org.jmol.modelsetbio.BioExt
-
returns an array if we have special hybridization or charge
- getAminoAcidValenceAndCharge(String, String, int[]) - Method in class org.jmol.modelsetbio.BioModelSet
- getAndCheckValue(Map<String, Object>, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
- getAndCheckValue(Map<String, Object>, String) - Method in class org.jmol.util.JSONWriter
- getAndRegisterPlugin(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getAndSetNewVariable(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
- getAnglefromZ() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getAngleRadiansABC(double[], double[], double[]) - Static method in class org.jmol.minimize.Util
- getAngles() - Method in class org.jmol.minimize.Minimizer
- getAngleUnits() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getAngleUnitsList() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getAnimationInfo() - Method in class org.jmol.viewer.PropertyManager
- getAnimRunTimeSeconds() - Method in class org.jmol.viewer.AnimationManager
- getAnimState(AnimationManager, SB) - Method in class org.jmol.viewer.StateCreator
- getAnnotationBits(String, int, String) - Method in class org.jmol.modelsetbio.BioModelSet
- getAnnotationInfo(Object, int) - Method in class org.jmol.viewer.PropertyManager
- getAnnotationInfo(SV, String, int) - Method in class org.jmol.viewer.Viewer
- getAnnotationInfo(Viewer, SV, String, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
- getAnnotationInfo(Viewer, SV, String, int, int) - Method in class org.jmol.dssx.AnnotationParser
-
Get a string report of annotation data
- getAnnotationKVPairs(SV, String, String, SB, String, boolean, boolean, int) - Method in class org.jmol.dssx.AnnotationParser
-
Construct a nice listing for this annotation, including validation
- getAnnotationParser(boolean) - Method in class org.jmol.viewer.Viewer
- getAppletDefs(int, String, StringBuilder, JmolInstance) - Method in class org.openscience.jmol.app.webexport.PopInJmol
- getAppletDefs(int, String, StringBuilder, JmolInstance) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
- getAppletDefs(int, String, StringBuilder, JmolInstance) - Method in class org.openscience.jmol.app.webexport.WebPanel
- getAppletDocumentBase() - Method in class org.jmol.viewer.FileManager
- getAppletInfo() - Method in interface org.jmol.api.JmolAppletInterface
- getAppletInfo() - Method in class org.jmol.util.GenericApplet
- getAppletInfo() - Method in class org.jmol.viewer.PropertyManager
- getAppletPath(boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
- getAppropriateRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
- getArgb() - Method in class org.jmol.util.Rgb16
- getArgb(float) - Method in class org.jmol.util.ColorEncoder
- getArgb(short) - Static method in class org.jmol.util.C
- getArgbFromPalette(float, float, float, int) - Method in class org.jmol.util.ColorEncoder
- getArgbGreyscale(short) - Static method in class org.jmol.util.C
- getArgbHbondType(int) - Static method in class org.jmol.util.Edge
- getArgbMinMax(float, float, float) - Method in class org.jmol.util.ColorEncoder
- getArgbParam(int) - Method in class org.jmol.script.ScriptParam
- getArgbParamLast(int, boolean) - Method in class org.jmol.script.ScriptParam
- getArgbParamOrNone(int, boolean) - Method in class org.jmol.script.ScriptParam
- getArgbs(int) - Method in class org.jmol.modelsetbio.BioResolver
- getArgbs(int) - Method in class org.jmol.viewer.ColorManager
- getArguments(String) - Method in class org.jmol.viewer.PropertyManager
- getAromatic - Variable in class org.jmol.smiles.SmilesGenerator
- getAromaticDottedBondMask() - Method in class org.jmol.render.SticksRenderer
- getArrayDepth(T) - Static method in class org.jmol.script.SV
- getArrayFromStringList(String, int) - Static method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
turn "[1,2,3]" into [1.0,2.0,3.0] array will be truncated to n elements, or filled with zeros to pad to n, as necessary.
- getArrowScale() - Method in class org.jmol.renderspecial.DrawRenderer
- getAscent() - Method in class org.jmol.util.Font
- getAscent(Object) - Static method in class org.jmol.awt.AwtFont
- getAscent(Object) - Static method in class org.jmol.awtjs2d.JSFont
- getAsciiFileOrNull(String) - Method in class org.jmol.viewer.Viewer
- getAssocArray(int) - Method in class org.jmol.script.ScriptExpr
- getAssociatedNodeByIdx(int) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Find the node for this TAtom.
- getAssoiatedLinkByIdx(int) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Find the link for this TAtom.
- getAtom() - Method in class org.jmol.adapter.readers.simple.InputReader
- getAtom() - Method in class org.jmol.symmetry.UnitCellIterator
- getAtom(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getAtom(int) - Method in class org.jmol.modelset.AtomCollection
- getAtom(int) - Method in class org.jmol.modelset.Bond
- getAtom(int) - Method in class org.jmol.modelset.Measurement
- getAtom(int) - Method in class org.jmol.smiles.SmilesBond
- getAtom(int) - Method in interface org.jmol.util.SimpleEdge
-
Get the respective atom, 0 or 1
- getAtom(SymmetryInterface, int, int, T3) - Method in class org.jmol.symmetry.SymmetryDesc
- getAtom1() - Method in class org.jmol.smiles.SmilesBond
- getAtomAndStateCount(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Look through all named objects for molecules, counting atoms and also states; see if trajectories are compatible (experimental).
- getAtomAt(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getAtomBits(int, Object) - Method in class org.jmol.script.ScriptExpr
- getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in interface org.jmol.api.JmolAnnotationParser
- getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in class org.jmol.dssx.AnnotationParser
- getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in class org.jmol.dssx.DSSR1
- getAtomBitsBS(int, BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getAtomBitSet(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
- getAtomBitSet(Object) - Method in class org.jmol.script.ScriptEval
-
A general method to evaluate a string representing an atom set.
- getAtomBitSet(Object) - Method in class org.jmol.viewer.Viewer
- getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in interface org.jmol.api.JmolScriptManager
- getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in class org.jmol.script.ScriptManager
- getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in class org.jmol.viewer.Viewer
- getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.ModelSet
- getAtomBitsMDa(int, Object, BS) - Method in class org.jmol.modelset.AtomCollection
-
general unqualified lookup of atom set type
- getAtomBitsMDb(int, Object) - Method in class org.jmol.modelset.BondCollection
- getAtomBitsStr(int, String, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getAtomBondChirality(SimpleNode, Lst<int[]>, BS) - Method in class org.jmol.symmetry.CIPChirality
-
Get E/Z characteristics for specific atoms.
- getAtomChiralityLimited(SimpleNode, CIPChirality.CIPAtom, SimpleNode) - Method in class org.jmol.symmetry.CIPChirality
-
Determine R/S or one half of E/Z determination
- getAtomCIPChiralityCode(Atom) - Method in class org.jmol.modelset.ModelSet
-
Determine the Cahn-Ingold-Prelog R/S chirality of an atom
- getAtomCollectionReader(String, String, Object, Map<String, Object>, int) - Static method in class org.jmol.adapter.smarter.Resolver
-
the main method for reading files.
- getAtomCount() - Method in class org.jmol.modelset.ModelLoader
- getAtomCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the estimated number of atoms contained in the file.
- getAtomCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getAtomData(String, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getAtomData(String, String, boolean) - Method in class org.jmol.viewer.PropertyManager
-
use lower case to indicate coord data only (xyz, xyzrn, xyzvib, pdb.
- getAtomDefs(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- getAtomFromName(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- getAtomFromName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomFromNameCheckCase(String) - Method in class org.jmol.adapter.readers.cif.CifReader
-
From GEOM_BOND, check first for an exact match.
- getAtomFromOffsetIndex(int) - Method in class org.jmol.modelsetbio.Monomer
- getAtomGeneral(Atom, int, int) - Method in class org.jmol.adapter.readers.simple.InputReader
- getAtomGroupQuaternions(BS, int) - Method in class org.jmol.viewer.Viewer
- getAtomGroupQuaternions(BS, int, char) - Method in class org.jmol.modelset.ModelSet
- getAtomicAndIsotopeNumber() - Method in class org.jmol.modelset.Atom
- getAtomicAndIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
- getAtomicAndIsotopeNumber() - Method in interface org.jmol.util.Node
- getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
- getAtomicCharges() - Method in class org.jmol.modelset.AtomCollection
- getAtomicDSSRData(float[], String) - Method in class org.jmol.modelsetbio.BioModel
- getAtomicDSSRData(int) - Method in class org.jmol.modelset.ModelSet
- getAtomicDSSRData(ModelSet, int, float[], String) - Method in interface org.jmol.api.JmolAnnotationParser
- getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.AnnotationParser
- getAtomicDSSRData(ModelSet, int, float[], String) - Method in class org.jmol.dssx.DSSR1
- getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the atomic mass of the atom.
- getAtomicMass(int) - Static method in class org.jmol.util.Elements
- getAtomicNumber(String) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- getAtomicPotentials(String, String) - Method in class org.jmol.quantum.MepCalculation
- getAtomicPotentials(BS, BS, String) - Method in class org.jmol.scriptext.IsoExt
- getAtomicPropertyState(int, BS) - Method in class org.jmol.viewer.JmolStateCreator
- getAtomicPropertyState(int, BS) - Method in class org.jmol.viewer.StateCreator
- getAtomicPropertyState(SB, byte, BS, String, float[]) - Method in class org.jmol.viewer.Viewer
- getAtomicPropertyStateBuffer(SB, int, BS, String, float[]) - Method in class org.jmol.viewer.JmolStateCreator
- getAtomicPropertyStateBuffer(SB, int, BS, String, float[]) - Method in class org.jmol.viewer.StateCreator
- getAtomIdentityInfo(int, Map<String, Object>, P3) - Method in class org.jmol.modelset.AtomCollection
- getAtomIndex(int) - Method in class org.jmol.adapter.readers.simple.InputReader
- getAtomIndex(int) - Method in class org.jmol.modelset.Measurement
- getAtomIndex(String) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
- getAtomIndex(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- getAtomIndex(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomIndex(String, int) - Method in class org.jmol.modelset.Group
- getAtomIndex(String, int) - Method in class org.jmol.modelsetbio.Monomer
- getAtomIndex1() - Method in class org.jmol.modelset.Bond
- getAtomIndex1() - Method in class org.jmol.smiles.SmilesBond
- getAtomIndex1() - Method in class org.jmol.util.Edge
- getAtomIndex2() - Method in class org.jmol.modelset.Bond
- getAtomIndex2() - Method in class org.jmol.smiles.SmilesBond
- getAtomIndex2() - Method in class org.jmol.util.Edge
- getAtomIndexFromPrimitiveIndex(int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
Get the atom index from a primitive index.
- getAtomIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
- getAtomIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getAtomIndices(BS) - Method in class org.jmol.modelset.AtomCollection
- getAtomInfo(int) - Method in class org.jmol.viewer.Viewer
- getAtomInfo(int, String, P3) - Method in class org.jmol.modelset.AtomCollection
- getAtomInfoLong(int, P3, SymmetryInterface) - Method in class org.jmol.viewer.PropertyManager
- getAtomInfoXYZ(int, int) - Method in class org.jmol.viewer.Viewer
- getAtomIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomIterator(Object) - Method in class org.jmol.api.JmolAdapter
-
Get an AtomIterator for retrieval of all atoms in the file.
- getAtomLabel(int, int, int, int, float, int, boolean, String, boolean) - Static method in class org.jmol.smiles.SmilesAtom
-
called from SmilesGenerator
- getAtomList(String) - Method in class org.jmol.minimize.forcefield.Calculations
- getAtomList(String) - Method in class org.jmol.minimize.forcefield.ForceField
- getAtomMinMax(BS, BS[]) - Method in class org.jmol.jvxl.readers.AtomDataReader
- getAtomName() - Method in class org.jmol.adapter.smarter.AtomIterator
- getAtomName() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getAtomName() - Method in class org.jmol.modelset.Atom
- getAtomName() - Method in class org.jmol.smiles.SmilesAtom
- getAtomName() - Method in interface org.jmol.util.Node
- getAtomName() - Method in interface org.jmol.util.SimpleNode
- getAtomName(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getAtomName(String, String) - Static method in class org.jmol.adapter.readers.xtal.MagresReader
-
combine name and index
- getAtomNames() - Method in class org.jmol.adapter.readers.more.MdTopReader
- getAtomNumber() - Method in class org.jmol.modelset.Atom
- getAtomNumber() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the Jmol atom number
- getAtomNumber() - Method in interface org.jmol.util.Node
- getAtomNumber(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getAtomParity(Atom) - Method in class org.jmol.adapter.writers.MOLWriter
- getAtomPickingMode() - Method in class org.jmol.viewer.ActionManager
- getAtomPoint(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getAtomPointVector(BS) - Method in class org.jmol.modelset.AtomCollection
- getAtomPropertiesLike(String) - Static method in class org.jmol.script.T
- getAtomPropertyAsString(Atom, int) - Method in class org.jmol.adapter.writers.MOLWriter
- getAtomR0(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getAtomRecordMOL(int, ModelSet, SB, int, Atom, Quat, P3, boolean, boolean, SB, int, boolean) - Method in class org.jmol.adapter.writers.MOLWriter
- getAtomResidueInfo(SB, Atom) - Static method in class org.jmol.viewer.PropertyManager
- getAtoms(int, Object) - Method in class org.jmol.modelset.ModelSet
-
general lookup for integer type -- from Eval
- getAtoms(String) - Method in interface org.jmol.api.SmilesMatcherInterface
- getAtoms(String) - Method in class org.jmol.smiles.SmilesMatcher
- getAtoms(BS, boolean, boolean, boolean, boolean, boolean, boolean, float, M4) - Method in class org.jmol.jvxl.readers.AtomDataReader
- getAtomsConnected(float, float, int, BS) - Method in class org.jmol.modelset.BondCollection
- getAtomSetAtomCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetAtomIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetAuxiliaryInfo(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.api.JmolAdapter
-
Get the auxiliary information for a particular atomSet.
- getAtomSetAuxiliaryInfoValue(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetBondCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetCenter(BS) - Method in class org.jmol.modelset.ModelSet
- getAtomSetCollection() - Method in interface org.jmol.api.JmolFilesReaderInterface
- getAtomSetCollection() - Method in class org.jmol.io.FileReader
- getAtomSetCollection() - Method in class org.jmol.io.FilesReader
- getAtomSetCollection(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
Create the AtomSetCollection and return it
- getAtomSetCollection(Object) - Method in class org.jmol.api.JmolAdapter
- getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the auxiliary information for this atomSetCollection.
- getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
Direct DOM HTML4 page reading; Egon was interested in this at one point.
- getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
- getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
- getAtomSetCollectionFromReaderType(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
-
all in one -- for TestSmarterJmolAdapter
- getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]
- getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
- getAtomSetCollectionName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCollectionName(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the name of the atom set collection, if known.
- getAtomSetCollectionOrBufferedReaderFromZip(Viewer, InputStream, String, String[], Map<String, Object>, int, boolean) - Method in class org.jmol.io.JmolUtil
-
A rather complicated means of reading a ZIP file, which could be a single file, or it could be a manifest-organized file, or it could be a Spartan directory.
- getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
-
Read an atomSetCollection object from a bufferedReader and close the reader.
- getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
primary for String[] or File[] reading -- two options are implemented --- return a set of simultaneously open readers, or return one single collection using a single reader
- getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.api.JmolAdapter
-
Associate an atomSetCollection object with an array of BufferedReader.
- getAtomSetCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetCount(Object) - Method in class org.jmol.api.JmolAdapter
-
Get number of atomSets in the file.
- getAtomSetIndex() - Method in class org.jmol.adapter.smarter.AtomIterator
- getAtomSetIndex() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getAtomSetIndex() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
- getAtomSetName(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetName(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetName(Object, int) - Method in class org.jmol.api.JmolAdapter
-
Get the name of an atomSet.
- getAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getAtomSetNumber(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getAtomSetNumber(Object, int) - Method in class org.jmol.api.JmolAdapter
-
Get the number identifying each atomSet.
- getAtomsFromAtomNumberInFrame(int) - Method in class org.jmol.modelset.AtomCollection
- getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.JmolStateCreator
- getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.StateCreator
- getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.ShapeManager
- getAtomsInFrame(BS) - Method in class org.jmol.modelset.AtomCollection
- getAtomSite() - Method in class org.jmol.adapter.smarter.AtomIterator
- getAtomSite() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getAtomSite() - Method in class org.jmol.modelset.Atom
- getAtomSite() - Method in class org.jmol.smiles.SmilesAtom
- getAtomSite() - Method in interface org.jmol.util.Node
- getAtomSiteBase(BS) - Method in class org.jmol.modelset.ModelLoader
- getAtomSiteBS(BS) - Method in class org.jmol.quantum.NMRCalculation
-
Interaction tensors are not repeated for every possible combination.
- getAtomsNearPlane(float, P4) - Method in class org.jmol.modelset.AtomCollection
- getAtomsNearPt(float, P3, BS) - Method in class org.jmol.viewer.Viewer
- getAtomsNearPts(float, T3[], BS) - Method in class org.jmol.scriptext.MathExt
- getAtomsNearSurface(float, String) - Method in class org.jmol.scriptext.MathExt
- getAtomsStartingAt(int) - Method in class org.jmol.script.ScriptParam
- getAtomsWithin(float, T3, BS, int) - Method in class org.jmol.modelset.ModelSet
- getAtomsWithin(Polyhedron, float) - Method in class org.jmol.shapespecial.Polyhedra
- getAtomsWithinRadius(float, BS, boolean, RadiusData, BS) - Method in class org.jmol.modelset.ModelSet
-
Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms
- getAtomSymmetry(Atom, SymmetryInterface) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
When applying symmetry, this method allows us to use a set of symmetry operators unique to this particular atom -- or in this case, to its subsystem.
- getAtomSymmetry(Atom, SymmetryInterface) - Method in interface org.jmol.adapter.smarter.MSInterface
- getAtomTensor(int, String) - Method in class org.jmol.modelset.AtomCollection
- getAtomTensorList(int) - Method in class org.jmol.modelset.AtomCollection
- getAtomType() - Method in class org.jmol.modelset.Atom
- getAtomType() - Method in class org.jmol.smiles.SmilesAtom
- getAtomType() - Method in interface org.jmol.util.Node
- getAtomTypeDescriptions() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getAtomTypeDescs(int[]) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getAtomTypes() - Method in class org.jmol.adapter.readers.more.MdTopReader
- getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
- getAtomTypes() - Method in class org.jmol.modelset.AtomCollection
- getAtomUniqueID1() - Method in class org.jmol.adapter.smarter.BondIterator
- getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapterBondIterator
- getAtomUniqueID2() - Method in class org.jmol.adapter.smarter.BondIterator
- getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapterBondIterator
- getAtomValidation(String, Atom) - Method in class org.jmol.viewer.Viewer
- getAtomValidation(Viewer, String, Atom) - Method in interface org.jmol.api.JmolAnnotationParser
- getAtomValidation(Viewer, String, Atom) - Method in class org.jmol.dssx.AnnotationParser
-
Get all validation values corresponding to a specific validation type.
- getAtropicStereoFlag(Node[]) - Static method in class org.jmol.smiles.SmilesStereo
- getAtropIndex(SmilesBond) - Method in class org.jmol.smiles.SmilesSearch
- getAtropismCode(int) - Static method in class org.jmol.util.Edge
- getAtropismNode(int, Node, boolean) - Static method in class org.jmol.util.Edge
- getAtropismOrder(int, int) - Static method in class org.jmol.util.Edge
- getAtropismOrder12(int) - Static method in class org.jmol.util.Edge
- getAtropisomerKeys(String, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
-
called by SmilesParser to get nn in ^nn- base on match to actual structure
- getAttached(Atom, int, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
- getAttachedAtomForPDBH(String, String) - Method in class org.jmol.dssx.AnnotationParser
-
Finds the standard attached heavy atom for a PDB H atom; used in EBI clash validation.
- getAttr(String, String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- getAttribute(String, String) - Method in interface org.jmol.api.JmolJDXMOLParser
- getAttribute(String, String) - Method in class org.jmol.jsv.JDXMOLParser
- getAuxEneEndWinner(CIPChirality.CIPAtom, CIPChirality.CIPAtom, int[]) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Get the atom that is the highest priority of two atoms on the end of a double bond after sorting from Rule 1a through a given rule (Rule 3 or Rule 5)
- getAuxEneWinnerChirality(CIPChirality.CIPAtom, CIPChirality.CIPAtom, boolean, int[]) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Determine the winner on one end of an alkene or cumulene and return also the rule by which that was determined.
- getAuxiliaryData(int, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
- getAuxiliaryFileData() - Method in class org.jmol.export._IdtfExporter
- getAuxiliaryFileData() - Method in class org.jmol.export._PovrayExporter
- getAuxiliaryInfo(BS) - Method in class org.jmol.modelset.ModelSet
-
Retrieve the main modelset info Hashtable (or a new non-null Hashtable) with an up-to-date "models" key.
- getAuxiliaryInfoForAtoms(Object) - Method in class org.jmol.viewer.Viewer
- getAverageAtomPoint() - Method in class org.jmol.modelset.ModelSet
- getAxesState(SB) - Method in class org.jmol.shape.Axes
- getAxesState(Axes) - Method in class org.jmol.viewer.StateCreator
- getAxisEndPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
- getAxisPoint(int, boolean, P3) - Method in class org.jmol.shape.Axes
-
get actual point or 1/2 vector from origin to this point
- getAxisStartPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
- getAzacyclic() - Method in class org.jmol.symmetry.CIPData
-
Identify bridgehead nitrogens, as these may need to be given chirality designations.
- getBackgroundArgb() - Method in class org.jmol.api.JmolViewer
- getBackgroundArgb() - Method in class org.jmol.viewer.Viewer
- getBaseModelBitSet() - Method in class org.jmol.viewer.Viewer
- getBaseModelIndex(int) - Method in interface org.jmol.api.JmolJSpecView
- getBaseModelIndex(int) - Method in class org.jmol.jsv.JSpecView
- getBasePairInfo(BS) - Method in class org.jmol.viewer.PropertyManager
- getBasePairs() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getBasePairs(Viewer, int) - Method in interface org.jmol.api.JmolAnnotationParser
- getBasePairs(Viewer, int) - Method in class org.jmol.dssx.AnnotationParser
- getBasePairs(Viewer, int) - Method in class org.jmol.dssx.DSSR1
- getBaseRing6Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getBaseSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
-
Get the symmetry that was in place prior to any supercell business
- getBasisAtom(int) - Method in class org.jmol.modelset.ModelSet
- getBBoxVertices() - Method in class org.jmol.modelset.ModelSet
- getBetter4bList() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Create Mata-style linear atom.listRS and return the better of R-ref or S-ref.
- getBfactor() - Method in class org.jmol.adapter.smarter.AtomIterator
- getBfactor() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getBfactor100() - Method in class org.jmol.modelset.Atom
- getBfactor100Hi() - Method in class org.jmol.modelset.AtomCollection
- getBfactor100Lo() - Method in class org.jmol.modelset.AtomCollection
- getBFactors() - Method in class org.jmol.modelset.AtomCollection
- getBgContrast(int) - Static method in class org.jmol.util.C
- getBinaryType(InputStream) - Static method in class org.jmol.adapter.smarter.Resolver
- getBindingInfo(String) - Method in class org.jmol.viewer.ActionManager
- getBindingInfo(String) - Method in class org.jmol.viewer.Viewer
- getBindingInfo(String[], String[], String) - Method in class org.jmol.viewer.binding.Binding
- getBindings() - Method in class org.jmol.viewer.binding.Binding
- getBioBranches(Lst<BS>) - Method in class org.jmol.modelsetbio.BioModel
- getBioExt() - Method in class org.jmol.modelsetbio.BioModelSet
- getBioModel(int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelsetbio.BioResolver
- getBioModelSet(ModelSet) - Method in class org.jmol.modelsetbio.BioResolver
- getBioPolymerCount() - Method in class org.jmol.modelsetbio.BioModel
- getBioPolymerCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getBioPolymerCountInModel(int) - Method in class org.jmol.modelsetbio.BioModelSet
- getBioPolymerIndexInModel() - Method in class org.jmol.modelset.Group
- getBioPolymerIndexInModel() - Method in class org.jmol.modelsetbio.Monomer
- getBioPolymerLength() - Method in class org.jmol.modelset.Group
- getBioPolymerLength() - Method in class org.jmol.modelsetbio.Monomer
- getBioShape(int) - Method in class org.jmol.shapebio.BioShapeCollection
- getBioShapeState(String, boolean, Map<String, BS>, Map<String, BS>) - Method in class org.jmol.shapebio.BioShape
- getBioSmiles(BS) - Method in class org.jmol.viewer.Viewer
- getBioSmiles(BS, String, int) - Method in class org.jmol.smiles.SmilesGenerator
- getBioSmilesType() - Method in class org.jmol.modelset.Atom
- getBioSmilesType() - Method in class org.jmol.smiles.SmilesAtom
- getBioSmilesType() - Method in interface org.jmol.util.Node
- getBioStructureTypeName() - Method in class org.jmol.modelset.Atom
- getBioStructureTypeName() - Method in class org.jmol.smiles.SmilesAtom
- getBioStructureTypeName() - Method in interface org.jmol.util.Node
- getBioStructureTypeName(boolean) - Method in enum org.jmol.c.STR
- getBitSet(SV, boolean) - Static method in class org.jmol.script.SV
- getBitSetForMF(Atom[], BS, String) - Static method in class org.jmol.util.JmolMolecule
- getBitsetIdent(BS, String, Object, boolean, int, boolean) - Method in class org.jmol.scriptext.CmdExt
- getBitsetIdentFull(BS, String, Object, boolean, int, boolean, String[]) - Method in class org.jmol.scriptext.CmdExt
- getBitsetProperty(BS, Lst<SV>, int, P3, P4, Object, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptExpr
- getBitsetPropertyFloat(BS, int, String, float, float) - Method in class org.jmol.scriptext.CmdExt
- getBitsetPropertySelector(int, int) - Method in class org.jmol.script.ScriptExpr
- getBitSetTrajectories() - Method in class org.jmol.modelset.ModelSet
- getBlock(String, String) - Method in class org.jmol.adapter.readers.quantum.NBOParser
- getBond(int) - Method in class org.jmol.smiles.SmilesAtom
-
Returns the bond at index
number
. - getBond(Atom) - Method in class org.jmol.modelset.Atom
- getBondChiralityLimited(SimpleEdge, SimpleNode) - Method in class org.jmol.symmetry.CIPChirality
-
Determine the axial or E/Z chirality for this bond, with the given starting atom a
- getBondColix1(int) - Method in class org.jmol.modelset.BondCollection
- getBondColix2(int) - Method in class org.jmol.modelset.BondCollection
- getBondCount() - Method in class org.jmol.modelset.Atom
- getBondCount() - Method in class org.jmol.modelset.Model
- getBondCount() - Method in class org.jmol.smiles.SmilesAtom
- getBondCount() - Method in interface org.jmol.util.SimpleNode
-
Get the total number of bonds, including hydrogen bonds.
- getBondCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getBondCountInModel(int) - Method in class org.jmol.modelset.BondCollection
-
for general use
- getBondCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getBondDipoles() - Method in class org.jmol.shapespecial.Dipoles
- getBondedAtomIndex(int) - Method in class org.jmol.modelset.Atom
- getBondedAtomIndex(int) - Method in class org.jmol.smiles.SmilesAtom
- getBondedAtomIndex(int) - Method in interface org.jmol.util.Node
- getBondedAtomIndexes() - Method in class org.jmol.minimize.MinAtom
- getBondIndex(int) - Method in class org.jmol.minimize.MinAtom
- getBondInfo(int, P3) - Method in class org.jmol.viewer.PropertyManager
- getBondInfo(JmolAdapter, String, Object) - Method in class org.jmol.modelsetbio.BioResolver
- getBondingRadFromTable(int, int, short[]) - Static method in class org.jmol.util.Elements
- getBondingRadii() - Method in class org.jmol.modelset.AtomCollection
- getBondingRadius() - Method in class org.jmol.modelset.Atom
- getBondingRadius(int, int) - Static method in class org.jmol.api.JmolAdapter
- getBondingRadius(int, int) - Static method in class org.jmol.util.Elements
-
This method is used by: (1) the CIF reader to create molecular systems when no bonding information is present (2) Atom.getBondingRadiusFloat, used by AtomCollection.findMaxRadii and getWorkingRadius, BondCollection.deleteConnections, ModelCollection.autoBond and makeConnections (3) the MMFF minimizer for unidentified atoms In terms of bondingVersion, the critical ones are the first two.
- getBondIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getBondIterator(Object) - Method in class org.jmol.api.JmolAdapter
-
Get a BondIterator for retrieval of all bonds in the file.
- getBondIterator(BS) - Method in class org.jmol.modelset.BondCollection
- getBondIteratorForType(int, BS) - Method in class org.jmol.modelset.BondCollection
- getBondLabel(Atom[]) - Method in class org.jmol.modelkit.ModelKit
- getBondLabelValues() - Static method in class org.jmol.modelset.LabelToken
- getBondList() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getBondList(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getBondList(Object) - Method in class org.jmol.api.JmolAdapter
- getBondList(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create the bond set.
- getBondNotTo(SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesAtom
- getBondOrder(String) - Method in class org.jmol.adapter.readers.cif.CifReader
- getBondOrder(Edge, int, int, boolean) - Method in class org.jmol.smiles.SmilesGenerator
- getBondOrder(SimpleEdge) - Method in class org.jmol.symmetry.CIPData
- getBondOrder(SimpleEdge) - Method in class org.jmol.symmetry.CIPDataSmiles
- getBondOrderFromFloat(float) - Static method in class org.jmol.util.Edge
- getBondOrderFromString(String) - Static method in class org.jmol.script.ScriptParam
- getBondOrderFromString(String) - Static method in class org.jmol.util.Edge
- getBondOrderNameFromOrder(int) - Static method in class org.jmol.util.Edge
- getBondOrderNumberFromOrder(int) - Static method in class org.jmol.util.Edge
-
used for formatting labels and in the connect PARTIAL command
- getBondOrderString(int) - Static method in class org.jmol.smiles.SmilesBond
- getBondPickingMode() - Method in class org.jmol.viewer.ActionManager
- getBondRadius() - Method in class org.jmol.adapter.smarter.AtomIterator
- getBondRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getBondRecordMOL(SB, int, Bond, int[], boolean, boolean, boolean) - Method in class org.jmol.adapter.writers.MOLWriter
- getBonds() - Method in class org.jmol.minimize.Minimizer
- getBondsForSelectedAtoms(BS) - Method in class org.jmol.viewer.Viewer
- getBondsForSelectedAtoms(BS, boolean) - Method in class org.jmol.modelset.BondCollection
- getBondsPickable() - Method in class org.jmol.viewer.Viewer
- getBondState(Sticks) - Method in class org.jmol.viewer.StateCreator
- getBondStereochemistry(Edge, SimpleNode) - Method in class org.jmol.smiles.SmilesGenerator
-
Retrieves the saved character based on the index of the bond.
- getBondTo(int) - Method in class org.jmol.minimize.MinAtom
- getBondTo(SmilesAtom) - Method in class org.jmol.smiles.SmilesAtom
-
if atom is null, return bond TO this atom (bond.atom2 == this) otherwise, return bond connecting this atom with that atom
- getBondType() - Method in class org.jmol.util.Edge
- getBondType() - Method in interface org.jmol.util.SimpleEdge
-
Get the order of the bond.
- getBondType(String, int) - Static method in class org.jmol.adapter.readers.cif.TopoCifParser
- getBondType(Bond, AtomType, AtomType, int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
-
Get the bond type: 1 biphenyl or 0 any other
- getBondTypeFromCode(char) - Static method in class org.jmol.smiles.SmilesBond
- getBoolean(boolean) - Static method in class org.jmol.script.SV
- getBoolean(int) - Method in class org.jmol.api.JmolViewer
- getBoolean(int) - Method in class org.jmol.viewer.Viewer
- getBoolean(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- getBooleanProperty(String) - Method in class org.jmol.api.JmolViewer
- getBooleanProperty(String) - Method in class org.jmol.viewer.Viewer
- getBooleanValue(String, boolean) - Method in class org.jmol.util.GenericApplet
- getBoolName(int) - Static method in class org.jmol.viewer.JC
- getBoundBox(SV) - Method in class org.jmol.script.ScriptMathProcessor
- getBoundBoxCenter() - Method in class org.jmol.api.JmolViewer
- getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
- getBoundBoxCenter() - Method in class org.jmol.viewer.Viewer
- getBoundBoxCenter(int) - Method in class org.jmol.modelset.ModelSet
- getBoundBoxCenterX() - Method in class org.jmol.viewer.Viewer
- getBoundBoxCenterY() - Method in class org.jmol.viewer.Viewer
- getBoundBoxCommand(boolean) - Method in class org.jmol.modelset.ModelSet
- getBoundBoxCornerVector() - Method in class org.jmol.api.JmolViewer
- getBoundBoxCornerVector() - Method in class org.jmol.modelset.ModelSet
- getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
- getBoundBoxCornerVector() - Method in class org.jmol.viewer.Viewer
- getBoundBoxInfo() - Method in class org.jmol.viewer.PropertyManager
- getBoundBoxOrientation(int, BS) - Method in class org.jmol.modelset.ModelSet
- getBoundBoxPoints(boolean) - Method in class org.jmol.util.BoxInfo
-
Return basic info on boundbox in the form of an array.
- getBoundBoxVertices() - Method in class org.jmol.util.BoxInfo
- getBoundingBox() - Method in class org.jmol.shape.Mesh
- getBoundingBox() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getBox(int) - Method in class org.jmol.shape.Labels
- getBoxFacesFromOABC(P3[]) - Method in class org.jmol.util.MeshSlicer
- getBoxInfo() - Method in class org.jmol.modelset.ModelSet
- getBoxInfo(BS, float) - Method in class org.jmol.modelset.ModelSet
- getBoxPoints(int, SymmetryInterface, BS, float) - Method in class org.jmol.scriptext.IsoExt
- getBoxVec() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getBranch2dZ(int, int, BS, BS, V3, V3, V3, int) - Method in class org.jmol.modelset.ModelLoader
- getBranchBitSet(int, int, boolean) - Method in class org.jmol.viewer.Viewer
-
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself,deliver the set of atoms constituting this branch.
- getBranchBitSet(Node[], int, BS, Lst<BS>, int, boolean, boolean) - Static method in class org.jmol.util.JmolMolecule
-
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself, deliver the set of atoms constituting this branch.
- getBranchesForInversion(Node[], int, BS) - Static method in class org.jmol.util.JmolMolecule
- getBreakableContext(int) - Method in class org.jmol.script.ScriptFlowContext
- getBrickValue(int) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
- getBridge(int[][][][], int, int, int, int, Lst<Bridge>, Atom, Atom, AminoPolymer, AminoPolymer, Map<String, Boolean>, boolean) - Method in class org.jmol.dssx.DSSP
- getBridges(int[][][][]) - Method in class org.jmol.dssx.DSSP
-
(p.
- getBS(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getBSAll() - Method in class org.jmol.adapter.smarter.StructureIterator
- getBSAll() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getBSAromaticRings() - Method in class org.jmol.smiles.SmilesSearch
- getBsAtoms(Lst<Object>, int[], BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getBsBranches(float[]) - Method in class org.jmol.modelset.ModelSet
- getBsOK() - Method in class org.jmol.quantum.NciCalculation
-
grid-based discrete SCF calculation needs to know which atoms to consider inter and which intramolecular
- getBsReps(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getBSSideChain() - Method in class org.jmol.modelset.Group
- getBSSideChain() - Method in class org.jmol.modelsetbio.AminoMonomer
- getBsSurfaceClone() - Method in interface org.jmol.api.JmolEnvCalc
- getBsSurfaceClone() - Method in class org.jmol.geodesic.EnvelopeCalculation
- getBufferedFileInputStream(String) - Method in interface org.jmol.api.GenericPlatform
- getBufferedFileInputStream(String) - Static method in class org.jmol.awt.AwtFile
- getBufferedFileInputStream(String) - Method in class org.jmol.awt.Platform
- getBufferedFileInputStream(String) - Method in class org.jmol.awtjs2d.Platform
- getBufferedInputStream(String) - Method in interface org.jmol.atomdata.AtomDataServer
- getBufferedInputStream(String) - Method in class org.jmol.viewer.FileManager
- getBufferedInputStream(String) - Method in class org.jmol.viewer.Viewer
- getBufferedInputStreamOrErrorMessageFromName(String, String, boolean, boolean, byte[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getBufferedReader(String) - Method in class org.jmol.minimize.forcefield.ForceField
- getBufferedReaderForResource(Viewer, Object, String, String) - Static method in class org.jmol.viewer.FileManager
- getBufferedReaderOrBinaryDocument(int, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
- getBufferedReaderOrBinaryDocument(int, boolean) - Method in class org.jmol.io.FilesReader
-
called by SmartJmolAdapter to request another buffered reader or binary document, rather than opening all the readers at once.
- getBufferedReaderOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
- getBufferedReaderOrErrorMessageFromName(String, String[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getBundle(String) - Method in class org.jmol.modelkit.ModelKitPopup
- getBundle(String) - Method in class org.jmol.popup.JmolGenericPopup
- getBundle(String) - Method in class org.jmol.popup.JmolPopup
- getButtonGroup() - Method in class org.jmol.awt.AwtPopupHelper
- getButtonGroup() - Method in class org.jmol.awtjs2d.JSPopupHelper
- getButtonGroup() - Method in interface org.jmol.popup.PopupHelper
- getButtonMods(int) - Static method in class org.jmol.viewer.binding.Binding
- getByteCount() - Method in class org.jmol.export.___Exporter
- getC1P() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getC2() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getC4P() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getC5() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getC6() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getC8() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getCachedAnnotationMap(String, Object) - Method in class org.jmol.modelsetbio.BioModel
- getCachedPngjBytes(String) - Method in class org.jmol.viewer.FileManager
- getCachedPngjBytes(FileManager, String) - Method in class org.jmol.io.JmolUtil
- getCalcType(Atom[], String[], int) - Static method in class org.jmol.quantum.NMRCalculation
- getCalcValue() - Method in class org.openscience.jmol.app.janocchio.Measure
- getCallback(String) - Static method in enum org.jmol.c.CBK
- getCameraDepth() - Method in class org.jmol.viewer.TransformManager
- getCameraFactors() - Method in class org.jmol.viewer.TransformManager
-
This method returns data needed by the VRML, X3D, and IDTF/U3D exporters.
- getCameraPosition() - Method in class org.jmol.export.__CartesianExporter
- getCanonicalCopy(float, boolean) - Method in interface org.jmol.api.SymmetryInterface
- getCanonicalCopy(float, boolean) - Method in class org.jmol.symmetry.Symmetry
- getCanonicalCopy(float, boolean) - Method in class org.jmol.symmetry.UnitCell
- getCanonicalCopy(P3[], float) - Static method in class org.jmol.util.BoxInfo
-
Change points references to canonical form used in Triangulator, while also scaling.
- getCanonicalName(String) - Method in class org.jmol.viewer.FileManager
- getCanonicalSeitz(int) - Static method in class org.jmol.symmetry.SpaceGroup
- getCanonicalSeitzList() - Method in class org.jmol.symmetry.SpaceGroup
- getCapOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getCapSlabInfo(String) - Method in class org.jmol.shapesurface.Isosurface
- getCapSlabObject(int, boolean) - Method in class org.jmol.scriptext.IsoExt
- getCapSlabObject(String, boolean) - Method in class org.jmol.shapesurface.Isosurface
-
legacy -- for some scripts with early isosurface slabbing
- getCarbonylCarbonAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
- getCarbonylOxygenAtom() - Method in class org.jmol.modelset.Group
- getCarbonylOxygenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
- getCaretPosition() - Method in interface org.jmol.api.js.GenericConsoleTextArea
- getCaretPosition() - Method in interface org.jmol.console.GenericTextArea
- getCartesianOffset() - Method in interface org.jmol.api.SymmetryInterface
- getCartesianOffset() - Method in class org.jmol.symmetry.Symmetry
- getCartesianOffset() - Method in class org.jmol.symmetry.UnitCell
- getCartoonType(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getCartoonType(int) - Method in interface org.jmol.api.PymolAtomReader
- getCel() - Method in class org.jmol.util.GData
- getCellProjection(P4, T3[]) - Method in class org.jmol.util.Triangulator
- getCellRange() - Method in interface org.jmol.api.SymmetryInterface
- getCellRange() - Method in class org.jmol.symmetry.Symmetry
- getCellStyle(int, int, GridBagConstraints) - Method in interface org.jmol.awtjs.swing.TableCellRenderer
- getCellTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
-
Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this
- getCellWeight(P3) - Static method in class org.jmol.util.SimpleUnitCell
-
calculate weighting of 1 (interior), 0.5 (face), 0.25 (edge), or 0.125 (vertex)
- getCellWeights(BS) - Method in class org.jmol.modelset.ModelSet
- getCelPower() - Method in class org.jmol.util.GData
- getCenter() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.modelset.ModelSet
- getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.viewer.Viewer
- getCentering() - Method in class org.jmol.symmetry.SymmetryOperation
-
assumption here is that these are in order of sets, as in ITA
- getCenters() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getCenterText() - Method in class org.jmol.modelkit.ModelKit
- getCenterText() - Method in class org.jmol.viewer.TransformManager
- getCEState(ColorEncoder, SB) - Method in class org.jmol.viewer.StateCreator
- getChain(int) - Method in class org.jmol.modelset.Model
- getChainAt(int) - Method in class org.jmol.modelset.Model
- getChainBits(int) - Method in class org.jmol.modelset.AtomCollection
- getChainCount(boolean) - Method in class org.jmol.modelset.Model
- getChainCountInModelWater(int, boolean) - Method in class org.jmol.modelset.ModelSet
- getChainID() - Method in class org.jmol.adapter.smarter.AtomIterator
- getChainID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getChainID() - Method in class org.jmol.modelset.Atom
- getChainID() - Method in class org.jmol.smiles.SmilesAtom
- getChainID() - Method in interface org.jmol.util.Node
- getChainID(String, boolean) - Method in class org.jmol.viewer.Viewer
-
Create a unique integer for any chain string.
- getChainIDStr() - Method in class org.jmol.modelset.Atom
- getChainIDStr() - Method in class org.jmol.smiles.SmilesAtom
- getChainIDStr() - Method in interface org.jmol.util.Node
- getChainIDStr(int) - Method in class org.jmol.viewer.Viewer
- getChainInfo(int, BS) - Method in class org.jmol.viewer.PropertyManager
- getChangeableColix(int, int) - Method in class org.jmol.util.GData
- getChangeableColixIndex(short) - Static method in class org.jmol.util.C
- getChangeableReader(Viewer, String, String) - Static method in class org.jmol.io.FileReader
- getChar(String, int) - Static method in class org.jmol.smiles.SmilesParser
- getCharge() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the charge of the atom.
- getCharges() - Method in class org.jmol.adapter.readers.more.MdTopReader
- getCheckBox(String) - Method in class org.jmol.awt.AwtPopupHelper
- getCheckBox(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getCheckBox(String) - Method in interface org.jmol.popup.PopupHelper
- getCheckBox(AwtPopupHelper, String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
- getChemicalInfo(String, String, BS) - Method in class org.jmol.viewer.Viewer
- getChemicalShift(Atom) - Method in interface org.jmol.api.JmolNMRInterface
-
If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shielding
- getChemicalShift(Atom) - Method in class org.jmol.quantum.NMRCalculation
- getChimeInfo(int) - Method in class org.jmol.viewer.Viewer
- getChimeInfo(int, BS) - Method in interface org.jmol.api.JmolPropertyManager
- getChimeInfo(int, BS) - Method in class org.jmol.viewer.PropertyManager
- getChimeInfoA(Atom[], int, BS) - Method in class org.jmol.viewer.PropertyManager
-
Get information in the style of Chime for SHOW selected|atoms|groups|group1| chains|residues|sequence
- getChimeMessenger() - Method in class org.jmol.viewer.Viewer
- getChiralClass() - Method in class org.jmol.smiles.SmilesAtom
- getChiralClass(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
- getChiralityClass(String) - Static method in class org.jmol.smiles.SmilesStereo
- getChiralityForAtoms(CIPData) - Method in class org.jmol.symmetry.CIPChirality
-
A general determination of chirality that involves ultimately all of Rules 1-6.
- getCifData(int) - Method in class org.jmol.viewer.Viewer
- getCifData(String, Object) - Method in class org.jmol.jvxl.readers.BCifDensityReader
- getCifData(String, Object) - Method in class org.jmol.jvxl.readers.CifDensityReader
- getCifDataParser() - Method in class org.jmol.adapter.readers.cif.Cif2Reader
- getCifDataParser() - Method in class org.jmol.adapter.readers.cif.CifReader
- getCifFloat(String) - Method in class org.jmol.jvxl.readers.BCifDensityReader
- getCifFloat(String) - Method in class org.jmol.jvxl.readers.CifDensityReader
- getCifMap(String) - Method in class org.jmol.jvxl.readers.BCifDensityReader
- getCifMap(String) - Method in class org.jmol.jvxl.readers.CifDensityReader
- getCIPChirality(boolean) - Method in class org.jmol.modelset.Atom
-
Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlags
- getCIPChirality(boolean) - Method in class org.jmol.modelset.Bond
-
Not implemented.
- getCIPChirality(boolean) - Method in class org.jmol.smiles.SmilesAtom
- getCIPChirality(boolean) - Method in class org.jmol.util.Edge
- getCIPChirality(boolean) - Method in interface org.jmol.util.Node
- getCIPChirality(Viewer) - Method in class org.jmol.symmetry.Symmetry
- getCIPChiralityCode() - Method in class org.jmol.modelset.Atom
- getCIPChiralityCode() - Method in class org.jmol.smiles.SmilesAtom
- getCIPChiralityCode() - Method in interface org.jmol.util.Node
- getCIPChiralityCode(char) - Static method in class org.jmol.viewer.JC
- getCIPChiralityName(int) - Static method in class org.jmol.viewer.JC
- getCIPChiralityRule() - Method in class org.jmol.modelset.Atom
- getCIPRuleName(int) - Static method in class org.jmol.viewer.JC
- getCircleData() - Static method in class org.jmol.export.MeshData
-
Calculates the data (faces, vertices, normals) for a circle.
- getCircleResource() - Method in class org.jmol.export._IdtfExporter
- getClassifiedName(String, boolean) - Method in class org.jmol.viewer.FileManager
-
[0] and [2] may return same as [1] in the case of a local unsigned applet.
- getClickableSet(boolean) - Method in class org.jmol.modelset.AtomCollection
- getClickCount(int) - Static method in class org.jmol.viewer.binding.Binding
- getClip() - Method in class org.jmol.util.JmolAudio
- getClipboardText() - Method in class org.jmol.api.JmolViewer
- getClipboardText() - Static method in class org.jmol.awt.AwtClipboard
-
Get the String residing on the clipboard.
- getClipboardText() - Method in class org.jmol.viewer.OutputManager
- getClipboardText() - Method in class org.jmol.viewer.OutputManagerAwt
- getClipboardText() - Method in class org.jmol.viewer.OutputManagerJS
- getClipboardText() - Method in class org.jmol.viewer.Viewer
- getClone() - Method in class org.jmol.adapter.smarter.Atom
- getCmd(int) - Method in class org.jmol.shapesurface.Isosurface
- getCmdExt() - Method in class org.jmol.script.ScriptExpr
- getCmlBondOrder(int) - Static method in class org.jmol.util.Edge
- getCode() - Method in enum org.jmol.c.FIL
- getCodeFromName(String) - Static method in enum org.jmol.util.Edge.EnumBondOrder
- getColix() - Method in class org.jmol.adapter.smarter.BondIterator
- getColix() - Method in class org.jmol.api.JmolAdapterBondIterator
- getColix(boolean) - Method in class org.jmol.rendercgo.CGORenderer
- getColix(int) - Static method in class org.jmol.util.C
- getColix(int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getColix(short[], int, Atom) - Static method in class org.jmol.shape.Shape
- getColix2(int, Atom, boolean) - Method in class org.jmol.shape.Labels
- getColixA(short, byte, Atom) - Method in class org.jmol.shape.Shape
- getColixArray(String) - Static method in class org.jmol.util.C
- getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.ColorManager
- getColixB(short, int, Bond) - Method in class org.jmol.shape.Shape
- getColixBondPalette(Bond, int) - Method in class org.jmol.viewer.ColorManager
- getColixI(short, byte, int) - Method in class org.jmol.shape.Shape
- getColixInherited(short, short) - Static method in class org.jmol.util.C
- getColixO(Object) - Static method in class org.jmol.util.C
- getColixS(String) - Static method in class org.jmol.util.C
- getColixTranslucencyFractional(short) - Static method in class org.jmol.util.C
- getColixTranslucencyLabel(short) - Static method in class org.jmol.util.C
- getColixTranslucencyLevel(short) - Static method in class org.jmol.util.C
- getColixTranslucent(int) - Static method in class org.jmol.util.C
- getColixTranslucent3(short, boolean, float) - Static method in class org.jmol.util.C
- getColor() - Method in enum org.jmol.c.STR
- getColor(short) - Method in class org.jmol.export.JSExporter
- getColor(String) - Static method in class org.jmol.jvxl.readers.JvxlXmlReader
- getColor(String) - Method in class org.jmol.jvxl.readers.KinemageReader
- getColor1(int) - Method in interface org.jmol.api.GenericGraphics
- getColor1(int) - Method in class org.jmol.awt.AwtG2D
- getColor1(int) - Method in class org.jmol.awtjs2d.JsG2D
- getColor3(int, int, int) - Method in interface org.jmol.api.GenericGraphics
- getColor3(int, int, int) - Method in class org.jmol.awt.AwtG2D
- getColor3(int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- getColor4(int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
- getColor4(int, int, int, int) - Method in class org.jmol.awt.AwtG2D
- getColor4(int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- getColorArgbOrGray(short) - Method in class org.jmol.util.GData
- getColorCommand(String, byte, short, boolean) - Static method in class org.jmol.shape.Shape
- getColorCommandUnk(String, short, boolean) - Static method in class org.jmol.shape.Shape
- getColorEncoder(String) - Method in class org.jmol.viewer.ColorManager
- getColorIndex(float) - Method in class org.jmol.util.ColorEncoder
- getColorIndexFromPalette(float, float, float, int, boolean) - Method in class org.jmol.util.ColorEncoder
- getColorKey() - Method in class org.jmol.util.ColorEncoder
- getColorList(int, short[], int, BS, Map<Short, Integer>) - Method in class org.jmol.export.___Exporter
-
input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color index
- getColorPhaseIndex(String) - Static method in class org.jmol.jvxl.readers.SurfaceReader
- getColorPointForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
- getColorPt(Object, P3) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getColorRange(int) - Method in class org.jmol.script.ScriptEval
- getColors(short[]) - Method in class org.jmol.export.JSExporter
- getColorScheme() - Method in class org.jmol.util.ColorEncoder
- getColorSchemeArray(int) - Method in class org.jmol.util.ColorEncoder
- getColorSchemeList(int[]) - Static method in class org.jmol.util.ColorEncoder
- getColorSchemeList(String) - Method in class org.jmol.viewer.ColorManager
- getColorSchemeName(int) - Method in class org.jmol.util.ColorEncoder
- getColorState(ColorManager, SB) - Method in class org.jmol.viewer.StateCreator
- getColorTrans(ScriptEval, int, boolean, int[]) - Method in class org.jmol.scriptext.ScriptExt
-
Checks color, translucent, opaque parameters.
- getColorTriad(int) - Method in class org.jmol.script.ScriptParam
- getColourString(double) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- getColumn(int) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
- getColumn(int) - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
- getColumn(int) - Method in class org.jmol.awtjs.swing.JTable
- getColumnClass(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- getColumnClass(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- getColumnClass(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getColumnClass(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
- getColumnCount() - Method in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- getColumnCount() - Method in class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- getColumnCount() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getColumnCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
- getColumnModel() - Method in class org.jmol.awtjs.swing.JTable
- getColumnName(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- getColumnName(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- getColumnName(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getColumnName(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
- getCommand() - Method in class org.jmol.util.CommandHistory
-
Calculates the command to return.
- getCommand(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- getCommand(int, boolean, boolean) - Method in class org.jmol.script.ScriptEval
-
used for recall of commands in the application console
- getCommand(Mesh) - Method in class org.jmol.shapecgo.CGO
- getCommand(Mesh) - Method in class org.jmol.shapespecial.Draw
- getCommand2(Mesh, int) - Method in class org.jmol.shapecgo.CGO
- getCommand2(Mesh, int) - Method in class org.jmol.shapespecial.Draw
- getCommandDown() - Method in class org.jmol.util.CommandHistory
-
Retrieves the following command from the top of the list, updates list position.
- getCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Generates a commandline from the options set for povray path etc and sets in the textField.
- getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.JmolStateCreator
- getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.StateCreator
- getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.Viewer
- getCommands2(Map<String, BS>, SB, String, String) - Method in class org.jmol.viewer.StateCreator
- getCommandSet(String) - Static method in class org.jmol.script.T
-
retrieves an unsorted list of viable commands that could be completed by this initial set of characters.
- getCommandString() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- getCommandString() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- getCommandUp() - Method in class org.jmol.util.CommandHistory
-
Retrieves the following command from the bottom of the list, updates list position.
- getComparator(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getComparison(T, int, int, String, float[]) - Method in class org.jmol.script.ScriptExpr
- getComponent(int) - Method in interface org.jmol.api.SC
- getComponent(int) - Method in class org.jmol.awt.AwtSwingComponent
- getComponent(int) - Method in class org.jmol.awtjs.swing.Container
- getComponentCount() - Method in interface org.jmol.api.SC
- getComponentCount() - Method in class org.jmol.awt.AwtSwingComponent
- getComponentCount() - Method in class org.jmol.awtjs.swing.Container
- getComponents() - Method in interface org.jmol.api.SC
- getComponents() - Method in class org.jmol.awt.AwtSwingComponent
- getComponents() - Method in class org.jmol.awtjs.swing.Container
- getComposition - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- getConeData() - Static method in class org.jmol.export.MeshData
-
Calculates the data (faces, vertices, normals) for a cone.
- getConeMesh(P3, M3, short) - Static method in class org.jmol.export.___Exporter
- getConeResource() - Method in class org.jmol.export._IdtfExporter
- getConformation(int, boolean, BS, BS) - Method in class org.jmol.modelsetbio.BioModel
- getConformation(int, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
- getConnectionPoints() - Method in class org.jmol.renderspecial.DrawRenderer
- getConsole() - Method in class org.jmol.viewer.Viewer
- getConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getConsoleFontScale() - Method in class org.jmol.viewer.Viewer
- getConstraint(SymmetryInterface, int, int) - Method in class org.jmol.modelkit.ModelKit
-
This constraint will be set for the site only.
- getConstraintList() - Method in class org.jmol.minimize.forcefield.Calculations
- getContentPane() - Method in class org.jmol.awtjs.swing.JDialog
- getContext(boolean) - Method in class org.jmol.scriptext.CmdExt
- getContext(String) - Method in class org.jmol.viewer.StateManager
- getContextTrace(Viewer, ScriptContext, SB, boolean) - Static method in class org.jmol.script.ScriptEval
- getContextVariableAsVariable(String, boolean) - Method in class org.jmol.script.ScriptParam
- getContourList(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getContourPoint(T3[], int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
- getContourPoint(T3[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
- getContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
create a set of contour data.
- getContractionNormalization(int, int) - Method in class org.jmol.quantum.MOCalculation
-
NWCHEM only
- getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.AlphaPolymer
- getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.BioPolymer
- getControlPoints(boolean, float, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
- getControlPoints2(float) - Method in class org.jmol.modelsetbio.BioPolymer
- getConventionalUnitCell(String, M3) - Method in interface org.jmol.api.SymmetryInterface
- getConventionalUnitCell(String, M3) - Method in class org.jmol.symmetry.Symmetry
-
return a conventional lattice from a primitive
- getConventionalUnitCell(String, M3) - Method in class org.jmol.symmetry.UnitCell
-
return a conventional lattice from a primitive
- getCoord(int) - Method in class org.jmol.adapter.readers.xtal.CgdReader
- getCoordinateMap(T3[], int[], BS) - Method in class org.jmol.export.__CartesianExporter
- getCoordinatesAreFractional() - Method in interface org.jmol.api.SymmetryInterface
- getCoordinatesAreFractional() - Method in class org.jmol.symmetry.Symmetry
- getCoordinateState(BS) - Method in class org.jmol.viewer.Viewer
- getCorrelationMaps(String, Node[], int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- getCorrelationMaps(String, Node[], int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
-
Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.
- getCorrelationTime() - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
get the correlation time in seconds
- getCorrelationTimeTauPS() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
get the correlation time in picoseconds
- getCouples() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- getCoupleWeight() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- getCovalentBondCount() - Method in class org.jmol.modelset.Atom
- getCovalentBondCount() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the number of bonds of this atom.
- getCovalentBondCount() - Method in interface org.jmol.util.Node
- getCovalentBondCount() - Method in interface org.jmol.util.SimpleNode
-
Get the total number of covalent bonds, thus not including hydrogen bonds.
- getCovalentBondCountPlusMissingH() - Method in class org.jmol.modelset.Atom
- getCovalentBondCountPlusMissingH() - Method in class org.jmol.smiles.SmilesAtom
- getCovalentBondCountPlusMissingH() - Method in interface org.jmol.util.Node
-
includes actual + missing
- getCovalentBondOrder(int) - Static method in class org.jmol.util.Edge
- getCovalentBondsForAtoms(Bond[], int, BS) - Static method in class org.jmol.viewer.PropertyManager
- getCovalentHydrogenCount() - Method in class org.jmol.modelset.Atom
- getCovalentHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
- getCovalentHydrogenCount() - Method in interface org.jmol.util.Node
- getCovalentlyConnectedBitSet(Node[], Node, BS, boolean, boolean, Lst<BS>, BS, Node, Node) - Static method in class org.jmol.util.JmolMolecule
- getCovalentOrder() - Method in class org.jmol.modelset.Bond
- getCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
- getCovalentOrder() - Method in class org.jmol.util.Edge
- getCovalentOrder() - Method in interface org.jmol.util.SimpleEdge
- getCovalentRadius(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getCovalentRadius(int) - Static method in class org.jmol.util.Elements
-
Prior to Jmol 14.1.11, this was OpenBabel 1.100.1, but now it is BODR
- getCParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getCrossLinkGroup(int, Lst<Integer>, Group, boolean, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelset.Atom
-
Used by SMILES to get vector of cross-links
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelset.Group
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelsetbio.Monomer
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in class org.jmol.smiles.SmilesAtom
- getCrossLinkVector(Lst<Integer>, boolean, boolean) - Method in interface org.jmol.util.Node
- getCSSstyle(int, int) - Method in class org.jmol.awtjs.swing.Component
- getCStr(byte[], int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getCubeIterator(int) - Method in class org.jmol.bspt.Bspf
- getCurrentBondCount() - Method in class org.jmol.modelset.Atom
- getCurrentColorRange() - Method in class org.jmol.viewer.Viewer
- getCurrentColorSchemeName() - Method in class org.jmol.util.ColorEncoder
- getCurrentFileAsString(String) - Method in class org.jmol.viewer.Viewer
- getCurrentModelAuxInfo() - Method in class org.jmol.viewer.Viewer
- getCurrentModelFileAsString() - Method in class org.jmol.scriptext.CmdExt
- getCurrentModelIndex() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getCurrentStep() - Method in class org.jmol.minimize.forcefield.ForceField
- getCurrentStructureFile() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getCurrentUnitCell() - Method in class org.jmol.viewer.Viewer
- getCurrentX() - Method in class org.jmol.viewer.ActionManager
- getCurrentY() - Method in class org.jmol.viewer.ActionManager
- getCursorX() - Method in class org.jmol.viewer.Viewer
- getCursorY() - Method in class org.jmol.viewer.Viewer
- getCutoff() - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
get the cutoff distance
- getCutoffAng() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
get the cutoff distance
- getCutoffField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getCylinderData(boolean) - Static method in class org.jmol.export.MeshData
-
Calculates the data (faces, vertices, normals) for a cylinder.
- getCylinderResource(boolean) - Method in class org.jmol.export._IdtfExporter
- getData() - Method in class org.jmol.adapter.readers.cif.CifReader
- getData() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- getData() - Method in class org.jmol.quantum.NMRCalculation
-
Creates the data set necessary for doing NMR calculations.
- getData(int, int, BioPolymer, char, char, int, BS, BS, boolean, boolean, boolean, boolean, boolean, boolean, float, boolean, boolean, LabelToken[], OC, SB, BS, P3) - Method in class org.jmol.modelsetbio.BioExt
- getData(InputStream, String[]) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
-
called by SmarterJmolAdapter via JmolUtil to open a Spartan directory and get all the needed data as a string.
- getData(Object[]) - Static method in class org.jmol.shapecgo.CGOMesh
- getData(String) - Method in class org.jmol.adapter.writers.PWMATWriter
- getData(String) - Method in class org.jmol.script.ScriptCompiler
- getData(String, String) - Method in class org.jmol.api.JmolViewer
- getData(String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getData(String, String) - Method in class org.jmol.viewer.Viewer
- getData(String, String, String, int) - Method in class org.jmol.adapter.readers.quantum.NBOParser
- getData(String, BS, int) - Method in interface org.jmol.api.JmolDataManager
- getData(String, BS, int) - Method in class org.jmol.viewer.DataManager
- getDataBlock() - Method in class org.jmol.adapter.readers.more.MdTopReader
- getDataKey(int) - Method in class org.jmol.dssx.AnnotationParser
- getDataManager() - Method in class org.jmol.viewer.Viewer
- getDataMinMax() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getDataObj(String, BS, int) - Method in class org.jmol.viewer.Viewer
-
Retrieve a data object
- getDataRange() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getDataRange(IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
- getDataSeparator() - Method in class org.jmol.viewer.Viewer
- getDataState(SB) - Method in class org.jmol.viewer.StateCreator
- getDataState(JmolStateCreator, SB) - Method in interface org.jmol.api.JmolDataManager
- getDataState(JmolStateCreator, SB) - Method in class org.jmol.viewer.DataManager
- getDataValue(byte) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Read the data value.
- getDateFormat(String) - Method in interface org.jmol.api.GenericPlatform
- getDateFormat(String) - Method in class org.jmol.awt.Platform
- getDateFormat(String) - Method in class org.jmol.awtjs2d.Platform
- getDE(float[], int, int, int, int, boolean) - Method in class org.jmol.util.MeshSlicer
- getDE(MinAtom, int, int, double) - Method in class org.jmol.minimize.forcefield.ForceField
- getDebugFooter(int, double) - Method in class org.jmol.minimize.forcefield.Calculations
- getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.Calculations
- getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
- getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
- getDebugHeader2(int) - Method in class org.jmol.minimize.forcefield.Calculations
- getDebugLine(int, Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
- getDebugLine(int, Calculation) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
- getDebugLineC(int, Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
- getDef(String) - Method in class org.jmol.export._VrmlExporter
- getDef(String) - Method in class org.jmol.export.UseTable
-
This Hashtable contains references to _n where n is a number.
- getDefaultBoundBox() - Method in class org.jmol.modelset.ModelSet
-
The default bounding box is created when the LOAD ....
- getDefaultColix() - Method in class org.jmol.shapesurface.Isosurface
- getDefaultCount(int, boolean) - Static method in class org.jmol.smiles.SmilesAtom
- getDefaultDirectory() - Method in class org.jmol.viewer.Viewer
- getDefaultDirectory(String) - Method in class org.jmol.viewer.FileManager
- getDefaultLabelState(Labels) - Method in class org.jmol.viewer.StateCreator
- getDefaultLargePDBRendering(SB, int) - Method in class org.jmol.modelsetbio.BioModel
- getDefaultLattice() - Method in class org.jmol.viewer.Viewer
- getDefaultMadFromOrder(int) - Method in class org.jmol.modelset.BondCollection
-
When creating a new bond, determine bond diameter from order
- getDefaultMeasurementLabel(int) - Method in class org.jmol.viewer.Viewer
- getDefaultModel() - Method in class org.jmol.modelkit.ModelKit
- getDefaultPropertyParam(int) - Method in interface org.jmol.api.JmolPropertyManager
- getDefaultPropertyParam(int) - Method in class org.jmol.viewer.PropertyManager
- getDefaultPropertyParam(int) - Method in class org.jmol.viewer.Viewer
- getDefaultSetting(int, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
-
All settings that Jmol uses should go here
- getDefaultSettingPt(int, int, P3) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
- getDefaultSettingS(int, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
- getDefaultStructure(BS, BS) - Method in class org.jmol.modelset.ModelSet
- getDefaultUnitCell() - Method in class org.jmol.adapter.readers.cif.MSRdr
- getDefaultVdwNameOrData(int, VDW, BS) - Method in class org.jmol.viewer.Viewer
- getDefaultVdwNameOrData(VDW, BS) - Method in interface org.jmol.api.JmolDataManager
- getDefaultVdwNameOrData(VDW, BS) - Method in class org.jmol.viewer.DataManager
- getDefaultVdwType(int) - Method in class org.jmol.modelset.ModelSet
- getDefinedAtomSet(String) - Method in class org.jmol.viewer.Viewer
- getDefinedState(SB, boolean) - Method in class org.jmol.viewer.StateCreator
- getDefRet(String, String[]) - Method in class org.jmol.export.UseTable
-
Used by JSExporter for WebGL
- getDegrees(float, boolean) - Method in class org.jmol.multitouch.ActionManagerMT
- getDegrees(float, boolean) - Method in class org.jmol.viewer.ActionManager
-
Transform a screen pixel change to an angular change such that a full sweep of the dimension (up to 500 pixels) corresponds to 180 degrees of rotation.
- getDelayMaximumMs() - Method in class org.jmol.viewer.Viewer
- getDerivedSpaceGroup() - Method in class org.jmol.symmetry.SpaceGroup
- getDesc(ModelSet) - Method in class org.jmol.symmetry.Symmetry
- getDescent() - Method in class org.jmol.util.Font
- getDescent(Object) - Static method in class org.jmol.awt.AwtFont
- getDescent(Object) - Static method in class org.jmol.awtjs2d.JSFont
- getDescription() - Method in class org.jmol.dialog.Dialog.TypeFilter
- getDescription() - Method in class org.openscience.jmol.app.janocchio.MyFileFilter
- getDfCoefMaps() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- getDFMap(String, String, int, String, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
-
finds the position in the Jmol-required list of function types.
- getDialog() - Method in class org.jmol.dialog.FileChooser
- getDialogs() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getDialogs() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getDiameter() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- getDiameter(int, int) - Method in class org.jmol.render.FontLineShapeRenderer
- getDictRefValue() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- getDiff() - Method in class org.openscience.jmol.app.janocchio.Measure
- getDiffusePercent() - Method in class org.jmol.util.GData
- getDigits(String, int, int[]) - Static method in class org.jmol.smiles.SmilesParser
- getDihedralCouple(Atom[]) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- getDihedralMap(int[]) - Method in class org.jmol.modelset.ModelSet
- getDimensionValue(int) - Method in class org.jmol.modelset.Atom
- getDimensionValue(T3, int) - Static method in class org.jmol.bspt.Node
- getDipolarConstantHz(Atom, Atom) - Method in interface org.jmol.api.JmolNMRInterface
- getDipolarConstantHz(Atom, Atom) - Method in class org.jmol.quantum.NMRCalculation
- getDipolarCouplingHz(Atom, Atom, V3) - Method in interface org.jmol.api.JmolNMRInterface
- getDipolarCouplingHz(Atom, Atom, V3) - Method in class org.jmol.quantum.NMRCalculation
- getDipoleIndex(int, int) - Method in class org.jmol.shapespecial.Dipoles
- getDipoleIndexFor(String, String) - Method in class org.jmol.shapespecial.Dipoles
- getDirect() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- getDirective(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getDisplayModelIndex() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getDistance(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
- getDistanceJMolecule(BS, String[], boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getDistances() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- getDistanceUnits(String) - Method in class org.jmol.viewer.Viewer
- getDocument() - Method in class org.jmol.awtjs.swing.JTextPane
- getDOMAttributesA(Object[]) - Method in class org.jmol.adapter.readers.xml.XmlReader
- getDoTranslate() - Static method in class org.jmol.i18n.GT
- getDotsConvexMaps() - Method in class org.jmol.geodesic.EnvelopeCalculation
- getDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
- getDouble(Map<String, Object>, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- getDouble(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getDragDropFileTypeName(String) - Method in class org.jmol.script.ScriptManager
- getDragSelected() - Method in class org.jmol.viewer.Viewer
- getDrawHover() - Method in class org.jmol.viewer.Viewer
- getDSSRForModel(Viewer, int) - Method in class org.jmol.dssx.DSSR1
- getDSSRFrame(Map<String, Object>) - Method in interface org.jmol.api.JmolAnnotationParser
- getDSSRFrame(Map<String, Object>) - Method in class org.jmol.dssx.AnnotationParser
- getDSSRFrame(Map<String, Object>) - Method in class org.jmol.dssx.DSSR1
- getDSSRFrame(Viewer) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getDualHydrogenBondArray() - Method in class org.jmol.dssx.DSSP
-
(p.
- getDX(int, int) - Method in class org.jmol.viewer.Gesture
- getDY(int, int) - Method in class org.jmol.viewer.Gesture
- getEchoName(int) - Static method in class org.jmol.viewer.JC
- getEchoState(SB, Text) - Method in class org.jmol.viewer.StateCreator
- getEchoStateActive() - Method in class org.jmol.modelset.ModelSet
- getEdgeData() - Method in class org.jmol.jvxl.calc.MarchingCubes
- getEdgePoints(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getEdges() - Method in class org.jmol.jvxl.readers.IsoSolventReader
- getEdges() - Method in class org.jmol.modelset.Atom
- getEdges() - Method in class org.jmol.smiles.SmilesAtom
- getEdges() - Method in interface org.jmol.util.Node
- getEdges() - Method in interface org.jmol.util.SimpleNode
-
Get the bond array, including hydrogen bonds.
- getEigenSort() - Static method in class org.jmol.util.Tensor
- getElectronCount(int[]) - Method in class org.jmol.smiles.SmilesRingSet
- getElement(String) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
- getElement(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
-
allow for any number of characters, for which the first one or two are an element symbol.
- getElementCounts() - Method in class org.jmol.symmetry.PointGroup
- getElementFromUser() - Method in class org.jmol.modelkit.ModelKit
- getElementName(int) - Method in class org.jmol.modelset.AtomCollection
- getElementNumber() - Method in class org.jmol.adapter.smarter.AtomIterator
- getElementNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getElementNumber() - Method in class org.jmol.modelset.Atom
- getElementNumber() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the atomic number of the element or 0
- getElementNumber() - Method in interface org.jmol.util.Node
- getElementNumber() - Method in interface org.jmol.util.SimpleNode
- getElementNumber(int) - Static method in class org.jmol.util.Elements
- getElementNumber(String) - Static method in class org.jmol.api.JmolAdapter
- getElementsPresentBitSet(int) - Method in class org.jmol.api.JmolViewer
- getElementsPresentBitSet(int) - Method in class org.jmol.modelset.ModelSet
- getElementsPresentBitSet(int) - Method in class org.jmol.viewer.Viewer
- getElementSymbol() - Method in class org.jmol.adapter.smarter.Atom
- getElementSymbol() - Method in class org.jmol.modelset.Atom
- getElementSymbol(int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getElementSymbol(int) - Static method in class org.jmol.api.JmolAdapter
- getElementSymbol(int) - Static method in class org.jmol.util.Elements
- getElementSymbol(Atom, String) - Method in class org.jmol.adapter.readers.more.ForceFieldReader
- getElementSymbolIso(boolean) - Method in class org.jmol.modelset.Atom
- getElemNos() - Method in class org.jmol.shapespecial.Polyhedron
- getEllipsoidForAtomTensor(Tensor, Atom) - Static method in class org.jmol.shapespecial.Ellipsoid
- getEllipsoidShade(float, float, float, int, M4) - Method in class org.jmol.util.Shader
- getEmbeddedFileState(String, boolean, String) - Method in class org.jmol.viewer.FileManager
-
Get the specified SPT file of a Jmol zip collection or the embedded script for any other file that is embeddable.
- getEmbeddedScript(String) - Static method in class org.jmol.viewer.FileManager
-
Extract a Jmol script embedded using JC.EMBEDDED_SCRIPT_TAG.
- getEmptyEllipsoid(String, int) - Static method in class org.jmol.shapespecial.Ellipsoid
- getEncodedOrder() - Method in class org.jmol.adapter.smarter.BondIterator
- getEncodedOrder() - Method in class org.jmol.api.JmolAdapterBondIterator
- getEncodedVertexData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within
element - getEncoding(String) - Static method in class org.jmol.jvxl.readers.JvxlXmlReader
- getEndChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
- getEndChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getEndInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
- getEndInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getEndSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
- getEndSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getEneChirality(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, boolean, boolean) - Method in class org.jmol.symmetry.CIPChirality
-
Determine the stereochemistry of a bond
- getEneKekule() - Method in class org.jmol.symmetry.CIPData
-
Look for conjugated loops of any size that have atoms not already in aromatic rings
- getEnergies(int, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
-
Get the energy of a given type or types.
- getEnergy() - Method in class org.jmol.minimize.forcefield.Calculation
- getEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
- getEnergy() - Method in class org.jmol.modelset.Bond
- getEnergy() - Method in class org.jmol.modelset.HBond
- getEnergy(double, double, double, double) - Static method in class org.jmol.modelset.HBond
- getEnergyDiff() - Method in class org.jmol.minimize.forcefield.ForceField
- getEnergyOnly() - Method in class org.jmol.minimize.Minimizer
- getEneTop() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Check ene for first nonduplicate.
- getEntryIcon(String[]) - Method in class org.jmol.popup.GenericPopup
- getEquationForQuadricWithCenter(float, float, float, M3, V3, M3, double[], M4) - Static method in class org.jmol.shapespecial.Ellipsoid
- getEquivalentType(int, int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
-
equivalent types for OOP and torsions
- getEquivPointList(Lst<P3>, int, String) - Method in interface org.jmol.api.SymmetryInterface
- getEquivPointList(Lst<P3>, int, String) - Method in class org.jmol.symmetry.Symmetry
- getEquivPoints(Lst<P3>, P3, String) - Method in interface org.jmol.api.SymmetryInterface
- getEquivPoints(Lst<P3>, P3, String) - Method in class org.jmol.symmetry.Symmetry
- getEquivPoints(P3, String, M4[], Lst<P3>, int, int) - Method in class org.jmol.symmetry.UnitCell
- getErrorLineMessage(String, String, int, int, String) - Static method in class org.jmol.script.ScriptError
- getErrorLineMessage2() - Method in class org.jmol.script.ScriptEval
- getErrorMessage() - Method in interface org.jmol.api.JmolScriptEvaluator
- getErrorMessage() - Method in class org.jmol.api.JmolViewer
- getErrorMessage() - Method in class org.jmol.script.ScriptError
- getErrorMessage() - Method in class org.jmol.viewer.Viewer
- getErrorMessageUn() - Method in class org.jmol.api.JmolViewer
- getErrorMessageUn() - Method in class org.jmol.viewer.Viewer
- getErrorMessageUntranslated() - Method in interface org.jmol.api.JmolScriptEvaluator
- getErrorMessageUntranslated() - Method in class org.jmol.script.ScriptError
- getErrorMessageUntranslated() - Method in exception org.jmol.script.ScriptException
- getEvalContextAndHoldQueue(JmolScriptEvaluator) - Method in class org.jmol.viewer.Viewer
- getEventName(int) - Static method in class org.jmol.multitouch.ActionManagerMT
- getExecutor() - Method in interface org.jmol.api.JmolParallelProcessor
- getExecutor() - Method in class org.jmol.script.ScriptParallelProcessor
- getExitRate() - Method in class org.jmol.viewer.ActionManager
- getExpCouple(int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getExpDist(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getExplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
- getExplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
- getExplicitHydrogenCount() - Method in interface org.jmol.util.Node
-
[CH2] for example
- getExplicitNH() - Method in class org.jmol.modelsetbio.AminoMonomer
- getExpNoe(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getExportDate() - Method in class org.jmol.export.___Exporter
- getExportDriverList() - Method in class org.jmol.viewer.Viewer
- getExportName() - Method in interface org.jmol.api.JmolRendererInterface
- getExportName() - Method in class org.jmol.export.Export3D
- getExportName() - Method in class org.jmol.g3d.Graphics3D
- getExportType() - Method in interface org.jmol.api.JmolRendererInterface
- getExportType() - Method in class org.jmol.export.Export3D
- getExportType() - Method in class org.jmol.g3d.Graphics3D
- getExpValue() - Method in class org.openscience.jmol.app.janocchio.Measure
- getExt(String) - Method in class org.jmol.script.ScriptExpr
- getFace(Mesh) - Method in class org.jmol.shapesurface.Pmesh
-
return a cycle of points generating this face used after slabbing
- getFaces() - Method in class org.jmol.jvxl.readers.IsoSolventReader
- getFaces() - Method in class org.jmol.util.MeshSurface
- getFaces(int[][], int, Map<Integer, Object[]>) - Method in class org.jmol.shapespecial.Polyhedra
-
Face: a CCW loop of edges all (within tolerance) in the same plane.
- getFaceTriangles(int, Map<Integer, Object[]>, int) - Method in class org.jmol.shapespecial.Polyhedra
- getFaceVertexes(int) - Static method in class org.jmol.util.Geodesic
- getFactoredValue(int) - Method in class org.jmol.util.Tensor
-
Returns a factored eigenvalue; thermal ellipsoids use sqrt(abs(eigenvalue)) for ellipsoid axes; others use just use abs(eigenvalue); all cases get factored by typeFactor
- getField(byte) - Method in class org.jmol.adapter.readers.cif.CifReader
- getField(String) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
- getFile() - Method in class org.openscience.jmol.app.HistoryFile
- getFile() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- getFile(int) - Method in class org.jmol.console.JmolConsole.FileChecker
- getFile31() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- getFile46() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
read the labels from xxxx.46
- getFileAsBytes(String, OC) - Method in class org.jmol.viewer.FileManager
- getFileAsMap(String, String) - Method in class org.jmol.viewer.FileManager
- getFileAsString(String) - Method in class org.jmol.viewer.Viewer
- getFileAsString3(String, boolean, String) - Method in class org.jmol.viewer.Viewer
- getFileAsString4(String, int, boolean, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
- getFileData() - Method in class org.jmol.viewer.Viewer
- getFileData(int) - Method in class org.jmol.modelset.ModelSet
- getFileData(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- getFileDataAsString(String[], int, boolean, boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getFileHeader() - Method in class org.jmol.viewer.Viewer
- getFileHeader(int) - Method in class org.jmol.modelset.ModelSet
- getFileInfo() - Method in class org.jmol.viewer.FileManager
- getFileInfo(Object, String) - Static method in class org.jmol.viewer.PropertyManager
- getFileList(String, boolean) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
-
get a complete critical file list for a spartan file Mac directory based on file extension ".spardir.zip" or ".spardir"
- getFileName() - Method in class org.jmol.viewer.FileManager
- getFileName() - Method in exception org.jmol.viewer.JmolAsyncException
- getFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
- getFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
- getFilePath(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getFileReader(String) - Method in class org.jmol.shapesurface.Isosurface
- getFileReferences(String, Lst<String>, Lst<String>) - Static method in class org.jmol.viewer.FileManager
- getFiles() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- getFileState(SB) - Method in class org.jmol.viewer.StateCreator
- getFileType() - Method in class org.jmol.viewer.FileManager
- getFileType(BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
-
From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issues
- getFileTypefromFilter(String) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
Just get the resolved file type; if a file, does NOT close the reader
- getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the type of this file or molecular model, if known.
- getFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getFilterWithCase(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getFirstAtomIndex(int) - Method in class org.jmol.modelset.ModelLoader
- getFirstAtomIndexFromAtomNumber(int, BS) - Method in class org.jmol.modelset.AtomCollection
- getFlag(int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
safely get a one-character 0 or 1 as a boolean
- getFlags(String) - Static method in class org.jmol.smiles.SmilesParser
- getFlexFitList(BS, BS, String, boolean) - Method in class org.jmol.scriptext.SmilesExt
- getFloat() - Method in class org.jmol.adapter.readers.more.MdCrdReader
- getFloat() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
- getFloat() - Method in class org.jmol.jvxl.readers.PmeshReader
- getFloat(int) - Method in class org.jmol.api.JmolViewer
- getFloat(int) - Method in class org.jmol.shapecgo.CGOMesh
- getFloat(int) - Method in class org.jmol.viewer.Viewer
- getFloat(int, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- getFloat(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- getFloat(Lst<Object>, int) - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
- getFloatEncodedInt(String) - Static method in class org.jmol.script.ScriptParam
-
Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders.
- getFloatProperty(String) - Method in class org.jmol.modelset.Atom
- getFloatProperty(String) - Method in class org.jmol.smiles.SmilesAtom
- getFloatProperty(String) - Method in interface org.jmol.util.Node
- getFont(float) - Method in class org.jmol.shape.Frank
- getFont3D(float) - Method in class org.jmol.util.GData
- getFont3D(int) - Static method in class org.jmol.util.Font
- getFont3D(String, String, float) - Method in class org.jmol.viewer.Viewer
- getFont3DCurrent() - Method in class org.jmol.util.GData
- getFont3DFS(String, float) - Method in class org.jmol.util.GData
- getFont3DFSS(String, String, float) - Method in class org.jmol.util.GData
- getFont3DScaled(Font, float) - Method in class org.jmol.util.GData
- getFontAscent(Object) - Method in interface org.jmol.api.FontManager
- getFontAscent(Object) - Method in class org.jmol.awt.Platform
- getFontAscent(Object) - Method in class org.jmol.awtjs2d.Platform
- getFontCommand(String, Font) - Static method in class org.jmol.shape.Shape
- getFontDescent(Object) - Method in interface org.jmol.api.FontManager
- getFontDescent(Object) - Method in class org.jmol.awt.Platform
- getFontDescent(Object) - Method in class org.jmol.awtjs2d.Platform
- getFontFaceID(String) - Static method in class org.jmol.util.Font
- getFontFidFS(String, float) - Method in class org.jmol.util.GData
- getFontFidI(float) - Method in class org.jmol.util.GData
- getFontLineShapeState(FontLineShape) - Method in class org.jmol.viewer.StateCreator
- getFontMetrics() - Method in class org.jmol.modelset.Text
- getFontMetrics() - Method in class org.jmol.util.Font
- getFontMetrics(Font, Object) - Method in interface org.jmol.api.FontManager
- getFontMetrics(Font, Object) - Static method in class org.jmol.awt.AwtFont
- getFontMetrics(Font, Object) - Method in class org.jmol.awt.Platform
- getFontMetrics(Font, Object) - Static method in class org.jmol.awtjs2d.JSFont
- getFontMetrics(Font, Object) - Method in class org.jmol.awtjs2d.Platform
- getFontState(String, Font) - Method in class org.jmol.viewer.StateCreator
- getFontStyleID(String) - Static method in class org.jmol.util.Font
- getForceField(String) - Method in class org.jmol.minimize.Minimizer
- getFormalCharge() - Method in class org.jmol.adapter.smarter.AtomIterator
- getFormalCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getFormalCharge() - Method in class org.jmol.modelset.Atom
- getFormalCharge() - Method in class org.jmol.smiles.SmilesAtom
- getFormalCharge() - Method in interface org.jmol.util.Node
- getFormalCharge() - Method in interface org.jmol.util.SimpleNode
- getFormatType(String) - Static method in class org.jmol.script.SV
- getFortranFormatLengths(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
get all integers after letters negative entries are spaces (1Xn)
- getFractional(Atom, P3) - Method in class org.jmol.modelset.Trajectory
- getFractional2DValue(float, float, float, float, float, float) - Static method in class org.jmol.jvxl.data.VolumeData
- getFractionalCoord(boolean, char, boolean, P3) - Method in class org.jmol.modelset.Atom
- getFractionalCoord(V3) - Method in class org.jmol.adapter.readers.xtal.CastepReader
- getFractionalCoordPt(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
- getFractionalOffset() - Method in interface org.jmol.api.SymmetryInterface
- getFractionalOffset() - Method in class org.jmol.symmetry.Symmetry
- getFractionalOffset() - Method in class org.jmol.symmetry.UnitCell
- getFractionalOrigin() - Method in interface org.jmol.api.SymmetryInterface
- getFractionalOrigin() - Method in class org.jmol.symmetry.Symmetry
- getFractionalOrigin() - Method in class org.jmol.util.SimpleUnitCell
- getFractionalPoint(int) - Method in class org.jmol.script.ScriptParam
-
Could return a P4 for large 1100100100 type indicators
- getFractionalUnitCoord(boolean, char, P3) - Method in class org.jmol.modelset.Atom
- getFractionalUnitCoordPt(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
- getFractionalUnitDistance(T3, T3, T3) - Method in class org.jmol.modelset.Atom
- getFrame() - Method in interface org.jmol.awt.JmolFrame
- getFrame() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- getFrame() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- getFrame() - Static method in class org.openscience.jmol.app.webexport.WebExport
- getFrameActions() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getFrameActions() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getFrameAtomCount() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getFrameAtomIndex(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getFrameAtoms() - Method in class org.jmol.viewer.Viewer
- getFrameBase(int) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getFrameCount() - Method in class org.jmol.viewer.AnimationManager
- getFrameDelayMs(int) - Method in class org.jmol.modelset.ModelSet
- getFrameModelInfo(String) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getFrameNumber() - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- getFrameNumber() - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- getFrameOffsets(BS, boolean) - Method in class org.jmol.modelset.ModelSet
- getFrameScenes(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
remove all scenes that do not define a frame.
- getFrameStep(int) - Method in class org.jmol.viewer.AnimationManager
- getFrameTitle() - Method in class org.jmol.viewer.Viewer
- getFrameTitle(int) - Method in class org.jmol.modelset.ModelSet
- getFreqField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getFullMap() - Method in class org.jmol.script.ScriptContext
- getFullName() - Method in class org.jmol.util.GenericApplet
- getFullPath() - Method in interface org.jmol.api.GenericFileInterface
- getFullPath() - Method in class org.jmol.awt.AwtFile
- getFullPath() - Method in class org.jmol.awtjs2d.JSFile
- getFullPathName(boolean) - Method in class org.jmol.script.ScriptEval
- getFullPathName(boolean) - Method in class org.jmol.viewer.FileManager
- getFullPathNameOrError(String) - Method in class org.jmol.viewer.Viewer
- getFullPathNameOrError(String, boolean, String[]) - Method in class org.jmol.viewer.FileManager
-
just check for a file as being readable.
- getFullPDBHeader() - Method in class org.jmol.modelsetbio.BioModel
- getFullPDBHeader(Map<String, Object>) - Method in class org.jmol.modelsetbio.BioExt
- getFullProteinStructureState(BS, int) - Method in class org.jmol.modelsetbio.BioModelSet
- getFullScreenDimensions(Object, int[]) - Method in interface org.jmol.api.GenericPlatform
- getFullScreenDimensions(Object, int[]) - Static method in class org.jmol.awt.Display
- getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awt.Platform
- getFullScreenDimensions(Object, int[]) - Static method in class org.jmol.awtjs2d.Display
- getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awtjs2d.Platform
- getFunction(String) - Method in class org.jmol.script.ScriptExpr
- getFunction(String) - Method in class org.jmol.viewer.Viewer
- getFunctionCalls(String) - Method in class org.jmol.viewer.JmolStateCreator
- getFunctionCalls(String) - Method in class org.jmol.viewer.StateCreator
-
A relatively static method that is only called on a new StateCreator so as to all StateCreator to be modular.
- getFunctionCalls(String) - Method in class org.jmol.viewer.Viewer
- getFunctions(boolean) - Method in class org.jmol.viewer.Viewer
- getFunctionZfromXY() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- getGestureType() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
- getGestureType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- getGhostOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getGLmolView() - Method in class org.jmol.util.GenericApplet
-
This method is only called by JmolGLmol applet._refresh();
- getGLmolView() - Method in class org.jmol.viewer.Viewer
-
This method is only called by JmolGLmol applet._refresh();
- getGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getGraphics(Object) - Method in interface org.jmol.api.GenericPlatform
- getGraphics(Object) - Static method in class org.jmol.awt.Image
- getGraphics(Object) - Method in class org.jmol.awt.Platform
- getGraphics(Object) - Method in class org.jmol.awtjs.Platform
- getGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
- getGraphicsForMetrics() - Method in class org.jmol.g3d.Platform3D
- getGraphicsForTextOrImage(int, int) - Method in class org.jmol.g3d.Platform3D
- getGroup(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getGroup1() - Method in class org.jmol.modelset.Group
- getGroup1() - Method in class org.jmol.modelsetbio.Monomer
- getGroup1(char) - Method in class org.jmol.modelset.Atom
- getGroup1(char) - Method in class org.jmol.smiles.SmilesAtom
- getGroup1(char) - Method in interface org.jmol.util.Node
- getGroup1b() - Method in class org.jmol.modelsetbio.Monomer
- getGroup1b() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getGroup3() - Method in class org.jmol.adapter.smarter.AtomIterator
- getGroup3() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getGroup3() - Method in class org.jmol.modelset.Group
- getGroup3(boolean) - Method in class org.jmol.modelset.Atom
- getGroup3(boolean) - Method in class org.jmol.smiles.SmilesAtom
- getGroup3(boolean) - Method in interface org.jmol.util.Node
- getGroup3(int) - Method in class org.jmol.modelset.ModelLoader
- getGroupBits(BS) - Method in class org.jmol.modelset.Atom
- getGroupBits(BS) - Method in class org.jmol.smiles.SmilesAtom
- getGroupBits(BS) - Method in interface org.jmol.util.Node
- getGroupCount() - Method in class org.jmol.modelset.Model
- getGroupCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getGroupID(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
- getGroupID(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
- getGroupID(Location) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- getGroupID(String) - Method in class org.jmol.modelsetbio.BioResolver
- getGroupIdFor(String) - Static method in class org.jmol.modelsetbio.BioResolver
- getGroupInfo(int, P3) - Method in class org.jmol.modelset.Group
- getGroupParameter(int) - Method in class org.jmol.modelset.Group
-
Monomers only
- getGroupParameter(int) - Method in class org.jmol.modelsetbio.Monomer
- getGroups() - Method in class org.jmol.modelset.ModelSet
-
In versions earlier than 12.1.51, groups[] was a field of ModelCollection.
- getGroupsWithin(int, BS) - Method in class org.jmol.modelset.ModelSet
- getGroupsWithin(int, BS) - Method in class org.jmol.viewer.Viewer
- getGroupsWithinAll(int, BS) - Method in class org.jmol.modelsetbio.BioModelSet
- getGroupsWithOps(String, float[], boolean) - Method in class org.jmol.symmetry.SpaceGroupFinder
-
Find all space groups that match EXACTLY or contain all of the operations specified.
- getHallLatticeEquivalent(int) - Static method in class org.jmol.symmetry.HallTranslation
- getHallTerms() - Static method in class org.jmol.symmetry.HallRotation
- getHallTerms() - Static method in class org.jmol.symmetry.HallTranslation
- getHallTranslation(char, int) - Static method in class org.jmol.symmetry.HallTranslation
- getHandedness(SimpleNode, SimpleNode, SimpleNode, SimpleNode, VTemp) - Static method in class org.jmol.smiles.SmilesStereo
-
determine the winding of the circuit a--b--c relative to point pt
- getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in interface org.jmol.api.JmolAnnotationParser
- getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in class org.jmol.dssx.AnnotationParser
- getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in class org.jmol.dssx.DSSR1
- getHeader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getHeader() - Method in class org.jmol.jvxl.readers.EfvetReader
- getHeaderRendererIcon(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getHeight() - Method in class org.jmol.awtjs.swing.Component
- getHeight() - Method in class org.jmol.util.Font
- getHeight(Object) - Static method in class org.jmol.awt.Image
- getHeight(Object) - Static method in class org.jmol.awtjs2d.Image
- getHelixData(int, char, int) - Method in class org.jmol.modelset.Group
- getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getHelixData(BS, int) - Method in class org.jmol.scriptext.MathExt
- getHelixData2(int, char, int) - Method in class org.jmol.modelsetbio.Monomer
- getHelixType(int) - Static method in class org.jmol.adapter.smarter.Structure
- getHelp(String) - Method in class org.jmol.viewer.Viewer
- getHermiteLevel() - Method in class org.jmol.viewer.Viewer
- getHermiteList(int, T3, T3, T3, T3, T3, T3[], int, int, boolean) - Static method in class org.jmol.util.GData
-
Used by Navigator, BioShapeRenderer, and DrawRenderer
- getHeteroList(int) - Method in class org.jmol.modelset.ModelSet
- getHexCode(short) - Static method in class org.jmol.util.C
- getHexCodes(short[]) - Static method in class org.jmol.util.C
- getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
- getHexitValue(char) - Static method in class org.jmol.util.Escape
- getHiddenSet() - Method in class org.jmol.viewer.SelectionManager
- getHideNotSelected() - Method in class org.jmol.viewer.SelectionManager
- getHigh - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
- getHighestOrder() - Method in class org.jmol.symmetry.PointGroup
- getHistoryWindowPosition(String) - Method in interface org.jmol.api.JmolAppAPI
- getHistoryWindowPosition(String) - Method in class org.openscience.jmol.app.JmolApp
- getHistoryWindowSize(String) - Method in interface org.jmol.api.JmolAppAPI
- getHistoryWindowSize(String) - Method in class org.openscience.jmol.app.JmolApp
- getHklPlane(T3, float, Lst<P3>) - Method in class org.jmol.script.ScriptParam
- getHorizAlignmentName(int) - Static method in class org.jmol.viewer.JC
- getHoverDelay() - Method in class org.jmol.viewer.Viewer
- getHoverLabel(int) - Method in class org.jmol.modelkit.ModelKit
-
Called by Viewer.hoverOn to set the special label if desired.
- getHtmlDisabled() - Method in class org.jmol.awtjs.swing.AbstractButton
- getHtmlDisabled() - Method in class org.jmol.awtjs.swing.JMenuItem
- getHtmlResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getHybridizationAndAxes(int, int, V3, V3, String, boolean, boolean, boolean, T3) - Method in class org.jmol.modelset.AtomCollection
- getHybridizationAndAxes(int, V3, V3, String) - Method in class org.jmol.viewer.Viewer
- getHybridizationAndAxesD(int, V3, V3, String) - Method in class org.jmol.modelset.AtomCollection
-
dsp3 (trigonal bipyramidal, see-saw, T-shaped) or d2sp3 (square planar, square pyramidal, octahedral)
- getHydrogenAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getHydrogenAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getHydrogenAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
-
Get the hydrogen atom count -- for ligand files
- getHydrophobicity() - Method in class org.jmol.modelset.Atom
- getHydrophobicity() - Method in class org.jmol.modelset.AtomCollection
- getHydrophobicity(int) - Static method in class org.jmol.util.Elements
- getIcon() - Method in interface org.jmol.api.SC
- getIcon() - Method in class org.jmol.awt.AwtSwingComponent
- getIcon() - Method in class org.jmol.awtjs.swing.AbstractButton
- getIcon(String) - Method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- getIcon(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getIconHeight() - Method in class org.openscience.jmol.app.janocchio.TableSorter.Arrow
- getIconWidth() - Method in class org.openscience.jmol.app.janocchio.TableSorter.Arrow
- getIconX(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getIconX(String) - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- getIconX(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getIconX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getId() - Method in enum org.jmol.c.STR
- getId(int) - Method in class org.jmol.shapesurface.MolecularOrbital
- getID(String, int) - Method in class org.jmol.shapesurface.LcaoCartoon
- getIdentifierOrNull(String) - Method in class org.jmol.modelset.AtomCollection
-
overhauled by RMH Nov 1, 2006.
- getIdentifierOrNull(String) - Method in class org.jmol.modelsetbio.BioModelSet
- getIdentity() - Method in class org.jmol.minimize.MinAtom
- getIdentity() - Method in class org.jmol.modelset.Bond
- getIdentity(int) - Method in class org.jmol.modelset.Atom
- getIdentityXYZ(P3, int) - Method in class org.jmol.modelset.Atom
- getIDStr() - Method in class org.jmol.modelset.Chain
- getImage(boolean, boolean) - Method in class org.jmol.viewer.Viewer
- getImage(Object, String, boolean) - Method in class org.jmol.viewer.FileManager
- getImage(String, boolean) - Method in class org.jmol.viewer.PropertyManager
- getImage(Viewer, Object, String, boolean) - Method in class org.jmol.io.JmolUtil
- getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.api.JmolViewer
- getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.viewer.OutputManager
-
Called when a simple image is required -- from x=getProperty("image") or for a simple preview PNG image for inclusion in a ZIP file from write xxx.zip or xxx.jmol, or for a PNGJ or PNG image that is being posted because of a URL that contains "?POST?_PNG_" or ?POST?_PNGJ_" or ?POST?_PNGJBIN_".
- getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.viewer.Viewer
- getImageDialog(String, Map<String, GenericImageDialog>) - Method in interface org.jmol.api.GenericPlatform
- getImageDialog(String, Map<String, GenericImageDialog>) - Method in class org.jmol.awt.Platform
- getImageDialog(String, Map<String, GenericImageDialog>) - Method in class org.jmol.awtjs2d.Platform
- getImageDialog(PlatformViewer, String, Map<String, GenericImageDialog>) - Static method in class org.jmol.awt.Image
- getImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Static method in class org.jmol.awtjs2d.Image
- getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in interface org.jmol.api.JmolDialogInterface
- getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in class org.jmol.dialog.Dialog
- getImageHeight(Object) - Method in interface org.jmol.api.GenericPlatform
- getImageHeight(Object) - Method in class org.jmol.awt.Platform
- getImageHeight(Object) - Method in class org.jmol.awtjs2d.Platform
- getImageIcon(String) - Method in class org.jmol.awt.AwtJmolPopup
- getImageIcon(String) - Method in class org.jmol.awt.AwtModelKitPopup
- getImageIcon(String) - Method in class org.jmol.awtjs2d.JSJmolPopup
- getImageIcon(String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
- getImageIcon(String) - Method in class org.jmol.popup.GenericPopup
- getImagePixels(Object, Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
- getImageURL(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getImageURLImpl(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getImageWidth(Object) - Method in interface org.jmol.api.GenericPlatform
- getImageWidth(Object) - Method in class org.jmol.awt.Platform
- getImageWidth(Object) - Method in class org.jmol.awtjs2d.Platform
- getImplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
- getImplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
- getImplicitHydrogenCount() - Method in interface org.jmol.util.Node
-
can be > 0 for PDB model with no H atoms or for SMILES string CCC
- getInchi(BS, String, String) - Method in class org.jmol.viewer.Viewer
-
Get an InChI or InChIKey for a set of atoms or MOL data.
- getInchi(Viewer, BS, String, String) - Method in interface org.jmol.api.JmolInChI
- getInchi(Viewer, BS, String, String) - Method in class org.jmol.inchi.InChIJNI
- getInchi(Viewer, BS, String, String) - Method in class org.jmol.inchi.InChIJS
- getInChI() - Method in interface org.jmol.api.GenericPlatform
- getInChI() - Method in class org.jmol.awt.Platform
- getInChI() - Method in class org.jmol.awtjs2d.Platform
- getIncrementalJValue(int, String, V3, V3, V3, double, int) - Static method in class org.jmol.quantum.NMRCalculation
- getIndex() - Method in class org.jmol.modelset.Atom
- getIndex() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the atom index of the atom.
- getIndex() - Method in interface org.jmol.util.Node
- getIndex() - Method in interface org.jmol.util.SimpleNode
- getIndex(int, int, int, int) - Method in class org.jmol.modelsetbio.BioPolymer
- getIndex(Monomer) - Method in class org.jmol.modelsetbio.ProteinStructure
- getIndexFromName(String) - Method in class org.jmol.shape.MeshCollection
- getIndexFromName(String) - Method in class org.jmol.shape.Shape
- getIndexFromName(String) - Method in class org.jmol.shapespecial.Dipoles
- getIndexFromName(String) - Method in class org.jmol.shapespecial.Ellipsoids
- getIndexFromName(String) - Method in class org.jmol.shapespecial.Polyhedra
- getIndexOf(int) - Method in class org.jmol.modelset.MeasurementPending
- getinfo() - Method in class org.jmol.modelkit.ModelKit
- getInfo() - Method in class org.jmol.modelset.Atom
- getInfo() - Method in class org.jmol.symmetry.SymmetryOperation
- getInfo() - Method in class org.jmol.symmetry.UnitCell
- getInfo() - Method in class org.jmol.util.Font
- getInfo() - Method in class org.jmol.util.Modulation
- getInfo(boolean) - Method in class org.jmol.shape.Mesh
- getInfo(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getInfo(int) - Method in class org.jmol.shape.Measures
- getInfo(int) - Method in class org.jmol.util.SimpleUnitCell
- getInfo(int, String) - Method in class org.jmol.modelset.ModelSet
- getInfo(int, String, boolean, String, int, float) - Method in class org.jmol.symmetry.PointGroup
- getInfo(Object[], int) - Static method in class org.jmol.symmetry.SymmetryDesc
-
Return information about a symmetry operator by type: array, angle, axis, center, draw, full, info, label, matrix4f, point, time, plane, translation, unitcell, xyz, all, or a negative number (-length, -1]: { "xyz", etc.
- getInfo(String) - Method in interface org.jmol.api.JmolNMRInterface
- getInfo(String) - Method in class org.jmol.quantum.NMRCalculation
- getInfo(String) - Method in class org.jmol.util.Tensor
-
returns an object of the specified type, including "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"
- getInfo(Map<String, Object>) - Method in class org.jmol.util.ModulationSet
- getInfo(Map<String, Object>) - Method in class org.jmol.util.Vibration
- getInfo(SpaceGroup, String, float[], boolean, boolean) - Static method in class org.jmol.symmetry.SpaceGroup
- getInfo(Viewer, String) - Method in class org.jmol.shapespecial.Polyhedron
- getInfoAsString(int) - Method in class org.jmol.shape.AtomShape
- getInfoAsString(int) - Method in class org.jmol.shape.Measures
- getInfoAsString(String) - Method in class org.jmol.modelset.Measurement
- getInfoB(int, String) - Method in class org.jmol.modelset.ModelSet
- getInfoBS(int) - Static method in class org.jmol.symmetry.SymmetryDesc
- getInfoHeight() - Method in class org.openscience.jmol.app.webexport.WebPanel
- getInfoI(int, String) - Method in class org.jmol.modelset.ModelSet
- getInfoIndex(String) - Static method in class org.jmol.util.Tensor
- getInfoM(String) - Method in class org.jmol.modelset.ModelSet
- getInfoWidth() - Method in class org.openscience.jmol.app.webexport.WebPanel
- getInfoXYZ(Atom) - Method in class org.jmol.viewer.ChimeMessenger
-
called when an atom is picked
- getInfoXYZ(Atom) - Method in interface org.jmol.viewer.JmolChimeMessenger
- getINI() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Save INI file
- getInitialJValue(int, double) - Static method in class org.jmol.quantum.NMRCalculation
- getInitiatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
- getInitiatorAtom() - Method in class org.jmol.modelsetbio.Monomer
- getInitiatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
- getInlineChar() - Method in class org.jmol.viewer.Viewer
- getInlineData(int) - Method in class org.jmol.modelset.ModelSet
- getInlineData(SB, String, boolean, Integer, String) - Method in class org.jmol.viewer.JmolStateCreator
- getInlineData(SB, String, boolean, Integer, String) - Method in class org.jmol.viewer.StateCreator
- getInMotion(boolean) - Method in class org.jmol.viewer.Viewer
- getInputPoint(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
-
for debugging
- getInputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
- getInputStreamOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
- getInsCode() - Method in class org.jmol.modelset.Group
- getInsertedCommand() - Method in class org.jmol.viewer.Viewer
- getInsertionCode() - Method in class org.jmol.adapter.smarter.AtomIterator
- getInsertionCode() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getInsertionCode() - Method in class org.jmol.modelset.Atom
- getInsertionCode() - Method in class org.jmol.modelset.Group
- getInsertionCode() - Method in class org.jmol.smiles.SmilesAtom
- getInsertionCode() - Method in interface org.jmol.util.Node
- getInsertionCodeChar(int) - Static method in class org.jmol.modelset.Group
- getInsertionCodeFor(int) - Static method in class org.jmol.modelset.Group
- getInsertionCodeIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
- getInsertionCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getInsertionListInModel(int) - Method in class org.jmol.modelset.ModelSet
- getInstance() - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- getInstance() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getInstance(JmolViewer, String, int, int, int) - Static method in class org.openscience.jmol.app.webexport.JmolInstance
- getInstanceList() - Method in class org.openscience.jmol.app.webexport.WebPanel
- getInstanceName(int) - Method in class org.openscience.jmol.app.webexport.WebPanel
- getInstanceWithParams(String, Class<?>[], Object...) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getInt() - Method in class org.jmol.jvxl.readers.EfvetReader
- getInt() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
- getInt() - Method in class org.jmol.jvxl.readers.PmeshReader
- getInt(int) - Method in class org.jmol.api.JmolViewer
- getInt(int) - Method in class org.jmol.shapecgo.CGOMesh
- getInt(int) - Method in class org.jmol.viewer.Viewer
- getInt(int, int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
safe int parsing of line.substring(col1, col2);
- getInt(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- getInt(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- getInt(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getInt(Map<String, Object>, String, int) - Static method in class org.jmol.viewer.OutputManager
- getIntArray2(int) - Method in class org.jmol.scriptext.ScriptExt
- getIntArrayFromStringList(String, int) - Static method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
turn "[1,2,3]" into [1,2,3] array will be truncated to n elements, or filled with zeros to pad to n, as necessary.
- getIntData() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- getIntegration() - Method in class org.jmol.quantum.QuantumCalculation
- getInteractionTensorList(String, BS) - Method in class org.jmol.quantum.NMRCalculation
-
Returns a list of tensors that are of the specified type and have both atomIndex1 and atomIndex2 in bsA.
- getInterface(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getInterface(String) - Static method in class org.jmol.jvxl.readers.SurfaceGenerator
- getInterface(String, Viewer, String) - Static method in class org.jmol.api.Interface
- getIntersection(float, P4, P3[], Lst<P3[]>, float[], BS, MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSlicer
- getIntKey(int, int, int) - Static method in class org.jmol.inchi.InChIJNI
- getIntTableNumber() - Method in interface org.jmol.api.SymmetryInterface
- getIntTableNumber() - Method in class org.jmol.symmetry.Symmetry
- getInvalidBS(BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getInvariantSymops(P3, int[]) - Method in interface org.jmol.api.SymmetryInterface
- getInvariantSymops(P3, int[]) - Method in class org.jmol.symmetry.Symmetry
- getInverseNormix(short) - Static method in class org.jmol.util.Normix
- getISCtype(Atom, String) - Method in class org.jmol.quantum.NMRCalculation
- getIsHetero() - Method in class org.jmol.adapter.smarter.AtomIterator
- getIsHetero() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getIsoExt() - Method in class org.jmol.script.ScriptExpr
- getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in interface org.jmol.api.JmolNMRInterface
-
If t is null, then a1, a2, and type are used to find the appropriate tensor.
- getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
- getIsosurfaceJvxl(int, String) - Method in class org.jmol.scriptext.CmdExt
- getIsosurfacePropertySmoothing(boolean) - Method in class org.jmol.viewer.Viewer
- getIsotopeData(Atom, int) - Method in class org.jmol.quantum.NMRCalculation
-
Get magnetogyricRatio (gamma/10^7 rad s^-1 T^-1) and quadrupoleMoment (Q/10^-2 fm^2) for a given isotope or for the default isotope of an element.
- getIsotopeNumber() - Method in class org.jmol.modelset.Atom
- getIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
- getIsotopeNumber() - Method in interface org.jmol.util.Node
- getIsotopeNumber() - Method in interface org.jmol.util.SimpleNode
- getIsotopeNumber(int) - Static method in class org.jmol.util.Elements
- getItem(int) - Method in class org.jmol.awtjs.swing.JMenu
- getItem(int) - Static method in class org.jmol.quantum.QS
- getItemCount() - Method in class org.jmol.awtjs.swing.JMenu
- getItemType(SC) - Method in class org.jmol.awt.AwtPopupHelper
- getItemType(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getItemType(SC) - Method in interface org.jmol.popup.PopupHelper
- getIterativeModels(boolean) - Method in class org.jmol.modelset.ModelSet
-
only some models can be iterated through.
- getIterator(Viewer, Atom, BS, float) - Method in interface org.jmol.api.SymmetryInterface
- getIterator(Viewer, Atom, BS, float) - Method in class org.jmol.symmetry.Symmetry
- getJavaConsole() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getJavaConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getJavaConsole(Jmol) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Deprecated.
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
- getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
-
Each Widget must implement this function and make sure to use the appletID number to specify the target applet i.e.
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
- getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
-
A COPY OF THIS .JS FILE MUST BE STORED IN THE html PART OF WEBEXPORT
- getJBR() - Method in class org.jmol.viewer.Viewer
- getJCouplingHz(Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
- getJDXBaseModelIndex(int) - Method in class org.jmol.viewer.Viewer
-
get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file.
- getJmol(int, int, String) - Static method in class org.openscience.jmol.app.JmolData
- getJmol(JFrame, int, int, Map<String, Object>) - Static method in class org.openscience.jmol.app.Jmol
- getJmol(JmolApp, JFrame) - Static method in class org.openscience.jmol.app.Jmol
- getJmolAtom(int) - Method in class org.jmol.smiles.SmilesStereo
- getJmolBondType(JniInchiBond) - Static method in class org.jmol.inchi.InChIJNI
- getJmolCanonicalXYZ(String) - Static method in class org.jmol.symmetry.SymmetryOperation
- getJmolDataFrameIndex(int, String) - Method in class org.jmol.modelset.ModelSet
- getJmolDataSourceFrame(int) - Method in class org.jmol.modelset.ModelSet
- getJmolDistance(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
- getJmolDistance(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
Calc using Jmol atom index
- getJmolFrameType(int) - Method in class org.jmol.modelset.ModelSet
- getJmolName(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getJmolNoe(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
- getJmolNoe(int, int) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- getJmolObject(int, BS, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getJmolOrRasmolArgb(int, int) - Method in class org.jmol.viewer.ColorManager
- getJmolParameter(String) - Method in class org.jmol.util.GenericApplet
- getJmolPerspective() - Method in class org.jmol.export.___Exporter
- getJmolProperty(String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getJmolScriptCallback(CBK) - Method in class org.jmol.viewer.StatusManager
- getJmolVersion() - Static method in class org.jmol.api.JmolViewer
- getJmolVersion() - Static method in class org.jmol.viewer.Viewer
- getJones() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
- getJSJSONParser() - Method in class org.jmol.viewer.Viewer
- getJSliderLabelTable(JSlider) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- getJsObjectInfo(Object[], String, Object[]) - Method in interface org.jmol.api.GenericPlatform
- getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awt.Platform
- getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awtjs2d.Platform
- getJsonNioServer() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getJspecViewProperties(Object) - Method in class org.jmol.viewer.Viewer
- getJspecViewProperties(String) - Method in class org.jmol.viewer.StatusManager
- getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolStatusListener
- getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolSyncInterface
- getJSpecViewProperty(String) - Method in class org.jmol.util.GenericApplet
-
JSpecView shares the JmolSyncInterface; used to get JSpecView
- getJSpecViewProperty(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- getJSV() - Method in class org.jmol.viewer.Viewer
- getJvalue() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule.DihedralCouple
- getJVXLCutoff() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getJVXLCutoff() - Method in class org.jmol.jvxl.readers.VolumeFileReader
- getJzt() - Method in class org.jmol.viewer.Viewer
- getJzu() - Method in class org.jmol.viewer.FileManager
- getKekuleElementNumber() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Calculate the average element numbers of associated double-bond atoms weighted by their most significant Kekule resonance contributor(s).
- getKey() - Method in interface org.jmol.api.JmolAbstractButton
- getKey() - Method in class org.jmol.console.JmolButton
- getKey() - Method in class org.jmol.console.JmolLabel
- getKey() - Method in class org.jmol.console.JmolToggleButton
- getKey() - Method in class org.jmol.console.KeyJCheckBox
- getKey() - Method in class org.jmol.console.KeyJCheckBoxMenuItem
- getKey() - Method in class org.jmol.console.KeyJMenu
- getKey() - Method in class org.jmol.console.KeyJMenuItem
- getKey() - Method in class org.jmol.console.KeyJRadioButtonMenuItem
- getKey(int, int) - Method in class org.jmol.util.MeshSlicer
- getKey(int, int, int, int, int) - Static method in class org.jmol.minimize.MinObject
- getKey(Object, int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getKey(Edge) - Static method in class org.jmol.smiles.SmilesRing
- getKeyList(boolean, Lst<String>, String) - Method in class org.jmol.script.SV
- getKeyMap() - Static method in class org.jmol.shapecgo.CGOMesh
- getKeys(boolean) - Method in class org.jmol.script.SV
- getKeys(String) - Method in class org.jmol.viewer.PropertyManager
- getKeyType(String) - Static method in class org.jmol.symmetry.SymmetryDesc
- getLabel() - Method in class org.jmol.symmetry.PointGroup.Operation
- getLabel(int) - Method in class org.jmol.shape.Labels
- getLabel(int, boolean, boolean) - Method in class org.jmol.modelset.Measurement
- getLabel(String) - Static method in class org.jmol.console.GenericConsole
- getLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getLabel(LabelToken[]) - Static method in class org.jmol.modelset.LabelToken
- getLabel1() - Method in class org.jmol.console.AppletConsole
- getLabel1() - Method in class org.jmol.console.GenericConsole
- getLabelArray() - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- getLabeler() - Method in class org.jmol.modelset.AtomCollection
- getLabelKey(String) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
- getLabelString() - Method in class org.jmol.modelset.Measurement
- getLabelText() - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- getLabelText() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- getLabelText() - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- getLabelText() - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- getLabelWithoutMnemonic(String) - Static method in class org.jmol.console.GenericConsole
- getLanguage() - Static method in class org.jmol.i18n.GT
- getLanguage() - Static method in class org.jmol.i18n.Resource
- getLanguageList() - Static method in class org.jmol.i18n.Language
-
This is the place to put the list of supported languages.
- getLanguageList(GT) - Static method in class org.jmol.i18n.GT
- getLastAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getLastAtomSetAtomIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getLastConventional - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- getLastCumuleneAtom(SimpleEdge, SimpleNode, int[], SimpleNode[]) - Method in class org.jmol.symmetry.CIPChirality
- getLastError() - Static method in exception org.jmol.smiles.InvalidSmilesException
- getLastException() - Method in interface org.jmol.api.SmilesMatcherInterface
- getLastException() - Method in class org.jmol.smiles.SmilesMatcher
- getLastIndex() - Method in class org.jmol.modelset.Measurement
- getLastPoint(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
-
Find the lowest ascender or descender above scan line bounding the region for this point.
- getLastVibrationVector(int, int) - Method in class org.jmol.modelset.ModelSet
- getLatticeCentering() - Method in interface org.jmol.api.SymmetryInterface
- getLatticeCentering() - Method in class org.jmol.symmetry.Symmetry
- getLatticeCentering(SymmetryOperation[]) - Static method in class org.jmol.symmetry.SymmetryOperation
- getLatticeCode(int) - Static method in class org.jmol.symmetry.HallTranslation
- getLatticeDesignation() - Method in interface org.jmol.api.SymmetryInterface
- getLatticeDesignation() - Method in class org.jmol.symmetry.HallInfo
- getLatticeDesignation() - Method in class org.jmol.symmetry.SpaceGroup
- getLatticeDesignation() - Method in class org.jmol.symmetry.Symmetry
- getLatticeDesignation(int) - Static method in class org.jmol.symmetry.HallTranslation
- getLatticeDesignation2(char, boolean) - Static method in class org.jmol.symmetry.HallTranslation
- getLatticeExtension(char, boolean) - Static method in class org.jmol.symmetry.HallTranslation
- getLatticeIndex(char) - Static method in class org.jmol.symmetry.HallTranslation
- getLatticeOp() - Method in interface org.jmol.api.SymmetryInterface
- getLatticeOp() - Method in class org.jmol.symmetry.Symmetry
- getLatticePoints(int) - Method in class org.jmol.util.BZone
-
Get the needed lattice points for n Brillouin zones.
- getLatticeType() - Method in interface org.jmol.api.SymmetryInterface
- getLatticeType() - Method in class org.jmol.symmetry.Symmetry
- getLeadAtom() - Method in class org.jmol.modelset.Group
- getLeadAtom() - Method in class org.jmol.modelsetbio.Monomer
- getLeadAtomIndices() - Method in class org.jmol.modelsetbio.BioPolymer
- getLeadAtomOr(Atom) - Method in class org.jmol.modelset.Group
- getLeadColix(int) - Method in class org.jmol.renderbio.BioShapeRenderer
- getLeadColixBack(int) - Method in class org.jmol.renderbio.BioShapeRenderer
- getLeadMidPoint(int, P3) - Method in class org.jmol.modelsetbio.BioPolymer
- getLeadMidpoints() - Method in class org.jmol.modelsetbio.BioPolymer
- getLeadPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
- getLeadPoints() - Method in class org.jmol.modelsetbio.BioPolymer
- getLeftPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
- getLength() - Method in class org.openscience.jvxl.MonitorInputStream
- getLength(int) - Method in class org.jmol.shapespecial.Ellipsoid
- getLevel(int) - Static method in class org.jmol.util.Logger
-
Returns the text corresponding to a level.
- getlexpNoes() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getLexStr(byte[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getLigandBondInfo(JmolAdapter, Object, String) - Method in class org.jmol.modelsetbio.BioResolver
-
reads PDB ligand CIF info and creates a bondInfo object.
- getLigandInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
- getLigandInfo(Object) - Method in class org.jmol.viewer.PropertyManager
- getLigandModel(String, String, String, String) - Method in class org.jmol.viewer.Viewer
-
obtain CIF data for a ligand for purposes of adding hydrogens or for any other purpose in terms of saving a data set for a file in a state
- getLightingInfo() - Method in class org.jmol.export._TachyonExporter
- getLightingState() - Method in class org.jmol.viewer.Viewer
- getLightingState(boolean) - Method in class org.jmol.viewer.JmolStateCreator
- getLightingState(boolean) - Method in class org.jmol.viewer.StateCreator
- getLightSource() - Method in class org.jmol.util.GData
- getLikeUnlike(BS, BS[], int) - Method in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- getLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- getLine() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- getLine() - Method in class org.jmol.jvxl.readers.XmlReader
- getLine() - Method in class org.jmol.jvxl.readers.XplorReader
- getLinearOffset(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- getLinenumber(ScriptContext) - Method in class org.jmol.script.ScriptEval
- getLinesUntil(String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- getLinkById(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- getLinkInfo() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- getList() - Method in class org.jmol.script.SV
- getList(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getList(String) - Method in class org.jmol.symmetry.CIPData
-
Retrieve an array of bit sets that match a given SMARTS
- getList(String) - Method in class org.jmol.symmetry.CIPDataSmiles
- getList(Lst<Object>, int) - Static method in class org.jmol.jvxl.readers.PyMOLMeshReader
- getList(Viewer, Object, String[], String) - Static method in class org.jmol.symmetry.SpaceGroupFinder
- getListCellRendererComponent(JList<?>, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
- getListCellRendererComponent(JList<?>, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
- getLoadFilesList(int, SB, SB, Map<String, Object>, Lst<String>) - Method in class org.jmol.script.ScriptEval
- getLoadModelIndex(int, SB, Map<String, Object>) - Method in class org.jmol.script.ScriptEval
- getLoadState(Map<String, Object>) - Method in class org.jmol.viewer.GlobalSettings
-
these settings are determined when the file is loaded and are kept even though they might later change.
- getLoadSymmetryParams(int, SB, Map<String, Object>) - Method in class org.jmol.scriptext.CmdExt
- getLocalDirectory(Viewer, boolean) - Static method in class org.jmol.viewer.FileManager
- getLocalPathForWritingFile(Viewer, String) - Static method in class org.jmol.viewer.FileManager
- getLocalUrl(String) - Method in interface org.jmol.api.GenericPlatform
- getLocalUrl(String) - Method in class org.jmol.awt.Platform
- getLocalUrl(String) - Method in class org.jmol.awtjs2d.Platform
- getLocalUrl(String) - Method in class org.jmol.viewer.Viewer
- getLocalUrl(GenericFileInterface) - Static method in class org.jmol.awt.AwtFile
- getLogData() - Method in class org.jmol.minimize.forcefield.Calculations
- getLogData() - Method in class org.jmol.minimize.forcefield.ForceField
- getLogFileName() - Method in class org.jmol.viewer.Viewer
- getLogLevel() - Static method in class org.jmol.util.Logger
- getLogPath(String) - Method in class org.jmol.viewer.OutputManager
- getLogPath(String) - Method in class org.jmol.viewer.OutputManagerAwt
- getLogPath(String) - Method in class org.jmol.viewer.OutputManagerJS
- getLong(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getM3() - Method in class org.jmol.symmetry.PointGroup.Operation
- getMacro(String) - Method in class org.jmol.viewer.Viewer
-
retrieve macros.json from the directory
- getMad(int, short) - Method in class org.jmol.shapebio.BioShape
- getMadBond() - Method in class org.jmol.api.JmolViewer
- getMadBond() - Method in class org.jmol.viewer.Viewer
- getMadParameter() - Method in class org.jmol.script.ScriptParam
- getMagneticOp() - Method in class org.jmol.symmetry.SymmetryOperation
-
Magnetic spin is a pseudo (or "axial") vector.
- getMagneticShielding(Atom) - Method in interface org.jmol.api.JmolNMRInterface
- getMagneticShielding(Atom) - Method in class org.jmol.quantum.NMRCalculation
- getMainItem(Map<String, SV>) - Method in class org.jmol.dssx.AnnotationParser
- getManifestScriptPath(String) - Static method in class org.jmol.viewer.FileManager
-
check a JmolManifest for a reference to a script file (.spt)
- getMap() - Method in class org.jmol.script.SV
- getMap(boolean) - Method in class org.jmol.adapter.readers.pymol.PickleReader
- getMapForJME(String, Atom[], BS) - Method in interface org.jmol.api.SmilesMatcherInterface
- getMapForJME(String, Atom[], BS) - Method in class org.jmol.smiles.SmilesMatcher
- getMapKeys(int, boolean) - Method in class org.jmol.script.SV
- getMapList(Map<String, Object>, String) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getMappedTopoAtoms(SmilesAtom, SmilesAtom, Node[], int[]) - Method in class org.jmol.smiles.SmilesStereo
- getMaps - Variable in class org.jmol.smiles.SmilesSearch
- getMapSafely(Map<String, Object>, String) - Static method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
Safely get a Map from a Map using a key.
- getMapSubset(Map<String, ?>, String, Map<String, Object>, Lst<Object>) - Static method in class org.jmol.viewer.PropertyManager
- getMark() - Method in class org.jmol.adapter.readers.pymol.PickleReader
- getMass() - Method in class org.jmol.modelset.Atom
- getMass() - Method in class org.jmol.smiles.SmilesAtom
- getMass() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
get the atomic mass only if needed by Rule 2, testing for three special conditions in the case of isotopes: If a duplicate, or an isotope that is 100% nat abundant is specified, or isotopic mass is not specified, just use the average mass.
- getMass() - Method in interface org.jmol.util.Node
- getMass() - Method in interface org.jmol.util.SimpleNode
- getMasses() - Method in class org.jmol.adapter.readers.more.MdTopReader
- getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the matching atom or null.
- getMatchingAtomIndex() - Method in class org.jmol.smiles.SmilesAtom
-
Returns the number of a matching atom in a molecule.
- getMatchingBond() - Method in class org.jmol.smiles.SmilesBond
- getMatchingBondedAtom(int) - Method in class org.jmol.smiles.SmilesAtom
- getMathExt() - Method in class org.jmol.script.ScriptExpr
- getMatrices(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getMatrix4f(M3, T3) - Static method in class org.jmol.script.ScriptMathProcessor
- getMatrixFromString(String, float[], boolean, int) - Method in interface org.jmol.api.SymmetryInterface
- getMatrixFromString(String, float[], boolean, int) - Method in class org.jmol.symmetry.Symmetry
- getMatrixFromString(SymmetryOperation, String, float[], boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
-
Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 format
- getMatrixFromXYZ(String) - Static method in class org.jmol.symmetry.SymmetryOperation
- getMaxDim() - Method in class org.jmol.util.BoxInfo
- getMaxMathParams(int) - Static method in class org.jmol.script.T
- getMaxVanderwaalsRadius() - Method in class org.jmol.modelset.AtomCollection
- getMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
- getMeasurementCount() - Method in class org.jmol.api.JmolViewer
- getMeasurementCount() - Method in class org.jmol.viewer.Viewer
- getMeasurementCountPlusIndices(int) - Method in class org.jmol.api.JmolViewer
- getMeasurementCountPlusIndices(int) - Method in class org.jmol.viewer.Viewer
- getMeasurementCountPlusIndices(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getMeasurementCountPlusIndices(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getMeasurementCountPlusIndices(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- getMeasurementCountPlusIndicesForTableRow(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- getMeasurementInfo() - Method in class org.jmol.viewer.PropertyManager
- getMeasurementInfoAsString() - Method in class org.jmol.viewer.Viewer
- getMeasurements(boolean, boolean) - Method in class org.jmol.modelset.MeasurementData
-
if this is the client, then this method can be called to get the result vector, either as a string or as an array.
- getMeasurementScript(String, boolean) - Method in class org.jmol.modelset.Measurement
-
Used by MouseManager and Picking Manager to build the script
- getMeasurementState(Measures) - Method in class org.jmol.viewer.StateCreator
- getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer
- getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer
- getMeasurementTable() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getMeasurementTable() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getMemo(int) - Method in class org.jmol.adapter.readers.pymol.PickleReader
- getMenu(String) - Method in class org.jmol.awt.AwtPopupHelper
- getMenu(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getMenu(String) - Method in interface org.jmol.popup.PopupHelper
- getMenu(String) - Method in class org.jmol.viewer.Viewer
- getMenu(String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
- getMenuAsText(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
- getMenuAsText(String) - Method in class org.jmol.popup.MainPopupResourceBundle
- getMenuAsText(String) - Method in class org.jmol.popup.PopupResource
- getMenuHTML() - Method in class org.jmol.awtjs.swing.AbstractButton
- getMenuIcon() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getMenuIcon() - Method in interface org.openscience.jmol.app.JmolPlugin
- getMenuItem(String) - Method in class org.jmol.awt.AwtPopupHelper
- getMenuItem(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getMenuItem(String) - Method in interface org.jmol.popup.PopupHelper
- getMenuItem(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Fetch the menu item that was created for the given command.
- getMenuItem(AwtPopupHelper, String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
- getMenuName() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
- getMenuName() - Method in class org.jmol.popup.MainPopupResourceBundle
- getMenuName() - Method in class org.jmol.popup.PopupResource
- getMenuPopup(String, char) - Method in interface org.jmol.api.GenericPlatform
- getMenuPopup(String, char) - Method in class org.jmol.awt.Platform
- getMenuPopup(String, char) - Method in class org.jmol.awtjs2d.Platform
- getMenuText() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getMenuText() - Method in interface org.openscience.jmol.app.JmolPlugin
- getMenuText(String) - Method in class org.jmol.popup.JmolPopup
- getMesh(String) - Method in class org.jmol.shape.MeshCollection
- getMeshCommand(SB, int) - Method in class org.jmol.shapesurface.Isosurface
- getMeshData(String, int[][], T3[], T3[]) - Method in class org.jmol.export._IdtfExporter
- getMeshHeader(String, int, int, int, int, SB) - Method in class org.jmol.export._IdtfExporter
- getMeshList(String, boolean) - Method in class org.jmol.shape.MeshCollection
-
Get matching list of meshes, order reversed
- getMeshSlicer() - Method in class org.jmol.util.MeshSurface
- getMessage() - Method in exception org.jmol.script.ScriptException
- getMessage() - Method in exception org.jmol.smiles.InvalidSmilesException
- getMessage(Measurement, boolean) - Static method in class org.jmol.shape.Measures
- getMF(Lst<TopoCifParser.TAtom>) - Static method in class org.jmol.adapter.readers.cif.TopoCifParser
- getMiddle() - Method in class org.openscience.jmol.app.surfacetool.Slice
- getMinDistance2ForVertexGrouping() - Method in class org.jmol.shape.Mesh
- getMinDistance2ForVertexGrouping() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getMinDistances(MeasurementData) - Method in interface org.jmol.api.JmolNMRInterface
- getMinDistances(MeasurementData) - Method in class org.jmol.quantum.NMRCalculation
- getMinimizationInfo() - Method in class org.jmol.viewer.Viewer
- getMinimizer(boolean) - Method in class org.jmol.viewer.Viewer
- getMinindex() - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- getMinindex() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getMiniPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
- getMinMax() - Method in class org.jmol.jvxl.calc.MarchingSquares
- getMinMax(Object, int, boolean) - Method in class org.jmol.scriptext.MathExt
- getMinMaxMappedValues(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getMinMaxPoint(Object, int) - Method in class org.jmol.scriptext.MathExt
-
calculates the statistical value for x, y, and z independently
- getMinMaxQuaternion(Lst<SV>, int) - Method in class org.jmol.scriptext.MathExt
- getMinZ(Atom[], int[]) - Method in class org.jmol.modelset.Group
- getMissingHydrogenCount() - Method in class org.jmol.smiles.SmilesSearch
- getMissingHydrogenCount(Atom, boolean) - Method in class org.jmol.modelset.AtomCollection
- getMixingTime() - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
get the mixing time
- getMixingTimeSec() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
get the mixing time
- getMKState() - Method in class org.jmol.modelkit.ModelKit
- getMMFF94AtomTypes(String[], Node[], int, BS, Lst<BS>, Lst<BS>[]) - Method in interface org.jmol.api.SmilesMatcherInterface
- getMMFF94AtomTypes(String[], Node[], int, BS, Lst<BS>, Lst<BS>[]) - Method in class org.jmol.smiles.SmilesMatcher
-
called by ForceFieldMMFF.setAtomTypes only
- getMMTFAtoms(boolean) - Method in class org.jmol.adapter.readers.cif.MMTFReader
-
set up all atoms, including bonding, within a group
- getMMTFBioAssembly() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- getMnemonic(String) - Static method in class org.jmol.console.GenericConsole
- getMod(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Modulation data keys are keyed by model number as well as type using [at]n, where n is the model number, starting with 0.
- getMod(String) - Method in interface org.jmol.adapter.smarter.MSInterface
- getModAtom(int) - Method in class org.jmol.render.MeasuresRenderer
- getModCalc() - Method in class org.jmol.util.ModulationSet
- getModel() - Method in class org.jmol.modelset.Group
-
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
- getModel(String, BS, Object[], OC) - Method in class org.jmol.viewer.PropertyManager
-
EXPERIMENTAL create a QCJSON file -- very preliminary
- getModelAdapter() - Method in class org.jmol.api.JmolViewer
- getModelAdapter() - Method in class org.jmol.viewer.Viewer
- getModelAtomBitSetIncludingDeleted(int, boolean) - Method in class org.jmol.modelset.ModelSet
-
Note that this method returns all atoms, included deleted ones.
- getModelAtomBitSetIncludingDeletedBs(BS) - Method in class org.jmol.modelset.ModelSet
-
note -- this method returns ALL atoms, including deleted.
- getModelAtomIndices() - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
-
prepare a list of starting atom indices for each model, adding one additional one to indicate 1 + last atom index
- getModelAuxiliaryInfo(int) - Method in class org.jmol.modelset.ModelSet
- getModelAuxiliaryInfoForAtom(int) - Method in class org.jmol.symmetry.CIPDataTracker
- getModelBS(int, BS) - Method in class org.jmol.modelset.Trajectory
-
set bits for all trajectories associated with this model
- getModelBS(BS, boolean) - Method in class org.jmol.modelset.ModelSet
-
Get the set of models associated with a set of atoms.
- getModelCellRange(int) - Method in class org.jmol.modelset.ModelSet
- getModelCenter() - Method in class org.jmol.export.__CartesianExporter
- getModelCml(BS, int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- getModelCml(BS, int, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getModelCml(BS, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
- getModelCount() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getModelData(boolean) - Method in class org.jmol.jsv.JDXMOLParser
- getModelDataBaseName(BS) - Method in class org.jmol.modelset.ModelSet
- getModelDipole() - Method in class org.jmol.viewer.Viewer
- getModelDipole(int) - Method in class org.jmol.modelset.ModelSet
- getModelExtract(Object, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
-
V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
- getModelExtract(BS, boolean, boolean, String, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getModelExtract(BS, boolean, boolean, String, boolean) - Method in class org.jmol.viewer.PropertyManager
-
V3000, SDF, MOL, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR, QCJSON, PWMAT, PWSLAB, XSF MOL67 is MOL with bonds of type 6 or 7 (aromatic single/double)
- getModelFileData(String, String, boolean) - Method in class org.jmol.viewer.Viewer
- getModelFileInfo() - Method in class org.jmol.viewer.Viewer
- getModelFileInfo(BS) - Method in interface org.jmol.api.JmolPropertyManager
- getModelFileInfo(BS) - Method in class org.jmol.viewer.PropertyManager
- getModelFileInfoAll() - Method in class org.jmol.viewer.Viewer
- getModelFileName(int) - Method in class org.jmol.modelset.ModelSet
- getModelFileNumber(int) - Method in class org.jmol.viewer.Viewer
- getModelFileType(int) - Method in class org.jmol.modelset.ModelSet
- getModelForAtomIndex(int) - Method in class org.jmol.viewer.Viewer
- getModelForMode(int, int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- getModelIndex() - Method in class org.jmol.modelset.Atom
-
SMILES only
- getModelIndex() - Method in class org.jmol.smiles.SmilesAtom
- getModelIndex() - Method in interface org.jmol.util.Node
- getModelIndex(ModelSet) - Method in class org.jmol.adapter.readers.pymol.JmolObject
- getModelIndexFromId(String) - Method in interface org.jmol.api.JmolAppletInterface
- getModelIndexFromId(String) - Method in class org.jmol.api.JmolViewer
- getModelIndexFromId(String) - Method in class org.jmol.modelset.ModelSet
- getModelIndexFromId(String) - Method in class org.jmol.util.GenericApplet
- getModelIndexFromId(String) - Method in class org.jmol.viewer.Viewer
- getModelIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
- getModelIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getModelInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
- getModelInfo(Object) - Method in class org.jmol.viewer.PropertyManager
- getModelInfo(String) - Method in class org.jmol.viewer.Viewer
-
get a value from the current model's Model.auxiliaryInfo
- getModelInfoAsString() - Method in class org.jmol.modelset.ModelSet
- getModelkit(boolean) - Method in class org.jmol.viewer.Viewer
- getModelkitProperty(String) - Method in class org.jmol.viewer.Viewer
-
Get a ModelKit property.
- getModelKitStateBitset(BS, BS) - Method in class org.jmol.modelset.ModelSet
- getModelName() - Method in class org.jmol.adapter.readers.pdb.PdbReader
-
A Jmol add-on -- allows for model name on MODEL line starting in column 15 (0-based)
- getModelName(int) - Method in class org.jmol.api.JmolViewer
- getModelName(int) - Method in class org.jmol.modelset.ModelSet
- getModelName(int) - Method in class org.jmol.viewer.Viewer
- getModelNumber() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- getModelNumber() - Method in class org.jmol.modelset.Atom
- getModelNumber(int) - Method in class org.jmol.api.JmolViewer
- getModelNumber(int) - Method in class org.jmol.modelset.ModelSet
- getModelNumber(int) - Method in class org.jmol.viewer.Viewer
- getModelNumberDotted(int) - Method in class org.jmol.api.JmolViewer
- getModelNumberDotted(int) - Method in class org.jmol.modelset.ModelSet
- getModelNumberDotted(int) - Method in class org.jmol.viewer.Viewer
- getModelNumberForAtomLabel(int) - Method in class org.jmol.modelset.ModelSet
- getModelNumberForLabel() - Method in class org.jmol.modelset.Atom
- getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
- getModelOrientation(int) - Method in class org.jmol.modelset.ModelSet
- getModelProperties(int) - Method in class org.jmol.api.JmolViewer
- getModelProperties(int) - Method in class org.jmol.viewer.Viewer
- getModelProperty(int, String) - Method in class org.jmol.modelset.ModelSet
- getModelSetAuxiliaryInfo() - Method in class org.jmol.api.JmolViewer
- getModelSetAuxiliaryInfo() - Method in class org.jmol.viewer.Viewer
- getModelSetFileName() - Method in class org.jmol.api.JmolViewer
- getModelSetFileName() - Method in class org.jmol.viewer.Viewer
- getModelSetPathName() - Method in class org.jmol.api.JmolViewer
- getModelSetPathName() - Method in class org.jmol.viewer.Viewer
- getModelSetProperties() - Method in class org.jmol.api.JmolViewer
- getModelSetProperties() - Method in class org.jmol.viewer.Viewer
- getModelSetTypeName() - Method in class org.jmol.modelset.ModelSet
- getModelSpecial(int) - Method in class org.jmol.viewer.AnimationManager
- getModelsSelected() - Method in class org.jmol.modelset.Trajectory
- getModelState(SB, boolean, boolean) - Method in class org.jmol.viewer.JmolStateCreator
- getModelState(SB, boolean, boolean) - Method in class org.jmol.viewer.StateCreator
- getModelSymmetryCount(int) - Method in class org.jmol.modelset.ModelSet
- getModelTitle(int) - Method in class org.jmol.modelset.ModelSet
- getModelToView() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getModelUndeletedAtomsBitSet(int) - Method in class org.jmol.viewer.Viewer
- getModelUndeletedAtomsBitSetBs(BS) - Method in class org.jmol.viewer.Viewer
- getModMatrices() - Method in class org.jmol.adapter.readers.cif.Subsystem
- getModPoint(boolean) - Method in interface org.jmol.api.JmolModulationSet
- getModPoint(boolean) - Method in class org.jmol.util.ModulationSet
- getModType(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getModType(String) - Method in interface org.jmol.adapter.smarter.MSInterface
- getModulation() - Method in class org.jmol.modelset.Atom
- getModulation(char, T3, boolean) - Method in interface org.jmol.api.JmolModulationSet
- getModulation(char, T3, boolean) - Method in class org.jmol.util.ModulationSet
- getModulation(int) - Method in class org.jmol.modelset.AtomCollection
- getModulationList(BS, char, P3) - Method in class org.jmol.modelset.ModelSet
- getModulationMap() - Method in class org.jmol.adapter.readers.cif.MSRdr
- getModulationMap() - Method in interface org.jmol.adapter.smarter.MSInterface
- getModulationReader() - Method in class org.jmol.adapter.readers.cif.CifReader
- getMOHeader(int, String[], Map<String, Object>[], int) - Method in class org.jmol.adapter.readers.quantum.MOReader
- getMoInfo(int) - Method in class org.jmol.shapesurface.MolecularOrbital
- getMoJvxl(int, boolean) - Method in class org.jmol.scriptext.CmdExt
- getMolecular(BS) - Method in class org.jmol.shapespecial.Dipoles
- getMolecularFormula() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- getMolecularFormula(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
- getMolecularFormula(String, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
- getMolecularFormula(String, boolean) - Method in class org.jmol.smiles.SmilesMatcher
- getMolecularFormulaAtoms(Node[], BS, float[], boolean) - Static method in class org.jmol.util.JmolMolecule
- getMolecularFormulaImpl(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
- getMoleculeBitSet(BS) - Method in class org.jmol.modelset.ModelSet
-
return cumulative sum of all atoms in molecules containing these atoms
- getMoleculeBitSetForAtom(int) - Method in class org.jmol.modelset.ModelSet
- getMoleculeCountInModel(int) - Method in class org.jmol.modelset.ModelSet
- getMoleculeIndex(int, boolean) - Method in class org.jmol.modelset.ModelSet
- getMoleculeInfo(Object) - Method in class org.jmol.viewer.PropertyManager
- getMoleculeNumber(boolean) - Method in class org.jmol.modelset.Atom
- getMoleculeNumber(boolean) - Method in class org.jmol.smiles.SmilesAtom
- getMoleculeNumber(boolean) - Method in interface org.jmol.util.Node
- getMolecules() - Method in class org.jmol.modelset.ModelSet
- getMolecules(Node[], BS[], Lst<BS>, BS) - Static method in class org.jmol.util.JmolMolecule
-
Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.
- getMolName() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
- getMonomerIndex() - Method in class org.jmol.modelset.Group
- getMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
- getMonomerSequenceAtoms(BS, BS) - Method in class org.jmol.modelsetbio.Monomer
- getMopacAtomZetaSPD(String) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
- getMoreInfo() - Method in interface org.jmol.api.SymmetryInterface
- getMoreInfo() - Method in class org.jmol.symmetry.Symmetry
- getMOString(float[]) - Static method in class org.jmol.quantum.QS
- getMotionEventNumber() - Method in class org.jmol.api.JmolViewer
- getMotionEventNumber() - Method in class org.jmol.viewer.Viewer
- getMotionFixedAtoms() - Method in class org.jmol.viewer.SelectionManager
- getMotionFixedAtoms() - Method in class org.jmol.viewer.Viewer
- getMoTokens(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- getMouseAction(int, int, int) - Static method in class org.jmol.viewer.binding.Binding
- getMouseActionName(int, boolean) - Static method in class org.jmol.viewer.binding.Binding
- getMouseActionStr(String) - Static method in class org.jmol.viewer.binding.Binding
-
create an action code from a string such as "CTRL-LEFT-double click"
- getMouseEnabled() - Method in class org.jmol.viewer.Viewer
- getMouseInfo() - Method in class org.jmol.viewer.PropertyManager
- getMouseManager(double, Object) - Method in interface org.jmol.api.GenericPlatform
- getMouseManager(double, Object) - Method in class org.jmol.awt.Platform
- getMouseManager(double, Object) - Method in class org.jmol.awtjs2d.Platform
- getMoveToText(boolean) - Method in class org.jmol.modelset.Orientation
- getMoveToText(float, boolean) - Method in class org.jmol.viewer.TransformManager
- getMP() - Method in class org.jmol.viewer.ActionManager
- getMpsShapeCount() - Method in class org.jmol.shapebio.BioShapeCollection
- getMSInfoB(String) - Method in class org.jmol.modelset.ModelSet
- getMultipleBondSettings(boolean) - Method in class org.jmol.render.SticksRenderer
- getMutationBackbone(AminoMonomer, Atom[]) - Static method in class org.jmol.modelsetbio.BioExt
- getMyExecutor() - Method in class org.jmol.script.ScriptParallelProcessor
- getMyInfo(P3) - Method in class org.jmol.modelsetbio.Monomer
- getMyValue() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
- getN0() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getN1() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getN2() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getN3() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getN4() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getN6() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getName() - Method in interface org.jmol.api.GenericFileInterface
- getName() - Method in interface org.jmol.api.JmolAbstractButton
- getName() - Method in interface org.jmol.api.JmolScriptFunction
- getName() - Method in interface org.jmol.api.SC
- getName() - Method in class org.jmol.awt.AwtSwingComponent
- getName() - Method in class org.jmol.awtjs.swing.Component
- getName() - Method in class org.jmol.awtjs2d.JSFile
- getName() - Method in enum org.jmol.c.STER
- getName() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
- getName() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- getName() - Method in class org.jmol.script.ScriptFunction
- getName() - Method in class org.jmol.symmetry.PointGroup
- getName() - Method in class org.jmol.symmetry.SpaceGroup
- getName() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getName() - Method in interface org.openscience.jmol.app.JmolPlugin
- getName(String) - Method in class org.jmol.adapter.readers.xtal.CgdReader
- getNameFromCode(int) - Static method in enum org.jmol.util.Edge.EnumBondOrder
- getNameList() - Static method in enum org.jmol.c.CBK
- getNameType(String, SymmetryInterface) - Method in class org.jmol.symmetry.SpaceGroup
- getNaturalIsotope(int) - Static method in class org.jmol.api.JmolAdapter
- getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
- getNav() - Method in class org.jmol.viewer.TransformManager
- getNavigationOffset() - Method in class org.jmol.viewer.TransformManager
- getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager
- getNavigationSlabOffsetPercent() - Method in class org.jmol.navigate.Navigator
- getNavigationState() - Method in interface org.jmol.api.JmolNavigatorInterface
- getNavigationState() - Method in class org.jmol.navigate.Navigator
- getNavigationState() - Method in class org.jmol.viewer.TransformManager
- getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager
- getNavPtHeight() - Method in class org.jmol.viewer.TransformManager
- getNBOAtomLabel(Atom) - Method in class org.jmol.adapter.readers.quantum.NBOParser
-
get the
- getNBOAtomLabel(Atom) - Method in class org.jmol.viewer.Viewer
- getNboCharges() - Method in class org.jmol.adapter.readers.quantum.MOReader
- getNBOCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
- getNBOOccupanciesStatic(Lst<Map<String, Object>>, int, int, String, int, int[]) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
- getNBOParser() - Method in class org.jmol.viewer.Viewer
- getNBOs - Variable in class org.jmol.adapter.readers.quantum.MOReader
- getNBOTypeFromName(String) - Static method in class org.jmol.viewer.JC
- getNboTypes() - Method in class org.jmol.adapter.readers.quantum.MOReader
- getNCIPlanes - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- getNegCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getNeighbors(AtomIndexIterator) - Method in class org.jmol.geodesic.EnvelopeCalculation
- getNeighborVertexArrays() - Static method in class org.jmol.util.Normix
- getNeighborVertexesArrays() - Static method in class org.jmol.util.Geodesic
- getNested(int) - Method in class org.jmol.smiles.SmilesSearch
- getNet() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- getNet() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- getNet() - Method in interface org.jmol.adapter.readers.cif.TopoCifParser.TPoint
- getNetByID(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Find or create a net with this netID, giving it a default name "Net"+id
- getNetFor(String, String, boolean) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Find or create a TNet for this id and label.
- getNewCubeIterator(int) - Method in class org.jmol.bspt.Bspf
- getNewDfCoefMap() - Static method in class org.jmol.quantum.QS
- getNewFixedRotationCenter() - Method in class org.jmol.viewer.TransformManager
- getNewLatticePoints(BZone) - Method in class org.jmol.util.BZone
-
Loop through all points, looking for non-excluded points using St.
- getNewSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getNextStatement() - Method in interface org.jmol.api.JmolScriptEvaluator
- getNextStatement() - Method in class org.jmol.script.ScriptEval
-
when paused, indicates what statement will be next
- getNextValue() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getNextVoxelValue() - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
- getNextVoxelValue() - Method in class org.jmol.jvxl.readers.VolumeFileReader
- getNHPoint(P3, V3, boolean, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
- getNitrogenAtom() - Method in class org.jmol.modelset.Group
- getNitrogenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
- getNitrogenHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
- getNMRCalculation() - Method in class org.jmol.viewer.Viewer
- getNmrDataJSON() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- getNMRfreq() - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
gets the NMR frequency
- getNMRfreqMHz() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
gets the NMR frequency
- getNMRPredict(String) - Method in class org.jmol.viewer.Viewer
- getNoCase(Map<String, Object>, String) - Static method in class org.jmol.viewer.StateManager
- getNode(int) - Method in class org.jmol.viewer.Gesture
- getNodeIndex(SimpleNode) - Static method in class org.jmol.inchi.InChIJNI
- getNodeWithSym(String, String, int, P3) - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
-
Find a node that already matches this id and symmetry
- getNoe(int, int) - Method in class org.jmol.quantum.NMRNoeMatrix
- getNoeExprefValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getnoeNPrefIndices() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getNOEorJHH(Atom[], int) - Method in interface org.jmol.api.JmolNMRInterface
- getNOEorJHH(Atom[], int) - Method in class org.jmol.quantum.NMRCalculation
- getNoesy() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
get if NOESY or ROESY was used for simulation
- getNoesy() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getNoeWeight() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- getNominalMass() - Method in class org.jmol.modelset.Atom
- getNormalizedDE() - Method in class org.jmol.minimize.forcefield.ForceField
- getNormalMap(T3[], int, BS, Lst<String>) - Method in class org.jmol.export.__CartesianExporter
- getNormals(T3[], P4) - Method in class org.jmol.shape.Mesh
- getNormalsTemp() - Method in class org.jmol.shape.Mesh
- getNormix() - Method in class org.jmol.rendercgo.CGORenderer
- getNormix(double, double, double, int, BS) - Static method in class org.jmol.util.Normix
- getNormixCount() - Static method in class org.jmol.util.Normix
- getNormixes() - Method in class org.jmol.shapespecial.Polyhedron
- getNormixV(V3, BS) - Static method in class org.jmol.util.Normix
- getNotInCentroid(BS, int[]) - Method in class org.jmol.modelset.ModelSet
- getNoValue() - Method in class org.jmol.quantum.NciCalculation
- getNoValue() - Method in class org.jmol.quantum.QuantumPlaneCalculation
-
Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
- getNPQ(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- getNPQd(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
for D orbitals, MOPAC adds 1 to n for noble gases but subtracts 1 from n for transition metals
- getNPQp(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
for P orbitals, MOPAC adds 1 to n for helium only
- getNPQs(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
for S orbitals, MOPAC adds 1 to n for noble gases other than helium
- getNucleic() - Method in class org.jmol.util.ColorEncoder
- getNucleicPhosphorusAtom(int) - Method in class org.jmol.modelsetbio.NucleicPolymer
- getNull(boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SpaceGroup
- getNumberFromCode(int) - Static method in enum org.jmol.util.Edge.EnumBondOrder
- getNumericalToken() - Method in class org.jmol.script.ScriptTokenParser
- getO2() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getO4() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getO6() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getObjectBoundingBox(String) - Method in class org.jmol.script.ScriptEval
- getObjectCenter(String, int, int) - Method in class org.jmol.script.ScriptEval
- getObjectColix(int) - Method in class org.jmol.viewer.Viewer
- getObjectID(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getObjectIdFromName(String) - Static method in class org.jmol.viewer.StateManager
- getObjectMad10(int) - Method in class org.jmol.viewer.Viewer
- getObjectMap(Map<String, ?>, boolean) - Method in class org.jmol.viewer.ShapeManager
- getObjectMap(Map<String, ?>, char) - Method in class org.jmol.viewer.Viewer
-
used in autocompletion in console using TAB
- getObjectNameFromId(int) - Static method in class org.jmol.viewer.StateManager
- getObjects(int) - Method in class org.jmol.adapter.readers.pymol.PickleReader
- getObjectSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getObjectSettings() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getObjectType(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getOccupancy() - Method in class org.jmol.adapter.smarter.AtomIterator
- getOccupancy() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getOccupancy(boolean) - Method in class org.jmol.util.ModulationSet
- getOccupancy100() - Method in class org.jmol.modelset.Atom
- getOccupancy100(boolean) - Method in class org.jmol.util.ModulationSet
- getOccupancy100(boolean) - Method in class org.jmol.util.Vibration
- getOccupancyFloat(int) - Method in class org.jmol.modelset.AtomCollection
- getOffset(int, int, boolean) - Static method in class org.jmol.viewer.JC
-
Construct an 32-bit integer packed with 10-byte x and y offsets (-500 to 500) along with flags to indicate if exact and, if not, a flag to indicate that the 0 in x or y indicates "centered".
- getOffsetResidueAtom(String, int) - Method in class org.jmol.modelset.Atom
- getOffsetResidueAtom(String, int) - Method in class org.jmol.smiles.SmilesAtom
- getOffsetResidueAtom(String, int) - Method in interface org.jmol.util.Node
- getOffsetVertices(P4) - Method in class org.jmol.shape.Mesh
- geTokens() - Method in interface org.jmol.api.JmolScriptFunction
- geTokens() - Method in class org.jmol.script.ScriptFunction
- getOp(int) - Static method in class org.jmol.symmetry.SpaceGroupFinder
- getOpacity255() - Method in class org.jmol.awt.AwtColor
- getOpacity255() - Method in class org.jmol.awtjs.swing.Color
- getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in interface org.jmol.api.JmolDialogInterface
- getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in class org.jmol.dialog.Dialog
- getOpenSmiles(BS) - Method in class org.jmol.api.JmolViewer
- getOpenSmiles(BS) - Method in class org.jmol.viewer.Viewer
- getOperation(int) - Method in class org.jmol.symmetry.SpaceGroup
- getOperationCount() - Method in class org.jmol.symmetry.SpaceGroup
- getOperationRsVs(int) - Method in interface org.jmol.api.SymmetryInterface
- getOperationRsVs(int) - Method in class org.jmol.symmetry.Symmetry
- getOperativeSymmetry() - Method in class org.jmol.viewer.Viewer
-
Only return symmetry that has operators.
- getOpMatrix(String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- getOption(String, Viewer, String) - Static method in class org.jmol.api.Interface
-
Note! Do not use this method with "viewer." or "util." because when the JavaScript is built, "org.jmol.util" and "org.jmol.viewer" are condensed to "JU" and "JV" (javajs.util is also JU)
- getOptions() - Method in class org.openscience.jmol.app.JmolApp
- getOrAddBond(Atom, Atom, int, short, BS, float, boolean) - Method in class org.jmol.modelset.BondCollection
- getOrAllocateChain(Model, int) - Method in class org.jmol.modelset.ModelLoader
- getOrbitals(float[], float[], int, int) - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- getOrCalcPartialCharges(BS, BS) - Method in class org.jmol.viewer.Viewer
- getOrder(int) - Static method in class org.jmol.inchi.InChIJNI
- getOrientation() - Method in class org.jmol.viewer.StateManager
- getOrientation(int, String, BS) - Method in class org.jmol.viewer.Viewer
- getOrientationFor(String) - Method in class org.jmol.viewer.StateManager
- getOrientationInfo() - Method in class org.jmol.viewer.TransformManager
- getOrientationText(int, boolean) - Method in class org.jmol.viewer.TransformManager
- getOriginFloat() - Method in class org.jmol.jvxl.data.VolumeData
- getOriginVaVbVc() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- getOrSaveImage(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
-
Creates an image of params.type form -- PNG, PNGJ, PNGT, JPG, JPG64, PDF, PPM, GIF, GIFT.
- getOtherAtom(int) - Method in class org.jmol.minimize.MinBond
- getOtherAtom(Atom) - Method in class org.jmol.modelset.Bond
- getOtherAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
- getOtherAtomIndex(Atom, Atom) - Method in class org.jmol.modelkit.ModelKit
- getOtherEneAtom(SmilesAtom[], int, int) - Static method in class org.jmol.inchi.InChIJNI
- getOtherNode(SimpleNode) - Method in class org.jmol.modelset.Bond
- getOtherNode(SimpleNode) - Method in class org.jmol.smiles.SmilesBond
- getOtherNode(SimpleNode) - Method in interface org.jmol.util.SimpleEdge
- getOutOfPlaneParameter(int[]) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getOutputChannel(String, String[]) - Method in class org.jmol.viewer.OutputManager
- getOutputChannel(String, String[]) - Method in class org.jmol.viewer.Viewer
- getOutputFileNameFromDialog(String, int, Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
- getOutputFromExport(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
- getOutputManager() - Method in class org.jmol.viewer.Viewer
- getOutputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
- getOverallSpan() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- getP() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getP(String) - Method in class org.jmol.viewer.Viewer
- getPageAuthorName() - Static method in class org.openscience.jmol.app.webexport.WebExport
- getPairs(BS, BS, RadiusData, int, boolean) - Method in class org.jmol.shapesurface.Contact
- getPalette(String) - Static method in enum org.jmol.c.PAL
- getPaletteAC() - Method in class org.jmol.util.ColorEncoder
- getPaletteAtoB(int, int, int) - Static method in class org.jmol.util.ColorEncoder
- getPaletteBW() - Method in class org.jmol.util.ColorEncoder
- getPaletteColorCount(int) - Method in class org.jmol.util.ColorEncoder
- getPaletteID(String) - Static method in enum org.jmol.c.PAL
- getPaletteName(byte) - Static method in enum org.jmol.c.PAL
- getPaletteWB() - Method in class org.jmol.util.ColorEncoder
- getPane() - Method in class org.jmol.console.JmolConsole
- getPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
- getPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
- getParam(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
- getParameter(float[], int, double, String) - Static method in class org.jmol.quantum.NciCalculation
- getParameter(int) - Method in class org.jmol.viewer.StatusManager
- getParameter(Object) - Method in class org.jmol.minimize.forcefield.Calculations
- getParameter(String) - Method in class org.jmol.api.JmolViewer
- getParameter(String) - Method in class org.jmol.viewer.Viewer
- getParameter(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
-
strictly a getter
- getParameter(String, int, boolean) - Method in class org.jmol.script.ScriptParam
- getParameterEscaped(String, int) - Method in class org.jmol.viewer.GlobalSettings
- getParameterObj(MinObject) - Method in class org.jmol.minimize.forcefield.Calculations
- getParameterObj(MinObject) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
- getParameterObj(MinObject) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
- getParameters() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
- getParameters(boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getParameterState(GlobalSettings, SB) - Method in class org.jmol.viewer.StateCreator
-
note that these are not user variables, only global jmol parameters
- getParams() - Method in class org.jmol.quantum.NMRNoeMatrix
- getParamType(int) - Static method in class org.jmol.script.T
- getParamType(int) - Static method in class org.jmol.viewer.PropertyManager
- getParent() - Method in interface org.jmol.api.SC
- getParent() - Method in class org.jmol.awt.AwtSwingComponent
- getParent() - Method in class org.jmol.awtjs.swing.Component
- getParentAsFile() - Method in interface org.jmol.api.GenericFileInterface
- getParentAsFile() - Method in class org.jmol.awt.AwtFile
- getParentAsFile() - Method in class org.jmol.awtjs2d.JSFile
- getParentItem(String, M4) - Method in class org.jmol.export._IdtfExporter
- getPartialBondDotted(int) - Static method in class org.jmol.util.Edge
- getPartialBondOrder(int) - Static method in class org.jmol.util.Edge
- getPartialBondOrderFromFloatEncodedInt(int) - Static method in class org.jmol.script.ScriptParam
-
reads standard n.m float-as-integer n*1000000 + m and returns (n % 7) << 5 + (m % 0x1F)
- getPartialBondOrderFromString(String) - Static method in class org.jmol.script.ScriptParam
- getPartialCharge() - Method in class org.jmol.adapter.smarter.AtomIterator
- getPartialCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getPartialCharge() - Method in class org.jmol.modelset.Atom
- getPartialCharges() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getPartialCharges() - Method in class org.jmol.modelset.AtomCollection
- getPartialCharges(BS) - Method in class org.jmol.script.ScriptEval
- getPartnerAtom(NucleicMonomer) - Method in class org.jmol.modelsetbio.BasePair
- getPathForAllFiles() - Method in class org.jmol.viewer.FileManager
- getPathHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Just recovers the path settings from last session.
- getPatternIndex() - Method in class org.jmol.smiles.SmilesAtom
- getPatternMatcher() - Method in class org.jmol.scriptext.MathExt
- getPdbAtomData(BS, OC, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getPdbAtomData(BS, OC, boolean, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
-
PDB or PQR only
- getPdbBondInfo(String, boolean) - Method in class org.jmol.modelsetbio.BioResolver
- getPdbCharge(String, String) - Method in class org.jmol.modelset.ModelLoader
-
Adjust known N and O atom formal charges.
- getPdbData(int, String, BS, Object[], OC, boolean) - Method in interface org.jmol.api.JmolPropertyManager
- getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.PropertyManager
- getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.Viewer
- getPdbData(String, char, boolean, BS, OC, LabelToken[], SB, BS) - Method in class org.jmol.modelsetbio.BioModel
- getPdbData(BioPolymer, char, char, int, int, BS, BS, boolean, boolean, boolean, LabelToken[], OC, SB, BS, P3) - Method in class org.jmol.modelsetbio.BioExt
- getPdbDataM(BioModel, Viewer, String, char, boolean, BS, OC, LabelToken[], SB, BS) - Method in class org.jmol.modelsetbio.BioExt
- getPDBGroupLength(String) - Method in class org.jmol.adapter.readers.more.Mol2Reader
- getPDBHeader(int) - Method in class org.jmol.modelset.ModelSet
- getPdbID() - Method in class org.jmol.viewer.Viewer
- getPeakAtomRecord(int) - Method in class org.jmol.jsv.JSpecView
- getPendingMeasurement() - Method in class org.jmol.viewer.Viewer
- getPercentageRead() - Method in class org.openscience.jvxl.MonitorInputStream
- getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.CastepDensityReader
- getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.VaspChgcarReader
- getPerspectiveDepth() - Method in class org.jmol.viewer.TransformManager
- getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager
-
calculate the perspective factor based on z
- getPhase(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getPhiPsiForHelixType(String) - Method in class org.jmol.modelsetbio.BioExt
- getPhongExponent() - Method in class org.jmol.util.GData
- getPickedPoint(T3, int) - Method in class org.jmol.shape.MeshCollection
- getPickingMode() - Method in class org.jmol.viewer.Viewer
- getPickingMode(String) - Static method in class org.jmol.viewer.ActionManager
- getPickingModeName(int) - Static method in class org.jmol.viewer.ActionManager
- getPickingState() - Method in class org.jmol.viewer.ActionManager
- getPickingStyle() - Method in class org.jmol.viewer.ActionManager
- getPickingStyleIndex(String) - Static method in class org.jmol.viewer.ActionManager
- getPickingStyleName(int) - Static method in class org.jmol.viewer.ActionManager
- getPlane(int) - Method in interface org.jmol.jvxl.api.VertexDataServer
- getPlane(int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- getPlane(int) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- getPlane(int) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
- getPlane(int) - Method in class org.jmol.jvxl.readers.IsoMOReader
- getPlane(int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- getPlane(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getPlane(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- getPlane(int) - Method in class org.jmol.shapesurface.Isosurface
- getPlane(int, boolean) - Method in class org.jmol.jvxl.calc.MarchingCubes
- getPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
- getPlane(int, float[]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
- getPlane(String) - Static method in class org.openscience.jvxl.Jvxl
- getPlane(V3) - Method in class org.jmol.symmetry.PointGroup
- getPlaneForObject(String, V3) - Method in class org.jmol.script.ScriptEval
- getPlaneNCI(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
-
Retrieve raw file planes and pass them to the calculation object for processing into new data.
- getPlaneNormals(P3, P3, P3, P3, VTemp) - Static method in class org.jmol.smiles.SmilesStereo
- getPlaneSR(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getPlaneValue(int) - Method in class org.jmol.quantum.NciCalculation
-
We always have four raw planes in hand; we just need to know which three to use in any particular case.
- getPlaneVFR(float[], boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- getPlotMinMax(float[], boolean, int) - Method in class org.jmol.scriptext.CmdExt
- getPlotText3D(int, int, Graphics3D, String, Font, boolean) - Static method in class org.jmol.g3d.TextRenderer
- getPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getPmeshData(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getPngjOrDroppedBytes(String, String) - Method in class org.jmol.viewer.FileManager
- getPoint() - Method in class org.jmol.adapter.readers.more.MdCrdReader
- getPoint(int, P3) - Method in class org.jmol.jvxl.data.VolumeData
- getPoint(int, P3, P3i) - Method in class org.jmol.rendercgo.CGORenderer
- getPoint(int, T3) - Method in class org.jmol.shapecgo.CGOMesh
- getPoint(String[], int) - Method in class org.jmol.jvxl.readers.Ras3DReader
- getPoint(String, int, int[], boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
- getPoint(Map<String, Object>) - Method in class org.jmol.viewer.ActionManager
- getPoint(Map<String, Object>, String, P3) - Method in class org.jmol.dssx.DSSR1
- getPoint3f(int, boolean) - Method in class org.jmol.scriptext.ScriptExt
- getPoint3f(int, boolean, boolean) - Method in class org.jmol.script.ScriptParam
-
Get an {x,y,z} value, possibly fractional, with option to throw an error.
- getPoint4f(int) - Method in class org.jmol.script.ScriptParam
- getPointArray(int, int, boolean) - Method in class org.jmol.script.ScriptParam
-
may return null values in some cases
- getPointCount() - Method in class org.jmol.viewer.Gesture
- getPointCount2(int, int) - Method in class org.jmol.viewer.Gesture
- getPointer(int) - Static method in class org.jmol.viewer.JC
- getPointerName(int) - Static method in class org.jmol.viewer.JC
- getPointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
- getPointers(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
- getPointGroup(PointGroup, T3, T3[], BS, boolean, float, float, int, boolean) - Static method in class org.jmol.symmetry.PointGroup
- getPointGroupAsString(BS, String, int, float, P3[], P3, String) - Method in class org.jmol.modelset.ModelSet
- getPointGroupInfo(int, String, boolean, String, int, float) - Method in interface org.jmol.api.SymmetryInterface
- getPointGroupInfo(int, String, boolean, String, int, float) - Method in class org.jmol.symmetry.Symmetry
- getPointGroupInfo(BS) - Method in class org.jmol.modelset.ModelSet
- getPointGroupName() - Method in interface org.jmol.api.SymmetryInterface
- getPointGroupName() - Method in class org.jmol.symmetry.Symmetry
- getPointIndex(int) - Method in class org.jmol.symmetry.PointGroup
- getPointIndex(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
- getPointOrBitsetOperation(T, SV) - Method in class org.jmol.script.ScriptMathProcessor
- getPointOrCenterVector(T) - Method in class org.jmol.script.ScriptParam
- getPointOrPlane(int, int) - Method in class org.jmol.script.ScriptParam
-
Get the point or plane at an index
- getPoints() - Method in interface org.jmol.api.JmolEnvCalc
- getPoints() - Method in class org.jmol.geodesic.EnvelopeCalculation
- getPoints() - Method in class org.jmol.render.MeasuresRenderer
- getPoints(byte[], P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getPointsAndElements(T3[]) - Method in class org.jmol.symmetry.PointGroup
- getPointTransf(int, Atom, Quat, P3) - Method in class org.jmol.modelset.ModelSet
-
pick up the appropriate value for this atom
- getPointVector(T, int) - Method in class org.jmol.script.ScriptParam
- getPolygonColorData(int, short[], int[][], BS) - Static method in class org.jmol.shapesurface.Isosurface
- getPolyhedralOrders() - Method in class org.jmol.smiles.SmilesStereo
-
experimental Jmol polySMILES
- getPolymerPointsAndVectors(int, BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioPolymer
- getPolymerPointsAndVectors(BS, Lst<P3[]>) - Method in class org.jmol.viewer.Viewer
- getPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelset.ModelSet
- getPolymerSequenceAtoms(int, int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
- getPopInHeight() - Static method in class org.openscience.jmol.app.webexport.WebExport
- getPopInWidth() - Static method in class org.openscience.jmol.app.webexport.WebExport
- getPopulation() - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- getPopup(String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
- getPopupMenu() - Method in interface org.jmol.api.SC
- getPopupMenu() - Method in class org.jmol.awt.AwtSwingComponent
- getPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
- getPopupMenu() - Method in class org.jmol.awtjs.swing.JMenu
- getPopupMenu() - Method in class org.jmol.viewer.Viewer
- getPOrNull(String) - Method in class org.jmol.viewer.Viewer
- getPort() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- getPort() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getPosCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getPosition() - Method in interface org.jmol.api.AtomIndexIterator
- getPosition() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- getPosition() - Method in class org.jmol.symmetry.UnitCellIterator
- getPosition() - Method in class org.openscience.jvxl.MonitorInputStream
- getPositionMin() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getPrecedence(int) - Static method in class org.jmol.script.T
- getPreference(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getPrefixToken() - Method in class org.jmol.script.ScriptCompiler
- getPreserveState() - Method in class org.jmol.viewer.Viewer
-
This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.
- getPrivateKey() - Method in class org.jmol.export.Export3D
- getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
- getProp(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- getPropC(String, int) - Method in class org.jmol.shapesurface.Contact
- getPropDataMC(String, Object[]) - Method in class org.jmol.shape.MeshCollection
- getProperties() - Method in class org.openscience.jmol.app.HistoryFile
- getproperty - Static variable in class org.jmol.script.T
- getProperty(int, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
- getProperty(Object) - Method in class org.jmol.viewer.ShapeManager
- getProperty(String) - Method in interface org.jmol.api.JmolAppletInterface
- getProperty(String) - Method in class org.jmol.modelkit.ModelKit
-
Get a property of the modelkit.
- getProperty(String) - Method in class org.jmol.util.GenericApplet
- getProperty(String, boolean) - Static method in class org.jmol.util.Logger
- getProperty(String, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
-
only called from org.openscience.jvxl.Jvxl.main
- getProperty(String, int) - Method in class org.jmol.minimize.Minimizer
- getProperty(String, int) - Method in class org.jmol.shape.Axes
- getProperty(String, int) - Method in class org.jmol.shape.Labels
- getProperty(String, int) - Method in class org.jmol.shape.Measures
- getProperty(String, int) - Method in class org.jmol.shape.Shape
- getProperty(String, int) - Method in class org.jmol.shape.Sticks
- getProperty(String, int) - Method in class org.jmol.shapecgo.CGO
- getProperty(String, int) - Method in class org.jmol.shapespecial.Dipoles
- getProperty(String, int) - Method in class org.jmol.shapespecial.Draw
- getProperty(String, int) - Method in class org.jmol.shapespecial.Polyhedra
- getProperty(String, int) - Method in class org.jmol.shapespecial.Vectors
- getProperty(String, int) - Method in class org.jmol.shapesurface.Contact
- getProperty(String, int) - Method in class org.jmol.shapesurface.Isosurface
- getProperty(String, int) - Method in class org.jmol.shapesurface.MolecularOrbital
- getProperty(String, int) - Method in class org.jmol.shapesurface.Pmesh
- getProperty(String, String) - Method in interface org.jmol.api.JmolAppletInterface
- getProperty(String, String) - Method in class org.jmol.util.BZone
- getProperty(String, String) - Method in class org.jmol.util.GenericApplet
- getProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
-
Get the value of a property
- getProperty(String, String, Object) - Method in interface org.jmol.api.JmolPropertyManager
- getProperty(String, String, Object) - Method in class org.jmol.api.JmolViewer
- getProperty(String, String, Object) - Method in class org.jmol.viewer.PropertyManager
- getProperty(String, String, Object) - Method in class org.jmol.viewer.Viewer
- getPropertyAsJSON(String) - Method in interface org.jmol.api.JmolAppletInterface
- getPropertyAsJSON(String) - Method in class org.jmol.util.GenericApplet
- getPropertyAsJSON(String, String) - Method in interface org.jmol.api.JmolAppletInterface
- getPropertyAsJSON(String, String) - Method in class org.jmol.util.GenericApplet
- getPropertyAsObject(String, Object, String) - Method in class org.jmol.viewer.PropertyManager
- getPropertyAsString(String) - Method in interface org.jmol.api.JmolAppletInterface
- getPropertyAsString(String) - Method in class org.jmol.util.GenericApplet
- getPropertyAsString(String, String) - Method in interface org.jmol.api.JmolAppletInterface
- getPropertyAsString(String, String) - Method in class org.jmol.util.GenericApplet
- getPropertyColorRange() - Method in class org.jmol.viewer.ColorManager
- getPropertyCount(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- getPropertyData(String, Object[]) - Method in class org.jmol.shape.Echo
- getPropertyData(String, Object[]) - Method in class org.jmol.shape.Shape
- getPropertyData(String, Object[]) - Method in class org.jmol.shapecgo.CGO
- getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Dipoles
- getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Draw
- getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Ellipsoids
- getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Polyhedra
- getPropertyData(String, Object[]) - Method in class org.jmol.shapesurface.Isosurface
- getPropertyManager() - Method in class org.jmol.viewer.Viewer
- getPropertyName(int) - Static method in class org.jmol.viewer.PropertyManager
- getPropertyNumber(String) - Method in interface org.jmol.api.JmolPropertyManager
- getPropertyNumber(String) - Method in class org.jmol.viewer.PropertyManager
- getPropertyNumber(String) - Method in class org.jmol.viewer.Viewer
- getPropI(String, int) - Method in class org.jmol.shapesurface.Isosurface
- getPropMC(String, int) - Method in class org.jmol.shape.MeshCollection
- getPropMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
- getPropShape(String, Object[]) - Method in class org.jmol.shape.Shape
- getProteinStructure(int) - Method in class org.jmol.modelsetbio.AlphaPolymer
- getProteinStructure(int) - Method in class org.jmol.modelsetbio.BioPolymer
- getProteinStructureState(BS, int) - Method in class org.jmol.modelset.ModelSet
- getProteinStructureSubType() - Method in class org.jmol.modelset.Group
- getProteinStructureSubType() - Method in class org.jmol.modelsetbio.AlphaMonomer
- getProteinStructureTag() - Method in class org.jmol.modelset.Group
- getProteinStructureTag() - Method in class org.jmol.modelsetbio.AminoMonomer
- getProteinStructureType() - Method in class org.jmol.modelset.Group
- getProteinStructureType() - Method in class org.jmol.modelsetbio.AlphaMonomer
- getProteinStructureType() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
- getProteinStructureType() - Method in class org.jmol.modelsetbio.Monomer
- getProteinStructureType() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getProteinStructureType() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getProteinStructureType(String) - Static method in enum org.jmol.c.STR
-
In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.
- getPymolScreenOffset(P3, P3i, int, P3, float) - Method in class org.jmol.modelset.Text
-
PyMOL will use 1 here for pymolOffset[0] for relative, 0 or absolute.
- getPymolView(Lst<Object>, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
adds depth_cue, fog, and fog_start
- getPymolXYOffset(float, int, float) - Method in class org.jmol.modelset.Text
- getQCoefs(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getQCoefs(String) - Method in interface org.jmol.adapter.smarter.MSInterface
- getQInfo(Quat) - Static method in class org.jmol.modelsetbio.BioExt
- getQuadrupolarConstant(Tensor) - Method in interface org.jmol.api.JmolNMRInterface
-
Quadrupolar constant, directly proportional to Vzz and dependent on the quadrupolar moment of the isotope considered
- getQuadrupolarConstant(Tensor) - Method in class org.jmol.quantum.NMRCalculation
- getQuadrupoleTensors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- getQuality(String) - Method in interface org.jmol.api.JmolDialogInterface
- getQuality(String) - Method in class org.jmol.dialog.Dialog
- getQuantumShell(String) - Static method in class org.jmol.quantum.QS
- getQuantumShellTag(int) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- getQuantumShellTag(int) - Static method in class org.jmol.quantum.QS
- getQuantumShellTagID(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- getQuantumShellTagID(String) - Static method in class org.jmol.quantum.QS
- getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.quantum.QS
- getQuaternion(char) - Method in class org.jmol.modelset.Group
- getQuaternion(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getQuaternion(char) - Method in class org.jmol.modelsetbio.AminoMonomer
- getQuaternion(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getQuaternion(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getQuaternion(int, char) - Method in class org.jmol.modelset.AtomCollection
- getQuaternion(V3, int) - Static method in class org.jmol.symmetry.PointGroup
- getQuaternionAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getQuaternionArray(Object, int) - Method in class org.jmol.script.ScriptEval
- getQuaternionFrame() - Method in class org.jmol.viewer.Viewer
- getQuaternionFrame(Atom[]) - Method in class org.jmol.modelset.Group
- getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AminoMonomer
- getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.Monomer
- getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getQuaternionFrameCenterAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
- getQuaternionP() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getQuaternionParameter(int, BS, boolean) - Method in class org.jmol.script.ScriptParam
- getQuaternionRotation(String) - Method in interface org.jmol.api.SymmetryInterface
- getQuaternionRotation(String) - Method in class org.jmol.symmetry.Symmetry
- getQuaternionRotation(String) - Method in class org.jmol.symmetry.UnitCell
-
Returns a quaternion that will take the standard frame to a view down a particular axis, expressed as its counterparts.
- getQuaternionStraightness(String, Quat, Quat) - Static method in class org.jmol.modelsetbio.BioExt
- getQuotedString(String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- getQuotedStringNext() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- getQuotedStringOrObject(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
final get for quoted object
- getR0(MinBond) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getRadio(String) - Method in class org.jmol.awt.AwtPopupHelper
- getRadio(String) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getRadio(String) - Method in interface org.jmol.popup.PopupHelper
- getRadio(AwtPopupHelper, String, Map<Object, SC>) - Static method in class org.jmol.awt.AwtSwingComponent
- getRadius() - Method in class org.jmol.adapter.smarter.AtomIterator
- getRadius() - Method in class org.jmol.adapter.smarter.BondIterator
- getRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getRadius() - Method in class org.jmol.api.JmolAdapterBondIterator
- getRadius() - Method in class org.jmol.modelset.Atom
- getRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
- getRadiusVdwJmol(Atom) - Method in class org.jmol.modelset.AtomCollection
- getRange(BS, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
- getRangeGroups(int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
- getRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS, int) - Method in class org.jmol.modelsetbio.BioModel
- getRasMolRadius() - Method in class org.jmol.modelset.Atom
- getRasmolScale() - Static method in class org.jmol.util.ColorEncoder
- getReader(String, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
-
Get a reader based on its name.
- getReaderClassBase(String) - Static method in class org.jmol.adapter.smarter.Resolver
- getReaderData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- getReaderFromType(String) - Static method in class org.jmol.adapter.smarter.Resolver
- getReadingTimeMillis() - Method in class org.openscience.jvxl.MonitorInputStream
- getRealCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
- getReciprocal(T3[], T3[], float) - Static method in class org.jmol.util.SimpleUnitCell
-
Generate the reciprocal unit cell, scaled as desired
- getRecord(String) - Method in interface org.jmol.api.JmolJDXMOLParser
- getRecord(String) - Method in class org.jmol.jsv.JDXMOLParser
- getRedField() - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- getRedField() - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- getRedValue() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getRedValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getRefreshing() - Method in class org.jmol.viewer.Viewer
- getRegistryInfo() - Method in interface org.jmol.api.JmolStatusListener
- getRegistryInfo() - Method in class org.jmol.util.GenericApplet
- getRegistryInfo() - Method in class org.jmol.viewer.StatusManager
- getRegistryInfo() - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- getRelationship(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
- getRelationship(String, String) - Method in class org.jmol.smiles.SmilesMatcher
- getRenderer(int) - Method in class org.jmol.render.RepaintManager
- getRenderer(String) - Method in class org.jmol.g3d.Graphics3D
- getRendering() - Method in class org.jmol.shape.Mesh
- getResidueLabels() - Method in class org.jmol.adapter.readers.more.MdTopReader
- getResiduePointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
- getResno() - Method in class org.jmol.modelset.Atom
- getResno() - Method in class org.jmol.modelset.Group
- getResno() - Method in class org.jmol.smiles.SmilesAtom
- getResno() - Method in interface org.jmol.util.Node
- getResolution() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getResolution() - Method in class org.jmol.util.MeshSurface
- getResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getResource(Object, String, boolean) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getResource(Viewer, String, String) - Static method in class org.jmol.i18n.Resource
- getResourceFromPO(String) - Static method in class org.jmol.i18n.Resource
-
applet only -- Simple reading of .po file; necessary for JavaScript; works in Java as well and avoids all those signed applets.
- getResourceString(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- getResult() - Method in class org.jmol.script.ScriptMathProcessor
- getRGB() - Method in class org.jmol.awtjs.swing.Color
- getRGB(int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
- getRhoStar() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getRhoStarField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getRiboseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- getRingCache(int, int, Map<String, Object[]>) - Method in class org.jmol.smiles.SmilesGenerator
- getRingData(Lst<BS>[], boolean, boolean) - Method in class org.jmol.smiles.SmilesSearch
- getRingKey(int, int) - Static method in class org.jmol.smiles.SmilesGenerator
- getRingNumber(String, int, char, int[]) - Static method in class org.jmol.smiles.SmilesParser
- getRingPointer(int) - Method in class org.jmol.smiles.SmilesGenerator
- getRna3dMap(String) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
- getRnd(float) - Method in class org.jmol.jvxl.readers.IsoMOReader
- getRootExt(String, String[], int) - Static method in class org.jmol.viewer.OutputManager
- getRootTrackerResult(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPData
-
CIPDataTracker only
- getRootTrackerResult(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPDataTracker
- getRotateBondIndex() - Method in class org.jmol.modelkit.ModelKit
- getRotateXyzText() - Method in class org.jmol.viewer.TransformManager
- getRotateZyzText(boolean) - Method in class org.jmol.viewer.TransformManager
- getRotation(M3) - Method in class org.jmol.viewer.TransformManager
- getRotationMatrix(P3, P3, float) - Method in class org.jmol.export.___Exporter
- getRotationMatrix(P3, P3, float, P3, P3) - Method in class org.jmol.export.___Exporter
- getRotationQ() - Method in class org.jmol.viewer.TransformManager
- getRotationText() - Method in class org.jmol.viewer.TransformManager
- getRowCount() - Method in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- getRowCount() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getRowCount() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getRowCount() - Method in class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- getRowCount() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getRowCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
- getRowFor(int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getRubberBand() - Method in class org.jmol.viewer.ActionManager
- getRubberBandSelection() - Method in class org.jmol.viewer.Viewer
- getRule6Descriptor(boolean) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
The original Rule 6 implementation; allows cubane, tetrahedrane, and bicyclo[2.2.2]octane to be ns.
- getRuleBondLength(MinAtom, MinAtom, int, boolean) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getRuleName(int) - Method in class org.jmol.symmetry.CIPChirality
- getSavedCoordinates(String) - Method in class org.jmol.viewer.StateManager
- getSavedOrientationText(String) - Method in class org.jmol.viewer.StateManager
- getSavedState(String) - Method in class org.jmol.viewer.StateManager
- getSavedStructure(String) - Method in class org.jmol.viewer.StateManager
- getSaveFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
- getSaveFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
- getScale() - Method in interface org.jmol.api.JmolModulationSet
- getScale() - Method in class org.jmol.util.ModulationSet
- getScaledCell(boolean) - Method in class org.jmol.symmetry.UnitCell
- getScalePixelsPerAngstrom(boolean) - Method in class org.jmol.viewer.Viewer
- getScaleText(String, boolean, float, float[]) - Method in class org.jmol.viewer.Viewer
-
Depending upon the measure text, we need to indicate |-------| 1 A or 0.1 A for example.
- getScaling(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
- getSceneScript(String[], Map<String, String>, Lst<Integer>) - Method in class org.jmol.viewer.OutputManagerAwt
- getSchemeIndex(String) - Static method in class org.jmol.util.ColorEncoder
- getScreenDim() - Method in class org.jmol.viewer.Viewer
- getScreenDimensions(Dimension) - Method in interface org.jmol.awtjs.swing.SwingController
-
Return the width and height of the window in d.
- getScreenHeight() - Method in class org.jmol.api.JmolViewer
- getScreenHeight() - Method in class org.jmol.viewer.Viewer
- getScreenImage() - Method in class org.jmol.viewer.Viewer
- getScreenImage() - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- getScreenImage(boolean) - Method in class org.jmol.g3d.Graphics3D
- getScreenImage(boolean) - Method in class org.jmol.util.GData
- getScreenImageBuffer(Object, boolean) - Method in class org.jmol.api.JmolViewer
- getScreenImageBuffer(Object, boolean) - Method in class org.jmol.viewer.Viewer
-
Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo
- getScreenNormal(T3, T3, float) - Method in class org.jmol.export.__RayTracerExporter
- getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager
- getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager4D
- getScreenWidth() - Method in class org.jmol.api.JmolViewer
- getScreenWidth() - Method in class org.jmol.viewer.Viewer
- getScript() - Method in interface org.jmol.api.JmolScriptEvaluator
- getScript() - Method in class org.jmol.script.ScriptEval
- getScriptBitSets(String, BS[]) - Method in class org.jmol.shapesurface.Isosurface
- getScriptButtonPercent() - Static method in class org.openscience.jmol.app.webexport.WebExport
- getScriptContext(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- getScriptContext(String) - Method in class org.jmol.script.ScriptEval
- getScriptContext(String) - Method in class org.jmol.viewer.Viewer
- getScriptEditor() - Method in interface org.jmol.api.JmolAppConsoleInterface
- getScriptEditor() - Method in class org.jmol.console.GenericConsole
- getScriptEditor() - Method in class org.jmol.console.JmolConsole
- getScriptEditor() - Method in class org.jmol.consolejs.AppletConsole
- getScriptFileInternal(String, String, String, String) - Method in class org.jmol.script.ScriptEval
-
Retrieve the uncompiled script or null if failed
- getScriptForCallback(SC, String, String) - Method in class org.jmol.modelkit.ModelKitPopup
-
Secondary processing of menu item click
- getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.GenericPopup
- getScriptForCallback(SC, String, String) - Method in class org.jmol.popup.JmolPopup
- getScriptID(ScriptContext) - Method in class org.jmol.scriptext.CmdExt
- getScriptItem(boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
- getScriptItem(boolean, boolean) - Method in class org.jmol.script.ScriptManager
- getScriptManager() - Method in class org.jmol.viewer.Viewer
- getScriptParams() - Method in class org.jmol.jvxl.readers.Parameters
- getScriptQueue() - Method in interface org.jmol.api.JmolScriptManager
- getScriptQueue() - Method in class org.jmol.script.ScriptManager
- getScriptQueueInfo() - Method in class org.jmol.viewer.Viewer
- getSearch(String, int, BS) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
- getSection(String, String, boolean) - Method in class org.jmol.adapter.readers.simple.JSONReader
- getSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
- getSelectCodeRange(int[]) - Method in class org.jmol.modelset.ModelSet
- getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in interface org.jmol.atomdata.AtomDataServer
- getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- getSelectedAtomIterator(BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
- getSelectedAtoms() - Method in class org.jmol.viewer.SelectionManager
- getSelectedAtomsNoSubset() - Method in class org.jmol.viewer.SelectionManager
- getSelectedIndex() - Method in class org.jmol.awtjs.swing.JComboBox
- getSelectedItem() - Method in class org.jmol.awtjs.swing.JComboBox
- getSelectedMonomerCount() - Method in class org.jmol.modelset.Group
- getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.BioPolymer
- getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.Monomer
- getSelectedMonomerIndex() - Method in class org.jmol.modelset.Group
- getSelectedMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
- getSelectionAtoms(Lst<Object>, int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Add selected atoms to a growing bit set.
- getSelectionCount() - Method in class org.jmol.viewer.SelectionManager
- getSelectionHalosEnabled() - Method in class org.jmol.viewer.Viewer
- getSelectionModel() - Method in interface org.jmol.awtjs.swing.ColumnSelectionModel
- getSelectionModel() - Method in class org.jmol.awtjs.swing.JTable
- getSelections() - Method in class org.jmol.smiles.SmilesSearch
-
htNested may contain $(select xxxx) primitives.
- getSelectionState(SelectionManager, SB) - Method in class org.jmol.viewer.StateCreator
- getSeqCode(T) - Static method in class org.jmol.script.ScriptExpr
- getSeqcodeBits(int, boolean) - Method in class org.jmol.modelset.AtomCollection
- getSeqcodeFor(int, char) - Static method in class org.jmol.modelset.Group
- getSeqcodeString() - Method in class org.jmol.modelset.Group
- getSeqcodeStringFor(int) - Static method in class org.jmol.modelset.Group
- getSeqID() - Method in class org.jmol.adapter.smarter.AtomIterator
- getSeqID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getSeqID() - Method in class org.jmol.modelset.Atom
- getSeqNo(int, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- getSeqNumberFor(int) - Static method in class org.jmol.modelset.Group
- getSequence() - Method in class org.jmol.modelsetbio.BioPolymer
- getSequence() - Method in class org.jmol.viewer.ActionManager
- getSequenceBits(String, BS, BS) - Method in class org.jmol.modelset.ModelSet
- getSequenceCode(boolean) - Method in class org.jmol.script.ScriptTokenParser
- getSequenceNumber() - Method in class org.jmol.adapter.smarter.AtomIterator
- getSequenceNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getSequenceNumber(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getSequenceNumber(int) - Method in interface org.jmol.api.PymolAtomReader
- getSerial() - Method in class org.jmol.adapter.smarter.AtomIterator
- getSerial() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getSerial(int, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- getSerialID() - Method in class org.jmol.adapter.smarter.StructureIterator
- getSerialID() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getServiceCommand(String) - Static method in class org.jmol.viewer.JC
- getSetAxesTypeMad10(int) - Method in class org.jmol.script.ScriptEval
- getSetByEdge(Edge, Hashtable<String, SmilesRingSet>) - Static method in class org.jmol.smiles.SmilesRing
- getSetHistory(int) - Method in class org.jmol.api.JmolViewer
- getSetHistory(int) - Method in class org.jmol.util.CommandHistory
-
Options include: all Integer.MAX_VALUE n prev n >= 1 next -1 set max to -2 - n n <= -3 just clear -2 clear and turn off; return "" 0 clear and turn on; return "" Integer.MIN_VALUE;
- getSetHistory(int) - Method in class org.jmol.viewer.Viewer
-
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
- getSettableTokFromString(String) - Static method in class org.jmol.script.T
- getSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getSettingFloat(int) - Method in class org.jmol.script.ScriptEval
- getSettingInt(int) - Method in class org.jmol.script.ScriptEval
- getSettings(String) - Method in class org.jmol.shapesurface.MolecularOrbital
- getSettingStr(int, boolean) - Method in class org.jmol.script.ScriptEval
-
Accept an unquoted string if there is just one parameter regardless of its type.
- getShadeB(float, float, float) - Method in class org.jmol.util.Shader
- getShadeF(float, float, float) - Method in class org.jmol.util.Shader
- getShadeFp8(float, float, float) - Method in class org.jmol.util.Shader
- getShadeIndex(float, float, float) - Method in class org.jmol.util.Shader
- getShadeIndex(short) - Method in class org.jmol.g3d.Graphics3D
- getShadeIndexP3(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
- getShadeN(float, float, float, float) - Method in class org.jmol.util.Shader
- getShades(short) - Method in class org.jmol.util.GData
- getShades(short) - Method in class org.jmol.util.Shader
- getShades2(int, boolean) - Method in class org.jmol.util.Shader
- getShadesG(short) - Method in class org.jmol.util.Shader
- getShape(int) - Method in class org.jmol.viewer.ShapeManager
- getShapeClassName(int, boolean) - Static method in class org.jmol.viewer.JC
- getShapeDetail() - Method in class org.jmol.shape.Echo
- getShapeDetail() - Method in class org.jmol.shape.Shape
- getShapeDetail() - Method in class org.jmol.shapecgo.CGO
- getShapeDetail() - Method in class org.jmol.shapespecial.Dipoles
- getShapeDetail() - Method in class org.jmol.shapespecial.Draw
- getShapeDetail() - Method in class org.jmol.shapespecial.Polyhedra
- getShapeDetail() - Method in class org.jmol.shapesurface.Isosurface
- getShapeErrorState() - Method in class org.jmol.viewer.Viewer
- getShapeIdFromObjectName(String) - Method in class org.jmol.viewer.ShapeManager
-
Returns the shape type index for a shape object given the object name.
- getShapeInfo() - Method in class org.jmol.viewer.PropertyManager
- getShapely() - Method in class org.jmol.util.ColorEncoder
- getShapeProperty(int, String) - Method in class org.jmol.script.ScriptEval
- getShapeProperty(int, String) - Method in class org.jmol.scriptext.ScriptExt
- getShapeProperty(int, String) - Method in class org.jmol.viewer.Viewer
- getShapePropertyAsInt(int, String) - Method in class org.jmol.viewer.Viewer
- getShapePropertyData(int, String, Object[]) - Method in class org.jmol.script.ScriptEval
- getShapePropertyData(int, String, Object[]) - Method in class org.jmol.viewer.ShapeManager
- getShapePropertyIndex(int, String, int) - Method in class org.jmol.viewer.ShapeManager
- getShapeState() - Method in class org.jmol.shape.AtomShape
- getShapeState() - Method in class org.jmol.shape.FontLineShape
- getShapeState() - Method in class org.jmol.shape.Frank
- getShapeState() - Method in class org.jmol.shape.Shape
- getShapeState() - Method in class org.jmol.shape.Sticks
- getShapeState() - Method in class org.jmol.shape.TextShape
- getShapeState() - Method in class org.jmol.shapebio.BioShape
- getShapeState() - Method in class org.jmol.shapebio.BioShapeCollection
- getShapeState() - Method in class org.jmol.shapecgo.CGO
- getShapeState() - Method in class org.jmol.shapespecial.Dipole
- getShapeState() - Method in class org.jmol.shapespecial.Dipoles
- getShapeState() - Method in class org.jmol.shapespecial.Dots
- getShapeState() - Method in class org.jmol.shapespecial.Draw
- getShapeState() - Method in class org.jmol.shapespecial.Ellipsoids
- getShapeState() - Method in class org.jmol.shapespecial.Polyhedra
- getShapeState() - Method in class org.jmol.shapesurface.Isosurface
- getShapeState() - Method in class org.jmol.shapesurface.LcaoCartoon
- getShapeState() - Method in class org.jmol.shapesurface.MolecularOrbital
- getShapeState(Shape) - Method in class org.jmol.viewer.StateCreator
- getShapeStatePriv(SB, boolean, int) - Method in class org.jmol.viewer.StateCreator
- getShapeType(int) - Method in class org.jmol.script.ScriptEval
- getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JC
- getSheetStructures() - Method in class org.jmol.dssx.DSSP
-
"sheet =: a set of one or more ladders connected by shared residues" (p.
- getShellOrder(int) - Static method in class org.jmol.quantum.MOCalculation
- getShowAxes() - Method in class org.jmol.viewer.Viewer
- getShowBbcage() - Method in class org.jmol.viewer.Viewer
- getShowFrank() - Method in class org.jmol.viewer.Viewer
- getShowNavigationPoint() - Method in class org.jmol.viewer.Viewer
- getShowSelectedOnce() - Method in class org.jmol.viewer.Viewer
- getShowUnitCell() - Method in class org.jmol.viewer.Viewer
- getSigma() - Method in class org.jmol.adapter.readers.cif.MSRdr
- getSignature() - Method in interface org.jmol.api.JmolScriptFunction
- getSignature() - Method in class org.jmol.script.ScriptFunction
- getSiteMultiplicity(P3) - Method in interface org.jmol.api.SymmetryInterface
- getSiteMultiplicity(P3) - Method in class org.jmol.symmetry.Symmetry
- getSiteMultiplicity(P3, UnitCell) - Method in class org.jmol.symmetry.SpaceGroup
- getSize(int) - Method in class org.jmol.shape.AtomShape
- getSize(int) - Method in class org.jmol.shape.Shape
-
overridden in Dots, CGOMesh, and AtomShape
- getSize(int) - Method in class org.jmol.shapespecial.Dots
- getSize(int, boolean) - Static method in class org.jmol.shapecgo.CGOMesh
- getSizeG(Group) - Method in class org.jmol.shape.Shape
- getSizeG(Group) - Method in class org.jmol.shapebio.BioShapeCollection
- getSlabColor() - Method in class org.jmol.util.MeshSurface
- getSlabDepthPlane(boolean) - Method in class org.jmol.viewer.TransformManager
- getSlabObjectType(int, Object, boolean, Object) - Static method in class org.jmol.util.TempArray
- getSlabPercentSetting() - Method in class org.jmol.viewer.TransformManager
- getSlabType() - Method in class org.jmol.util.MeshSurface
- getSlabWithinRange(float, float) - Static method in class org.jmol.util.TempArray
- getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
-
scales slater using double factorials involving quantum number n, l, and xyz exponents.
- getSlaterConstDSpherical(int, double, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
-
spherical scaling factors specifically for x2-y2 and z2 orbitals see http://openmopac.net/Manual/real_spherical_harmonics.html dz2 sqrt((1/2p)(5/8))(2cos2(q) -sin2(q)) sqrt(5/16p)(3z2-r2)/r2 dxz sqrt((1/2p)(15/4))(cos(q)sin(q))cos(f) sqrt(15/4p)(xz)/r2 dyz sqrt((1/2p)(15/4))(cos(q)sin(q))sin(f) sqrt(15/4p)(yz)/r2 dx2-y2 sqrt((1/2p)(15/16))sin2(q)cos2(f) sqrt(15/16p)(x2-y2)/r2 dxy sqrt((1/2p)(15/16))sin2(q)sin2(f) sqrt(15/4p)(xy)/r2 The fact() method returns sqrt(15/4p) for both z2 and x2-y2.
- getSlaters() - Method in class org.jmol.adapter.readers.quantum.SlaterReader
- getSlice() - Method in class org.openscience.jmol.app.surfacetool.Slice
- getSliceAngleXY() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getSliceMiddle() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getSlicePosition() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getSliceThickness() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getSmartsMap(String, BS, int) - Method in class org.jmol.viewer.Viewer
- getSmartsMatch(String, BS) - Method in class org.jmol.api.JmolViewer
- getSmartsMatch(String, BS) - Method in class org.jmol.viewer.Viewer
- getSmartsMatchForNodes(String, Node[]) - Method in class org.jmol.viewer.Viewer
- getSmiles(BS) - Method in class org.jmol.api.JmolViewer
- getSmiles(BS) - Method in class org.jmol.viewer.Viewer
- getSmiles(SmilesMatcher, Node[], int, BS, String, int) - Method in class org.jmol.smiles.SmilesGenerator
-
The main entry point from SmilesMatcher
- getSmiles(Node[], int, BS, String, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- getSmiles(Node[], int, BS, String, int) - Method in class org.jmol.smiles.SmilesMatcher
-
internal to Jmol -- called by org.jmol.Viewer.getSmiles
- getSmiles(Viewer, JniInchiOutputStructure, String) - Method in class org.jmol.inchi.InChIJNI
- getSmilesAt(SB, SimpleNode, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesGenerator
- getSmilesAtoms(String) - Method in class org.jmol.viewer.Viewer
- getSmilesChiralityArray() - Method in class org.jmol.symmetry.CIPDataSmiles
- getSmilesComponent(Node, BS, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesGenerator
-
creates a valid SMILES string from a model.
- getSmilesCorrelation(BS, BS, String, Lst<P3>, Lst<P3>, M4, Lst<BS>, boolean, int[][], P3, boolean, int) - Method in class org.jmol.scriptext.SmilesExt
-
The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.
- getSmilesExt() - Method in class org.jmol.script.ScriptExpr
- getSmilesMatcher() - Method in class org.jmol.viewer.Viewer
- getSmilesMatches(String, String, BS, BS, int, boolean, boolean) - Method in class org.jmol.scriptext.SmilesExt
- getSmilesOpt(BS, int, int, int, String) - Method in class org.jmol.viewer.Viewer
-
returns the SMILES string for a sequence or atom set does not include attached protons on groups
- getSolventPoints(IsoSolventReader.Edge, int, int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- getSortingStatus(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getSource(EventObject) - Method in class org.jmol.awt.AwtPopupHelper
-
returns the SwingComponent wrapper for this item
- getSourceActions(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- getSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupFromITAName(String) - Static method in class org.jmol.symmetry.SpaceGroup
- getSpaceGroupInfo(SymmetryInterface, int, String, int, P3, P3, String, float, int, boolean, boolean, int, SymmetryInterface, BS) - Method in class org.jmol.symmetry.SymmetryDesc
- getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupInfo(ModelSet, String, int, boolean, float[]) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupInfoObj(String, float[], boolean, boolean) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupInfoObj(String, float[], boolean, boolean) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupName() - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupName() - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupNameType(String) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupNameType(String) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupOperation(int) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupOperation(int) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupOperationCode(int) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupOperationCode(int) - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroupOperationCount() - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupOperationCount() - Method in class org.jmol.symmetry.Symmetry
- getSpaceGroups() - Static method in class org.jmol.symmetry.SpaceGroup
- getSpaceGroupXyz(int, boolean) - Method in interface org.jmol.api.SymmetryInterface
- getSpaceGroupXyz(int, boolean) - Method in class org.jmol.symmetry.Symmetry
- getSparseMatrix(CifReader, String, int, int) - Method in class org.jmol.adapter.readers.cif.MSCifParser
- getSpartanDirs(String) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
-
read the output file from the Spartan directory and decide from that what files need to be read and in what order - usually M0001 or a set of Profiles.
- getSpartanFileList(String, String[]) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
-
returns the list of files to read for every Spartan spardir.
- getSpartanSubfiles(String[]) - Method in class org.jmol.io.JmolUtil
-
Called to see if we have a zipped up Mac directory.
- getSpecialAtom(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
- getSpecialAtomName(int) - Static method in class org.jmol.modelsetbio.BioResolver
- getSpecialAtomPoint(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
- getSpecialLabel(String, String) - Method in class org.jmol.popup.JmolPopup
-
menus or menu items with SPECIAL in their name are sent here for on-the-fly labeling
- getSpecName(String) - Method in class org.jmol.modelset.AtomCollection
- getSpecNameOrNull(String, boolean) - Method in class org.jmol.modelset.AtomCollection
- getSpecular() - Method in class org.jmol.util.GData
- getSpecularExponent() - Method in class org.jmol.util.GData
- getSpecularPercent() - Method in class org.jmol.util.GData
- getSpecularPower() - Method in class org.jmol.util.GData
- getSpeedPixelsPerMillisecond(int, int) - Method in class org.jmol.viewer.Gesture
- getSPF(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- getSphereData(int) - Static method in class org.jmol.util.MeshSurface
-
Calculates the data (faces, vertices, normals) for a sphere.
- getSphereResource() - Method in class org.jmol.export._IdtfExporter
- getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
- getSpinAxis(String, int) - Method in class org.jmol.shapespecial.Draw
- getSpinCenter(String, int, int) - Method in class org.jmol.shapespecial.Draw
- getSpinDensities(int) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- getSpinOp(int) - Method in interface org.jmol.api.SymmetryInterface
- getSpinOp(int) - Method in class org.jmol.symmetry.Symmetry
- getSpinState() - Method in class org.jmol.viewer.Viewer
- getSpinState(boolean) - Method in class org.jmol.viewer.JmolStateCreator
- getSpinState(boolean) - Method in class org.jmol.viewer.StateCreator
- getSSMapAtom(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getStack(int) - Method in class org.jmol.viewer.StateManager
- getStandardLabelFormat(int) - Method in class org.jmol.viewer.Viewer
- getStandardPdbHydrogenCount(String) - Static method in class org.jmol.modelsetbio.BioResolver
- getStartChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStartChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStartInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStartInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStartSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStartSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getState() - Method in interface org.jmol.api.JmolGestureServerInterface
- getState() - Method in interface org.jmol.api.JmolModulationSet
- getState() - Method in class org.jmol.modelset.Trajectory
- getState() - Method in class org.jmol.symmetry.UnitCell
- getState() - Method in class org.jmol.util.ModulationSet
- getState(String) - Method in class org.jmol.shape.Mesh
- getState(SB) - Method in interface org.jmol.api.JmolNMRInterface
- getState(SB) - Method in class org.jmol.quantum.NMRCalculation
- getState(ModelSet, int, SB) - Method in interface org.jmol.api.SymmetryInterface
- getState(ModelSet, int, SB) - Method in class org.jmol.symmetry.Symmetry
- getState(Viewer) - Method in class org.jmol.shapespecial.Polyhedron
- getStateAtoms(SB) - Method in class org.jmol.shapespecial.Ellipsoids
- getStateCreator() - Method in class org.jmol.viewer.Viewer
- getStateID(SB) - Method in class org.jmol.shapespecial.Ellipsoids
- getStateInfo() - Method in class org.jmol.api.JmolViewer
- getStateInfo() - Method in class org.jmol.viewer.Viewer
- getStateInfo3(String, int, int) - Method in class org.jmol.viewer.Viewer
- getStateScript(String, int, int) - Method in class org.jmol.viewer.JmolStateCreator
- getStateScript(String, int, int) - Method in class org.jmol.viewer.StateCreator
- getStaticGraphics(Object, boolean) - Method in interface org.jmol.api.GenericPlatform
- getStaticGraphics(Object, boolean) - Static method in class org.jmol.awt.Image
- getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
- getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs.Platform
- getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs2d.Platform
- getStatusChanged(String) - Method in class org.jmol.viewer.StatusManager
- getStatusChanged(String) - Method in class org.jmol.viewer.Viewer
- getStereo() - Method in class org.jmol.smiles.SmilesAtom
- getStereoAtAt(SimpleNode[]) - Method in class org.jmol.smiles.SmilesAtom
- getStereoEdge(SimpleNode, SimpleNode) - Method in class org.jmol.symmetry.CIPDataSmiles
- getStereoFlag(SimpleNode, SimpleNode[], int, VTemp, boolean) - Static method in class org.jmol.smiles.SmilesStereo
- getStereoMode(String) - Static method in enum org.jmol.c.STER
- getStereoRotationMatrix(boolean) - Method in class org.jmol.viewer.TransformManager
- getStr(int, int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
safe string parsing of line.substring(col1, col2);
- getStraightness(float) - Static method in class org.jmol.modelsetbio.BioExt
- getStrandCount() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStrandCount() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStrandCount(int) - Method in class org.jmol.viewer.Viewer
- getStrFormatForState() - Method in class org.jmol.modelset.Measurement
- getString() - Method in class org.jmol.modelset.Measurement
- getString(String) - Method in class org.jmol.i18n.GT
- getString(String) - Method in class org.jmol.i18n.Resource
- getString(String) - Method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- getString(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getString(Map<String, Object>, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- getStringDetail() - Method in class org.jmol.modelset.Measurement
- getStringInfo(String, String, String, String, String, Map<String, Object[]>, String, Lst<Object[]>, String) - Method in class org.jmol.jsv.JDXMOLParser
- getStringObjectAsVariable(Object) - Method in class org.jmol.script.ScriptExpr
- getStrings(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getStringUsing(Viewer, String, String) - Method in class org.jmol.modelset.Measurement
- getStringX(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getStringX(String) - Static method in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- getStringX(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getStringX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- getStrucNo() - Method in class org.jmol.modelset.Group
- getStrucNo() - Method in class org.jmol.modelsetbio.AlphaMonomer
- getStructure() - Method in class org.jmol.adapter.readers.cif.MMTFReader
-
Get and translate the DSSP string from digit format input data
- getStructure() - Method in class org.jmol.modelset.Group
- getStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
- getStructure() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- getStructure(String) - Method in class org.jmol.popup.PopupResource
- getStructure(JniInchiStructure) - Method in class org.jmol.inchi.InChIJNI
- getStructuredModels() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStructuredModels() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStructureId() - Method in class org.jmol.modelset.Group
- getStructureId() - Method in class org.jmol.modelsetbio.AminoMonomer
- getStructureId() - Method in class org.jmol.modelsetbio.Monomer
- getStructureID() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStructureID() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter
-
Get a StructureIterator.
- getStructureLines(BS, SB, Lst<ProteinStructure>, STR, boolean, int) - Method in class org.jmol.modelsetbio.BioModelSet
- getStructureList() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- getStructureList() - Method in class org.jmol.modelset.ModelSet
- getStructureList() - Method in class org.jmol.viewer.GlobalSettings
- getStructureList() - Method in class org.jmol.viewer.Viewer
- getStructureMap(Lst<Object>, String, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
-
Find the map for a specified structure, producing a structure that can be used to generate lone pairs and bonds for a Lewis structure
- getStructureMidPoint(int) - Method in class org.jmol.modelsetbio.ProteinStructure
- getStructures(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- getStructures(String, String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
-
Reads the $NRTSTR $NRTSTRA, $NRTSTRB, and $CHOOSE blocks.
- getStructures46(String[], String, Lst<Object>, int) - Static method in class org.jmol.adapter.readers.quantum.NBOParser
-
Use the .46 file NBO alpha/beta labels to identify bonds, lone pairs, and lone valences.
- getStructureState() - Method in class org.jmol.viewer.Viewer
- getStructuresTOPO(String, String, Lst<Object>) - Method in class org.jmol.adapter.readers.quantum.NBOParser
- getStructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
- getStructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getStuctureAsText(String, String[][], String[][]) - Method in class org.jmol.popup.PopupResource
- getStyle(boolean) - Method in class org.jmol.awtjs.swing.GridBagConstraints
- getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Component
- getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.Container
- getSubcomponentHeight() - Method in class org.jmol.awtjs.swing.JSplitPane
- getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Component
- getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.Container
- getSubcomponentWidth() - Method in class org.jmol.awtjs.swing.JSplitPane
- getSublist(Lst<SV>, Lst<SV>) - Method in class org.jmol.scriptext.MathExt
-
[ {...},{...}...
- getSubPattern(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
- getSubsearch(SmilesSearch, String, int) - Method in class org.jmol.smiles.SmilesParser
- getSubSign(V3, V3, V3, int) - Static method in class org.jmol.quantum.NMRCalculation
-
Look for sign of (v23 x v21).dot.(sA_cA).
- getSubstructureSet(String, Node[], int, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- getSubstructureSet(String, Node[], int, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
-
Returns a bitset matching the pattern within a set of Jmol atoms.
- getSubstructureSetArray(String, BS, int) - Method in class org.jmol.viewer.Viewer
- getSubstructureSetArray(String, Node[], int, BS, BS, int) - Method in interface org.jmol.api.SmilesMatcherInterface
- getSubstructureSetArray(String, Node[], int, BS, BS, int) - Method in class org.jmol.smiles.SmilesMatcher
-
Returns a vector of bitsets indicating which atoms match the pattern.
- getSubstructureSetArrayForNodes(String, Node[], int) - Method in class org.jmol.viewer.Viewer
- getSubstructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
- getSubstructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
- getSubsystem(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getSubSystemUnitCell() - Method in interface org.jmol.api.JmolModulationSet
- getSubSystemUnitCell() - Method in class org.jmol.util.ModulationSet
- getSubzonePmeshes(BZone) - Method in class org.jmol.util.BZone
-
Loop through all planes, creating a pmesh for each face.
- getSubzones(BZone, BZone) - Method in class org.jmol.util.BZone
- getSupported(String) - Method in class org.jmol.i18n.GT
- getSupported(Language[], String) - Static method in class org.jmol.i18n.Language
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
- getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
-
The list of files returned by this function should contain the full path to each file.
- getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
- getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.SurfaceReader
- getSurfaceData() - Method in class org.jmol.jvxl.readers.EfvetReader
- getSurfaceData() - Method in class org.jmol.jvxl.readers.NffReader
- getSurfaceData() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
- getSurfaceData() - Method in class org.jmol.jvxl.readers.PmeshReader
- getSurfaceData() - Method in class org.jmol.jvxl.readers.PolygonFileReader
- getSurfaceData() - Method in class org.jmol.jvxl.readers.Ras3DReader
- getSurfaceDistance100() - Method in class org.jmol.modelset.Atom
- getSurfaceDistance100(int) - Method in class org.jmol.modelset.AtomCollection
- getSurfaceDistanceMax() - Method in class org.jmol.modelset.AtomCollection
- getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.IsoMOReader
- getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.IsoSolventReader
-
TEST: alternative EXACT position of fraction for spherical MarchingCubes FOR: ttest.xyz: 2 isosurface molecular test showing discontinuities C -2.70 0 0 C 2.75 0 0 RESULT: LINEAR (points slightly within R): $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.06620391572324] isosurfaceVolume = [41.639681683494324] NONLINEAR: $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.11873783245028] isosurfaceVolume = [41.727027252180655] revision 3/16/2014: isosurfaceArea = [75.13146821881998] isosurfaceVolume = [41.74598178064965] MSMS: msms -if ttest.xyzrn -of ttest -density 5 MSMS 2.6.1 started on Local PC Copyright M.F.
- getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
- getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.shapesurface.Isosurface
- getSurfaces() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getSurfaceSet() - Method in class org.jmol.jvxl.data.MeshData
- getSurfaceSetForLevel(int) - Method in class org.jmol.jvxl.data.MeshData
- getSurfaceSets() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- getSwingComponent(Object) - Method in class org.jmol.awt.AwtPopupHelper
- getSwingComponent(Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
- getSwingComponent(Object) - Method in interface org.jmol.popup.PopupHelper
- getSym - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
- getSymbol(String) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- getSymbolic() - Method in class org.jmol.adapter.readers.simple.InputReader
- getSymbolic(String) - Method in class org.jmol.adapter.readers.simple.InputReader
- getSymEditState() - Method in class org.jmol.modelkit.ModelKit
- getSymMatrices(int) - Method in class org.jmol.modelset.ModelSet
- getSymmetry() - Method in class org.jmol.adapter.readers.cif.Subsystem
- getSymmetry() - Method in class org.jmol.adapter.smarter.AtomIterator
- getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- getSymmetry() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getSymmetry(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getSymmetry(Viewer, boolean) - Method in class org.jmol.shapespecial.Polyhedron
- getSymmetry(Viewer, String) - Static method in class org.jmol.api.Interface
- getSymmetryEquivAtoms(BS) - Method in class org.jmol.modelset.ModelSet
- getSymmetryEquivPointList(Lst<P3>, String) - Method in class org.jmol.viewer.Viewer
- getSymmetryEquivPoints(P3, String) - Method in class org.jmol.viewer.Viewer
- getSymmetryFromCode(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
- getSymmetryFromCode(String) - Method in interface org.jmol.adapter.smarter.MSInterface
- getSymmetryInfo(int, String, int, P3, P3, P3, int, String, float, int, int) - Method in class org.jmol.viewer.Viewer
-
A general method for retrieving symmetry information with full capability of the symop() scripting function.
- getSymmetryInfo(SymmetryInterface, int, int, SymmetryInterface, String, int, P3, P3, P3, String, int, float, int, int) - Method in class org.jmol.symmetry.SymmetryDesc
-
multipurpose function handling a variety of tasks, including: processing of "lattice", "list", "atom", "point", and some "draw" output types finding the operator in the given space group creating a temporary space group for an xyz operator
- getSymmetryInfoAsString() - Method in class org.jmol.modelset.ModelSet
- getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, P3, String, int, float, int, int) - Method in interface org.jmol.api.SymmetryInterface
- getSymmetryInfoAtom(ModelSet, int, String, int, P3, P3, P3, String, int, float, int, int) - Method in class org.jmol.symmetry.Symmetry
- getSymmetryInfoStr() - Method in interface org.jmol.api.SymmetryInterface
- getSymmetryInfoStr() - Method in class org.jmol.symmetry.Symmetry
- getSymmetryInvariant(int) - Method in class org.jmol.modelset.ModelSet
- getSymmetryOperations() - Method in interface org.jmol.api.SymmetryInterface
- getSymmetryOperations() - Method in class org.jmol.symmetry.Symmetry
- getSymmetryOperatorList(boolean) - Method in class org.jmol.modelset.Atom
- getSymmetryTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
-
Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.
- getSymOp() - Method in class org.jmol.modelset.Atom
- getSymopInfo(int, String, int, P3, P3, P3, String, int, float, int, int) - Method in class org.jmol.symmetry.SymmetryDesc
- getSymopInfoForPoints(SymmetryInterface, int, int, P3, P3, P3, String, String, float, int, int, BS) - Method in class org.jmol.symmetry.SymmetryDesc
-
get information about a symmetry operation relating two specific points or atoms
- getSymopText() - Method in class org.jmol.modelkit.ModelKit
- getSymTemp() - Method in class org.jmol.viewer.Viewer
-
Retrieve a Symmetry object, possibly re-using an old one.
- getSymViewState() - Method in class org.jmol.modelkit.ModelKit
- getSyncMode() - Method in class org.jmol.viewer.StatusManager
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter.SortableHeaderRenderer
- getTableHeader() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getTableModel() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getTabulatedPotential(Atom) - Method in class org.jmol.quantum.MepCalculation
- getTaintedAtoms(int) - Method in class org.jmol.modelset.AtomCollection
- getTargetValence() - Method in class org.jmol.modelset.Atom
- getTauField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getTClone() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- getTensor(Atom, String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
- getTensor(Viewer, float[]) - Method in interface org.jmol.api.SymmetryInterface
- getTensor(Viewer, float[]) - Method in class org.jmol.symmetry.Symmetry
- getTensor(Viewer, float[]) - Method in class org.jmol.symmetry.UnitCell
- getTensorInfo(String, String, BS) - Method in interface org.jmol.api.JmolNMRInterface
- getTensorInfo(String, String, BS) - Method in class org.jmol.quantum.NMRCalculation
- getTensorList(Lst<Object>) - Static method in class org.jmol.modelset.AtomCollection
- getTensors() - Method in class org.jmol.adapter.smarter.AtomIterator
- getTensors() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getTensors() - Method in class org.jmol.modelset.Atom
- getTerminatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
- getTerminatorAtom() - Method in class org.jmol.modelsetbio.Monomer
- getTerminatorAtom() - Method in class org.jmol.modelsetbio.NucleicMonomer
- getTerminatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
- getText() - Method in interface org.jmol.api.JmolAppConsoleInterface
- getText() - Method in interface org.jmol.api.js.GenericConsoleTextArea
- getText() - Method in interface org.jmol.api.SC
- getText() - Method in class org.jmol.awt.AwtSwingComponent
- getText() - Method in class org.jmol.awtjs.swing.Component
- getText() - Method in class org.jmol.console.GenericConsole
- getText() - Method in interface org.jmol.console.GenericTextArea
- getText() - Method in class org.jmol.console.ScriptEditor
- getText() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- getText() - Static method in class org.openscience.jmol.app.webexport.LogPanel
- getText(String) - Static method in class org.jmol.modelkit.ModelKit
- getTextPixels(String, Font, Object, int, int, int) - Static method in class org.jmol.awtjs2d.Image
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in interface org.jmol.api.GenericPlatform
- getTextPixels(String, Font, Object, Object, int, int, int) - Static method in class org.jmol.awt.Image
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs.Platform
- getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
- getTextPosition() - Method in class org.jmol.util.GData
- getTextureName(short) - Method in class org.jmol.export._ObjExporter
-
Returns the name to be used for the texture associated with the given colix.
- getTextWrapper - Static variable in class org.jmol.i18n.GT
- getTextWrapper() - Static method in class org.jmol.i18n.GT
- getThermalRadius(int) - Static method in class org.jmol.shapespecial.Ellipsoid
- getTheta() - Method in class org.openscience.jmol.app.janocchio.NmrMolecule.DihedralCouple
- getThicknessMax() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getThisContext() - Method in interface org.jmol.api.JmolScriptEvaluator
- getThisContext() - Method in class org.jmol.script.ScriptEval
- getThisModelAtoms() - Method in class org.jmol.viewer.Viewer
- getThread() - Method in class org.jmol.minimize.Minimizer
- getTimeDifference(int) - Method in class org.jmol.viewer.Gesture
- getTimeFrom(String) - Static method in class org.jmol.util.Logger
- getTimerMsg(String, int) - Static method in class org.jmol.util.Logger
- getTlsGroups - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- gettMixField() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- getTok() - Method in interface org.jmol.api.JmolScriptFunction
- getTok() - Method in class org.jmol.script.ScriptFunction
- getToken() - Method in class org.jmol.script.ScriptTokenParser
-
gets the next token and sets global theToken and theValue
- getToken(int) - Method in class org.jmol.script.ScriptContext
- getToken(int) - Method in class org.jmol.script.ScriptParam
- getToken(int) - Method in class org.jmol.scriptext.ScriptExt
- getTokenCount() - Method in class org.jmol.script.ScriptContext
- getTokenFromName(String) - Static method in class org.jmol.script.T
- getTokens() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getTokens() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- getTokensFloat(String, float[], int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- getTokensLike(String) - Static method in class org.jmol.script.T
- getTokensType(Map<String, Object>, int) - Static method in class org.jmol.script.T
- getTokFromName(String) - Static method in class org.jmol.script.T
- getTopData() - Method in class org.jmol.adapter.readers.simple.FAHReader
- getToPlaneParameter() - Method in class org.jmol.jvxl.data.VolumeData
- getTopologyParser() - Method in class org.jmol.adapter.readers.cif.CifReader
- getTopoMapPt(int[], int, SmilesAtom, SmilesAtom, SmilesBond[], int) - Static method in class org.jmol.smiles.SmilesStereo
- getTopPopupMenu() - Method in class org.jmol.awtjs.swing.AbstractButton
- getTorsionAngleRadians(double[], double[], double[], double[], V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- getTorsionKey(int, int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getTorsions() - Method in class org.jmol.minimize.Minimizer
- getTorsions(Atom[], int[][], float[][], int) - Static method in class org.jmol.scriptext.SmilesExt
- getTotalHydrogenCount() - Method in class org.jmol.modelset.Atom
- getTotalHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
- getTotalHydrogenCount() - Method in interface org.jmol.util.Node
- getTotalValence() - Method in class org.jmol.modelset.Atom
- getTotalValence() - Method in class org.jmol.smiles.SmilesAtom
- getTotalValence() - Method in interface org.jmol.util.Node
- getTrackerKey(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Static method in class org.jmol.symmetry.CIPDataTracker
- getTrackerLine(CIPChirality.CIPAtom, BS, BS, int) - Method in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- getTrajectoryState() - Method in class org.jmol.viewer.Viewer
- getTrajectoryStep(P3[]) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- getTrajectoryStep(P3[], boolean) - Method in class org.jmol.adapter.readers.more.MdCrdReader
- getTransferData(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
- getTransferData(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
- getTransferDataFlavors() - Method in class org.jmol.awt.AwtClipboard
- getTransferDataFlavors() - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
- getTransform(P3, P3, boolean) - Method in interface org.jmol.api.SymmetryInterface
- getTransform(P3, P3, boolean) - Method in class org.jmol.symmetry.Symmetry
- getTransform(UnitCell, SymmetryOperation[], P3, P3, boolean) - Method in class org.jmol.symmetry.SymmetryDesc
- getTransformedVertexVectors() - Method in class org.jmol.util.GData
- getTransformManager(Viewer, int, int, boolean) - Static method in class org.jmol.viewer.TransformManager
- getTranslation(int) - Method in class org.jmol.modelset.ModelSet
- getTranslationScript() - Method in class org.jmol.viewer.TransformManager
- getTranslationXPercent() - Method in class org.jmol.viewer.TransformManager
- getTranslationYPercent() - Method in class org.jmol.viewer.TransformManager
- getTranslucentFlag(float) - Static method in class org.jmol.util.C
- getTranslucentLabel(short) - Static method in class org.jmol.shape.Shape
- getTranslucentLevel(int) - Method in class org.jmol.script.ScriptEval
- getTriad(int[]) - Method in class org.jmol.export._PovrayExporter
- getTriad(T3) - Method in class org.jmol.export.___Exporter
- getTriad(T3) - Method in class org.jmol.export._PovrayExporter
- getTriadC(T3) - Method in class org.jmol.export.___Exporter
- getTriangleData(T3, T3, T3) - Static method in class org.jmol.export.MeshData
-
Calculates the data (faces, vertices, normals) for a triangle.
- getTriangleResource(String, T3, T3, T3) - Method in class org.jmol.export._IdtfExporter
- getTriangles() - Method in class org.jmol.jvxl.readers.EfvetReader
- getTriangulator() - Method in class org.jmol.viewer.Viewer
- getTrigonality(SimpleNode, V3) - Method in class org.jmol.symmetry.CIPData
-
Determine the trigonality of an atom in order to determine whether it might have a lone pair.
- getTrimmedLineImpl() - Method in class org.jmol.g3d.LineRenderer
-
Cohen-Sutherland line clipping used to check visibility.
- getTrueAtomCount() - Method in class org.jmol.modelset.Model
-
not actually accessed -- just pointing out what it is
- getType() - Method in interface org.jmol.api.JmolDialogInterface
- getType() - Method in class org.jmol.dialog.Dialog
- getType() - Method in class org.jmol.modelsetbio.BioPolymer
- getType(int) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
- getType(Object[]) - Method in class org.jmol.viewer.DataManager
- getType(String) - Static method in class org.jmol.symmetry.SymmetryDesc
-
Determine the type of this request.
- getType(String) - Static method in class org.jmol.util.Tensor
- getType(Atom) - Static method in enum org.jmol.c.HB
- getUndeletedGroupAtomBits(BS) - Method in class org.jmol.viewer.Viewer
- getUndoInfo() - Method in class org.jmol.viewer.StateManager
- getUndoMax() - Method in class org.jmol.viewer.StateManager
- getUndoRedoState(int) - Method in class org.jmol.viewer.StateManager
- getUnescapedStringLiteral(boolean) - Method in class org.jmol.script.ScriptCompiler
-
lookingAtString returned true, and we need to unescape any t, r, n, ", ', x, u, or backslash after a backslash
- getUniqueFloatDef(int, int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getUniqueID() - Method in class org.jmol.adapter.smarter.AtomIterator
- getUniqueID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getUniqueID() - Method in class org.jmol.modelsetbio.Monomer
- getUniqueID(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getUniqueID(int) - Method in interface org.jmol.api.PymolAtomReader
- getUniquePoint(int, int, P3) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getUniqueTensorSet(BS) - Method in interface org.jmol.api.JmolNMRInterface
-
An attempt to find unique atoms using tensors.
- getUniqueTensorSet(BS) - Method in class org.jmol.quantum.NMRCalculation
- getUnitCell() - Method in class org.jmol.modelset.Atom
- getUnitCell() - Method in class org.jmol.shape.Mesh
- getUnitCell() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getUnitCell(int) - Method in class org.jmol.modelset.ModelSet
- getUnitCell(int) - Method in class org.jmol.viewer.Viewer
- getUnitCell(T3[], boolean, String) - Method in interface org.jmol.api.SymmetryInterface
- getUnitCell(T3[], boolean, String) - Method in class org.jmol.symmetry.Symmetry
- getUnitCellAsArray(boolean) - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellAsArray(boolean) - Method in class org.jmol.symmetry.Symmetry
- getUnitCellAsArray(boolean) - Method in class org.jmol.util.SimpleUnitCell
- getUnitCellAtomIndex() - Method in class org.jmol.viewer.AnimationManager
- getUnitCellForAtom(int) - Method in class org.jmol.modelset.ModelSet
- getUnitCellInfo() - Method in class org.jmol.viewer.PropertyManager
- getUnitCellInfo(boolean) - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellInfo(boolean) - Method in class org.jmol.symmetry.Symmetry
- getUnitCellInfo(int) - Method in class org.jmol.viewer.Viewer
- getUnitCellInfoMap() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellInfoMap() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellInfoText() - Method in class org.jmol.viewer.Viewer
- getUnitCellInfoType(int) - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellInfoType(int) - Method in class org.jmol.symmetry.Symmetry
- getUnitCellMultiplied() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellMultiplied() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellMultiplied() - Method in class org.jmol.symmetry.UnitCell
- getUnitCellMultiplier() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellMultiplier() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellMultiplier() - Method in class org.jmol.symmetry.UnitCell
- getUnitCellParams() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellParams() - Method in class org.jmol.modelset.ModelSet
-
deprecated due to multimodel issues, but required by an interface -- do NOT remove.
- getUnitCellParams() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellParams() - Method in class org.jmol.util.SimpleUnitCell
- getUnitCellPointsWithin(float, BS, P3, boolean) - Method in class org.jmol.modelset.ModelSet
- getUnitCellState() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellState() - Method in class org.jmol.modelkit.ModelKit
- getUnitCellState() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellVectors() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellVectors() - Method in class org.jmol.symmetry.Symmetry
- getUnitCellVectors() - Method in class org.jmol.symmetry.UnitCell
- getUnitCellVerticesNoOffset() - Method in interface org.jmol.api.SymmetryInterface
- getUnitCellVerticesNoOffset() - Method in class org.jmol.symmetry.Symmetry
- getUnitID(int) - Method in class org.jmol.modelset.Atom
- getUnitID(Atom, int) - Method in class org.jmol.modelsetbio.BioModel
-
Get a unitID.
- getUnitIDFlags(String) - Static method in class org.jmol.viewer.JC
-
Get a unitID type
- getUnits() - Method in class org.jmol.minimize.forcefield.Calculations
- getUnits() - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
- getUnits() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
- getUnitsymmetryInfo() - Method in class org.jmol.symmetry.Symmetry
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
- getUnknownCheckBoxScriptToRun(SC, String, String, boolean) - Method in class org.jmol.popup.GenericPopup
- getUnzippedReaderOrStreamFromName(String, Object, boolean, boolean, boolean, boolean, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
- getUParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getURLContents(URL, byte[], String) - Static method in class org.jmol.awt.AwtFile
- getURLContents(URL, byte[], String) - Static method in class org.jmol.awtjs2d.JSFile
-
Note that the JS equivalent passes back a javajs.util.SB
- getURLContents(URL, byte[], String, boolean) - Method in interface org.jmol.api.GenericPlatform
- getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awt.Platform
- getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awtjs2d.Platform
- getURLContentsStatic(URL, byte[], String, boolean) - Static method in class org.jmol.awtjs2d.Platform
-
In case this needs to be performed directly, without interface
- getUseMolecular() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- getUserDirectory() - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
-
Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
- getUserDirectory() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
- getUserFunctionResult(String, Lst<SV>, SV) - Method in class org.jmol.script.ScriptEval
- getUserSettableType(String) - Static method in class org.jmol.modelset.AtomCollection
- getUserVariable(String) - Method in class org.jmol.viewer.GlobalSettings
- getUtil(String, Viewer, String) - Static method in class org.jmol.api.Interface
- getUVBoxFromHKL(SymmetryInterface, P4, P4) - Method in class org.jmol.scriptext.CmdExt
-
create a uvw-space unit cell from an HKL plane
- getV0abc(int, Object) - Method in class org.jmol.viewer.Viewer
-
convert string abc;offset or M3 or M4 to origin and three vectors -- a, b, c.
- getV0abc(Object, M4) - Method in interface org.jmol.api.SymmetryInterface
- getV0abc(Object, M4) - Method in class org.jmol.symmetry.Symmetry
- getV0abc(Object, M4) - Method in class org.jmol.symmetry.UnitCell
- getV3() - Method in interface org.jmol.api.JmolModulationSet
- getV3() - Method in class org.jmol.util.ModulationSet
- getVal(float) - Method in class org.jmol.thread.MoveToThread.Slider
- getVal(MoveToThread.Slider) - Method in class org.jmol.thread.MoveToThread
- getValence() - Method in class org.jmol.modelset.Atom
-
return the total bond order for this atom
- getValence() - Method in class org.jmol.modelset.Bond
- getValence() - Method in class org.jmol.smiles.SmilesAtom
- getValence() - Method in class org.jmol.smiles.SmilesBond
- getValence() - Method in interface org.jmol.util.Node
- getValence() - Method in interface org.jmol.util.SimpleNode
- getValidValues(BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getValidVertices(BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getValue(double, boolean) - Method in class org.jmol.quantum.NciCalculation
- getValue(int) - Method in class org.jmol.adapter.readers.simple.InputReader
- getValue(int, int, int) - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
- getValue(int, int, int, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
-
for readers only
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- getValue(int, int, int, int) - Method in class org.jmol.shapesurface.Isosurface
- getValue(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- getValue(String, String) - Method in class org.jmol.util.GenericApplet
- getValue2(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getValueAB(float, float) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- getValueAB(float, float) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
- getValueArray(int, int, int, int, float[]) - Method in class org.jmol.jvxl.calc.MarchingCubes
- getValueAt(int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- getValueAt(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- getValueAt(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getValueAt(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
- getValueAtPoint(P3) - Method in class org.jmol.quantum.MepCalculation
- getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
- getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
- getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
- getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- getValueAtPoint2(T3, BS) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- getValueAtPoint2(T3, BS) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
- getValueLowerCase(String, String) - Method in class org.jmol.util.GenericApplet
- getValues() - Method in class org.jmol.jvxl.readers.IsoMOReader
- getValues(Mesh) - Method in class org.jmol.shape.MeshCollection
- getValues(Mesh) - Method in class org.jmol.shapesurface.Isosurface
- getVanderwaalsMar(int) - Method in class org.jmol.viewer.Viewer
- getVanderwaalsMar(int, VDW) - Static method in class org.jmol.util.Elements
- getVanderwaalsMarType(int, VDW) - Method in class org.jmol.viewer.Viewer
- getVanderwaalsRadiusFloat(Viewer, VDW) - Method in class org.jmol.modelset.Atom
- getVariable(Object) - Static method in class org.jmol.script.SV
- getVariable(String) - Method in class org.jmol.script.ScriptContext
-
Context variables go up the stack until a function is found.
- getVariableAB(byte[]) - Static method in class org.jmol.script.SV
- getVariableAD(double[]) - Static method in class org.jmol.script.SV
- getVariableADD(double[][]) - Static method in class org.jmol.script.SV
- getVariableAF(float[]) - Static method in class org.jmol.script.SV
- getVariableAFF(float[][]) - Static method in class org.jmol.script.SV
- getVariableAI(int[]) - Static method in class org.jmol.script.SV
- getVariableAII(int[][]) - Static method in class org.jmol.script.SV
- getVariableAO(Object[]) - Static method in class org.jmol.script.SV
- getVariableAP(T3[]) - Static method in class org.jmol.script.SV
- getVariableAS(String[]) - Static method in class org.jmol.script.SV
- getVariableASS(String[][]) - Static method in class org.jmol.script.SV
- getVariableAV(SV[]) - Static method in class org.jmol.script.SV
- getVariableList() - Method in class org.jmol.viewer.GlobalSettings
- getVariableList(Map<String, SV>, int, boolean, boolean) - Static method in class org.jmol.viewer.StateManager
- getVariableList(Lst<?>) - Static method in class org.jmol.script.SV
- getVariableMap(Map<String, ?>) - Static method in class org.jmol.script.SV
- getVariables(String) - Method in class org.jmol.viewer.PropertyManager
- getVarParameter(String, boolean) - Method in class org.jmol.script.ScriptParam
- getVArray(int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
- getVArrayB(int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
- getVDW(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- getVDW(int) - Method in interface org.jmol.api.PymolAtomReader
- getVdwClashRadius(ContactPair, double, double, double, double) - Static method in class org.jmol.shapesurface.Contact
-
well, heh, heh...
- getVdwLabel() - Method in enum org.jmol.c.VDW
- getVdwType(String) - Static method in enum org.jmol.c.VDW
- getVdwType(VDW) - Method in class org.jmol.modelset.Atom
- getVdwType2(String) - Static method in enum org.jmol.c.VDW
- getVectors(String) - Method in class org.jmol.adapter.writers.PWMATWriter
- getVectorsAndOrigin() - Method in class org.jmol.jvxl.readers.MapFileReader
- getVersion() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
- getVersion() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getVersion() - Method in interface org.openscience.jmol.app.JmolPlugin
- getVertex() - Method in class org.jmol.jvxl.readers.NffReader
- getVertex(short, short) - Static method in class org.jmol.util.Geodesic
- getVertexCount(int) - Static method in class org.jmol.util.Geodesic
- getVertexIndexFromNumber(int) - Method in class org.jmol.shape.Mesh
- getVertexList(DrawMesh, int, int) - Static method in class org.jmol.shapespecial.Draw
- getVertexValues(boolean) - Method in class org.jmol.jvxl.calc.MarchingSquares
- getVertexVector(int) - Static method in class org.jmol.util.Geodesic
- getVertexVectors() - Static method in class org.jmol.util.Geodesic
- getVertexVectors() - Static method in class org.jmol.util.Normix
- getVertices() - Method in class org.jmol.jvxl.readers.EfvetReader
- getVertices() - Method in class org.jmol.symmetry.UnitCell
- getVertices() - Method in class org.jmol.util.MeshSurface
- getVertices(Mesh) - Method in class org.jmol.shape.MeshCollection
- getVertices(Mesh) - Method in class org.jmol.shapesurface.Isosurface
- getVerticesFromOABC(T3[]) - Static method in class org.jmol.util.BoxInfo
- getVib() - Method in class org.jmol.adapter.smarter.AtomIterator
-
Note that atom.vib also serves to deliver specific data items.
- getVib() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getVib(char) - Method in class org.jmol.modelset.Atom
- getVibCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
-
also handles modulation info
- getVibration(boolean) - Method in interface org.jmol.api.JmolModulationSet
- getVibration(boolean) - Method in class org.jmol.util.ModulationSet
- getVibration(int, boolean) - Method in class org.jmol.modelset.AtomCollection
- getVibrationPoint(Vibration, T3, float) - Method in class org.jmol.viewer.TransformManager
-
return
- getVibrationVector() - Method in class org.jmol.modelset.Atom
- getViewerData() - Method in class org.jmol.popup.JmolPopup
- getViewerMeasurement(int, int) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getViewerRow(int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getViewerRow(int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getViewerRow(int, int) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getViewpoint() - Method in class org.jmol.export._VrmlExporter
- getViewScript(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- getViewState(TransformManager, SB) - Method in class org.jmol.viewer.StateCreator
- getViewToModel() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- getVisibleFramesBitSet() - Method in class org.jmol.api.JmolViewer
- getVisibleFramesBitSet() - Method in class org.jmol.viewer.Viewer
- getVisibleSet(boolean) - Method in class org.jmol.modelset.AtomCollection
- getVisibleVBS() - Method in class org.jmol.shape.Mesh
- getVisibleVertexBitSet() - Method in class org.jmol.shape.Mesh
- getVisibleVertexBitSet() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- getVolume() - Method in class org.jmol.shapespecial.Polyhedron
-
allows for n-gon, not just triangle; if last component index is negative, then that's a mesh code
- getVolume() - Method in class org.jmol.util.ContactPair
- getVolume(Viewer, VDW) - Method in class org.jmol.modelset.Atom
- getVolumetricVectorLengths() - Method in class org.jmol.jvxl.data.VolumeData
- getVoxel(int, int, int, int) - Method in class org.jmol.jvxl.readers.AtomDataReader
- getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- getVoxelCounts() - Method in class org.jmol.jvxl.data.VolumeData
- getVoxelData() - Method in class org.jmol.jvxl.data.VolumeData
- getVoxelDataAt(int) - Method in class org.jmol.jvxl.data.VolumeData
- getVoxelValue(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
- getVParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getWebSite() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- getWebSite() - Method in interface org.openscience.jmol.app.JmolPlugin
- getWidth() - Method in class org.jmol.awtjs.swing.Component
- getWidth(Object) - Static method in class org.jmol.awt.Image
- getWidth(Object) - Static method in class org.jmol.awtjs2d.Image
- getWindow(Container) - Static method in class org.jmol.awt.Platform
- getWindowBorder(String) - Method in class org.openscience.jmol.app.HistoryFile
- getWindowInnerDimension(String) - Method in class org.openscience.jmol.app.HistoryFile
- getWindowName() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- getWindowName() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- getWindowPosition(String) - Method in class org.openscience.jmol.app.HistoryFile
- getWindowSize(String) - Method in class org.openscience.jmol.app.HistoryFile
- getWindowState(SB, int, int) - Method in class org.jmol.viewer.StateCreator
- getWindowVisibility(String) - Method in class org.openscience.jmol.app.HistoryFile
- getWingAtom() - Method in class org.jmol.modelsetbio.Monomer
- getWingPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
- getWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
- getWithinDistanceVector(Lst<Object[]>, float, P3, BS, boolean) - Method in class org.jmol.scriptext.IsoExt
- getWord(String) - Method in class org.jmol.popup.PopupResource
- getWordContents() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
- getWordContents() - Method in class org.jmol.popup.MainPopupResourceBundle
- getWordContents() - Method in class org.jmol.popup.PopupResource
- getWorkingRadius(int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
- getWorkingRadius(Atom, AtomData) - Method in class org.jmol.modelset.AtomCollection
- getWrappedState(String, String[], Object, OC) - Method in class org.jmol.viewer.OutputManager
- getWrappedStateScript() - Method in class org.jmol.viewer.Viewer
- getX() - Method in class org.jmol.script.ScriptMathProcessor
- getXlink(String, String, boolean) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
- getXmlAttrib(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
- getXmlData(String, String, boolean, boolean) - Method in class org.jmol.jvxl.readers.XmlReader
- getXmlDataLF(String, String, boolean, boolean, boolean) - Method in class org.jmol.jvxl.readers.XmlReader
- getXmlPoint(String, String) - Method in class org.jmol.jvxl.readers.XmlReader
- getXmlType(String) - Static method in class org.jmol.adapter.smarter.Resolver
- getXOffset(int) - Static method in class org.jmol.viewer.JC
-
X offset in pixels.
- getXPlatformLook(JFileChooser) - Static method in class org.jmol.dialog.Dialog
- getXSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- getXTok() - Method in class org.jmol.script.ScriptMathProcessor
- getXyz(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
- getXyz(int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- getXYZ() - Method in class org.jmol.adapter.smarter.AtomIterator
- getXYZ() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- getXYZ() - Method in class org.jmol.modelset.Atom
- getXYZ() - Method in class org.jmol.smiles.SmilesAtom
- getXYZ() - Method in interface org.jmol.util.Node
- getXYZ() - Method in interface org.jmol.util.SimpleNode
- getXYZ(boolean) - Method in class org.jmol.symmetry.HallRotationTerm
- getXYZ(P3, float) - Method in class org.jmol.jvxl.readers.BCifDensityReader
- getXYZFromMatrix(M4, boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- getXYZFromRsVs(Matrix, Matrix, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- getxyzTrans(P3) - Method in class org.jmol.symmetry.SymmetryOperation
- getYellowField() - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- getYellowField() - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- getYellowValue() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- getYellowValue() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- getYOffset(int) - Static method in class org.jmol.viewer.JC
-
Y offset in pixels; negative of this is the actual screen offset
- getYzCount() - Method in class org.jmol.jvxl.data.VolumeData
- getZapName() - Method in class org.jmol.viewer.Viewer
- getZCurrent(float, float, int) - Method in class org.jmol.g3d.PrecisionRenderer
- getZipDirectory(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
- getZipDirectoryAsString(String) - Method in class org.jmol.viewer.Viewer
- getZoom(int, int, BS, float) - Method in class org.jmol.script.ScriptEval
- getZoomSetting() - Method in class org.jmol.viewer.TransformManager
- getZParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- getZshadeState(SB, TransformManager, boolean) - Method in class org.jmol.viewer.StateCreator
- ghemicalMMLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- GhemicalMMReader - Class in org.jmol.adapter.readers.simple
-
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
- GhemicalMMReader() - Constructor for class org.jmol.adapter.readers.simple.GhemicalMMReader
- ghostCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- ghostPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- gibbsEnergy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- gibbsEnergy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- gibbsEntropy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- gl_ambient - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- GL_LINE_LOOP - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_LINE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_LINES - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_POINTS - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_TRIANGLE_FAN - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_TRIANGLE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
- GL_TRIANGLES - Static variable in class org.jmol.shapecgo.CGOMesh
- GLOBAL - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- GLOBAL_AROMATICBONDS - Static variable in class org.jmol.viewer.JC
- GLOBAL_CONECT - Static variable in class org.jmol.viewer.JC
- GLOBAL_DOMAINS - Static variable in class org.jmol.viewer.JC
- GLOBAL_FRACTCOORD - Static variable in class org.jmol.viewer.JC
- GLOBAL_ISPDB - Static variable in class org.jmol.viewer.JC
- GLOBAL_MODULATED - Static variable in class org.jmol.viewer.JC
- GLOBAL_SUPERCELL - Static variable in class org.jmol.viewer.JC
- GLOBAL_SYMMETRY - Static variable in class org.jmol.viewer.JC
- GLOBAL_UNITCELLS - Static variable in class org.jmol.viewer.JC
- GLOBAL_VALIDATIONS - Static variable in class org.jmol.viewer.JC
- global3 - Variable in class org.jmol.adapter.readers.xtal.PWmatReader
- globalBooleans - Static variable in class org.jmol.viewer.JC
- globalDoApplySymmetry - Variable in class org.jmol.adapter.readers.xtal.AimsReader
- globalSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- GlobalSettings - Class in org.jmol.viewer
- GlobalSettings(Viewer, GlobalSettings, boolean) - Constructor for class org.jmol.viewer.GlobalSettings
- globalSlabValue - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- globalStrucNo - Static variable in class org.jmol.modelsetbio.ProteinStructure
- goButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- GOLD - Static variable in class org.jmol.util.C
- goPressed() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Save or else launch povray- ie do our thang!
- gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- gotocmd - Static variable in class org.jmol.script.T
- gotoCommand(int, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- gotoData(int, int) - Method in class org.jmol.jvxl.readers.XsfReader
- gotoParsedLine(int) - Method in class org.jmol.console.ScriptEditor
- gotoPosition(int, int) - Method in class org.jmol.console.ScriptEditor
- gotoTop() - Method in class org.jmol.console.ScriptEditor
- grabPixels(Object, int, int) - Static method in class org.jmol.awtjs2d.Image
- grabPixels(Object, int, int, int[]) - Method in interface org.jmol.api.GenericPlatform
- grabPixels(Object, int, int, int[]) - Static method in class org.jmol.awt.Image
- grabPixels(Object, int, int, int[]) - Method in class org.jmol.awt.Platform
- grabPixels(Object, int, int, int[]) - Method in class org.jmol.awtjs2d.Platform
- grad - Variable in class org.jmol.quantum.NciCalculation
- GRADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- gradient_max_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gradient_min_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gradient_min_slope - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gradient_normal_min_dot - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gradient_spacing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gradient_step_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gradient_symmetry - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- gradients - Variable in class org.jmol.minimize.forcefield.Calculations
- Graphics3D - Class in org.jmol.g3d
-
Provides high-level graphics primitives for 3D visualization for the software renderers.
- Graphics3D() - Constructor for class org.jmol.g3d.Graphics3D
- graphicsForMetrics - Variable in class org.jmol.util.GData
- graphicsForTextOrImage - Variable in class org.jmol.g3d.Platform3D
- GRAY - Static variable in class org.jmol.util.C
- GRAY - Static variable in class org.jmol.util.ColorEncoder
- green - Variable in class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- GREEN - Static variable in class org.jmol.util.C
- greyscalerendering - Static variable in class org.jmol.script.T
- greyscaleRendering - Variable in class org.jmol.viewer.GlobalSettings
- grid - Variable in class org.jmol.awtjs.swing.Grid
- grid - Variable in class org.jmol.awtjs.swing.JPanel
- Grid - Class in org.jmol.awtjs.swing
- Grid(int, int) - Constructor for class org.jmol.awtjs.swing.Grid
- grid_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- grid_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- grid_slot - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- GridBagConstraints - Class in org.jmol.awtjs.swing
- GridBagConstraints(int, int, int, int, double, double, int, int, Insets, int, int) - Constructor for class org.jmol.awtjs.swing.GridBagConstraints
- GridBagLayout - Class in org.jmol.awtjs.swing
- GridBagLayout() - Constructor for class org.jmol.awtjs.swing.GridBagLayout
- gridheight - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- gridpoints - Static variable in class org.jmol.script.T
- gridwidth - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- gridx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- gridy - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- gRight - Variable in class org.jmol.util.GenericApplet
- gRight - Variable in class org.jmol.viewer.Viewer
-
A graphics from a "slave" stereo display that has been synchronized with this this applet.
- GromacsReader - Class in org.jmol.adapter.readers.more
- GromacsReader() - Constructor for class org.jmol.adapter.readers.more.GromacsReader
- gromacsWideFormat - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- group - Variable in class org.jmol.modelset.Atom
- group - Static variable in class org.jmol.script.T
- group(String) - Method in class org.jmol.adapter.readers.xtal.CgdReader
- Group - Class in org.jmol.modelset
-
The essential container for every atom.
- Group() - Constructor for class org.jmol.modelset.Group
- GROUP - Enum constant in enum org.jmol.c.PAL
- group_arrow_prefix - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- group_auto_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- GROUP_COUNT - Static variable in class org.jmol.symmetry.SpaceGroupFinder
- group_full_member_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- GROUP_PDB - Static variable in class org.jmol.adapter.readers.cif.CifReader
- group1 - Variable in class org.jmol.modelset.Group
- group1 - Static variable in class org.jmol.script.T
- group3 - Variable in class org.jmol.adapter.smarter.Atom
- group3Count - Static variable in class org.jmol.modelsetbio.BioResolver
- group3Counts - Variable in class org.jmol.modelset.ModelLoader
- group3Counts - Variable in class org.jmol.popup.JmolPopup
- group3List - Variable in class org.jmol.popup.JmolPopup
- group3Lists - Variable in class org.jmol.modelset.ModelLoader
- group3NameCount - Static variable in class org.jmol.modelsetbio.BioResolver
- group3Names - Static variable in class org.jmol.modelset.Group
- group3Of - Variable in class org.jmol.modelset.ModelLoader
- group3s - Variable in class org.jmol.adapter.readers.more.MdTopReader
- groupByModel - Variable in class org.jmol.smiles.SmilesSearch
- groupCount - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- groupCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- groupCount - Variable in class org.jmol.modelset.Chain
- groupCount - Variable in class org.jmol.modelset.Model
- groupCount - Variable in class org.jmol.modelset.ModelLoader
- groupDSSP - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- groupid - Static variable in class org.jmol.script.T
- groupID - Variable in class org.jmol.modelset.Group
- groupID - Variable in class org.jmol.multitouch.ActionManagerMT
- GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JC
- GROUPID_ARGININE - Static variable in class org.jmol.viewer.JC
- GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JC
- GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JC
- GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JC
- GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JC
- GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JC
- GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JC
- GROUPID_ION_MAX - Static variable in class org.jmol.viewer.JC
- GROUPID_ION_MIN - Static variable in class org.jmol.viewer.JC
- GROUPID_LYSINE - Static variable in class org.jmol.viewer.JC
- GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JC
- GROUPID_PROLINE - Static variable in class org.jmol.viewer.JC
- GROUPID_SOLVENT_MIN - Static variable in class org.jmol.viewer.JC
- GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JC
- GROUPID_WATER - Static variable in class org.jmol.viewer.JC
- groupindex - Static variable in class org.jmol.script.T
- groupIndex - Variable in class org.jmol.modelset.Group
- groupMap - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- groupModels - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- groupNames - Static variable in class org.jmol.symmetry.SpaceGroupFinder
- groups - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- groups - Variable in class org.jmol.modelset.Chain
-
Groups form the essence of what a Chain is.
- groups - Variable in class org.jmol.modelset.ModelLoader
- growAtomArrays(int) - Method in class org.jmol.modelset.ModelSet
- GS - Static variable in class org.jmol.quantum.QS
- GS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- GT - Class in org.jmol.i18n
-
The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12 implementing translations in JavaScript
- GT() - Constructor for class org.jmol.i18n.GT
- GT(Viewer, String) - Constructor for class org.jmol.i18n.GT
- gti(String, int) - Method in class org.jmol.popup.JmolPopup
- gto(String, Object) - Method in class org.jmol.popup.JmolPopup
- GTO_EXP - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- gui - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- guimap - Variable in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- guimap - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- guimap - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- GuiMap - Class in org.openscience.jmol.app.jmolpanel
- GuiMap() - Constructor for class org.openscience.jmol.app.jmolpanel.GuiMap
- gulpContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- GulpReader - Class in org.jmol.adapter.readers.xtal
-
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.
- GulpReader() - Constructor for class org.jmol.adapter.readers.xtal.GulpReader
- gxTemp - Variable in class org.jmol.quantum.NciCalculation
- gxxTemp - Variable in class org.jmol.quantum.NciCalculation
- gxyTemp - Variable in class org.jmol.quantum.NciCalculation
- gxzTemp - Variable in class org.jmol.quantum.NciCalculation
- gyTemp - Variable in class org.jmol.quantum.NciCalculation
- gyyTemp - Variable in class org.jmol.quantum.NciCalculation
- gyzTemp - Variable in class org.jmol.quantum.NciCalculation
- gzTemp - Variable in class org.jmol.quantum.NciCalculation
- gzzTemp - Variable in class org.jmol.quantum.NciCalculation
H
- h_bar_planck - Static variable in class org.jmol.quantum.NMRCalculation
- h_bond_cone - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- h_bond_cutoff_center - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- h_bond_cutoff_edge - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- h_bond_exclusion - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- h_bond_from_proton - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- h_bond_max_angle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- h_bond_power_a - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- h_bond_power_b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- h_planck - Static variable in class org.jmol.quantum.NMRCalculation
- H_REGULAR - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- h1Count - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
a count of how many 1H atoms we have found on this atom; used to halt further processing of this atom
- H3T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- H5T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- half_bonds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- halfRoot5 - Static variable in class org.jmol.util.Geodesic
- hAlignNames - Static variable in class org.jmol.viewer.JC
- hallInfo - Variable in class org.jmol.symmetry.SpaceGroup
- HallInfo - Class in org.jmol.symmetry
- HallInfo(String) - Constructor for class org.jmol.symmetry.HallInfo
- HallRotation - Class in org.jmol.symmetry
- HallRotation(String, String) - Constructor for class org.jmol.symmetry.HallRotation
- HallRotationTerm - Class in org.jmol.symmetry
- HallRotationTerm(HallInfo, String, int, char) - Constructor for class org.jmol.symmetry.HallRotationTerm
- hallRotationTerms - Static variable in class org.jmol.symmetry.HallRotation
- hallSymbol - Variable in class org.jmol.symmetry.HallInfo
- hallSymbol - Variable in class org.jmol.symmetry.SpaceGroup
- HallTranslation - Class in org.jmol.symmetry
- HallTranslation(char, P3i) - Constructor for class org.jmol.symmetry.HallTranslation
- hallTranslationTerms - Static variable in class org.jmol.symmetry.HallTranslation
- halo - Static variable in class org.jmol.script.T
- Halos - Class in org.jmol.shape
- Halos() - Constructor for class org.jmol.shape.Halos
- HalosRenderer - Class in org.jmol.render
- HalosRenderer() - Constructor for class org.jmol.render.HalosRenderer
- halt - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- haltButton - Variable in class org.jmol.console.ScriptEditor
- haltButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- haltExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
- haltExecution() - Method in class org.jmol.script.ScriptEval
- haltScriptExecution() - Method in class org.jmol.api.JmolViewer
- haltScriptExecution() - Method in class org.jmol.viewer.Viewer
- handleAssignNew(MouseState, MouseState, MeasurementPending, int) - Method in class org.jmol.modelkit.ModelKit
-
handle a mouse-generated assignNew event
- handleDragAtom(MouseState, MouseState, int[]) - Method in class org.jmol.modelkit.ModelKit
- handleError() - Method in class org.jmol.script.ScriptCompiler
- handleError(Error, boolean) - Method in class org.jmol.viewer.Viewer
- handleEvent(Event) - Method in interface org.jmol.api.JmolAppletInterface
- handleEvent(Event) - Method in class org.jmol.util.GenericApplet
- handleEvent(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- handleOutputToFile(Map<String, Object>, boolean) - Method in class org.jmol.viewer.OutputManager
-
general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
- handleTlsMissingModels() - Method in class org.jmol.adapter.readers.pdb.PdbReader
-
for now, we just ignore TLS details if user has selected a specific model
- HAS_CLIENT - Static variable in interface org.jmol.api.JmolGestureServerInterface
- HAS_DRIVER - Static variable in interface org.jmol.api.JmolGestureServerInterface
- HAS_MAXGRID - Static variable in class org.jmol.jvxl.readers.Parameters
- hasAtoms - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- hasBfactorRange - Variable in class org.jmol.modelset.AtomCollection
- hasBfactorRange - Variable in class org.jmol.shapebio.BioShape
- hasChirality - Variable in class org.jmol.modelset.Model
- hasColorData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- hasColorRange - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- hasCONECT - Variable in class org.jmol.modelsetbio.BioResolver
- hasConstraint(int, boolean, boolean) - Method in class org.jmol.modelkit.ModelKit
- hasContent() - Method in class org.jmol.g3d.Graphics3D
- hasContent() - Method in class org.jmol.g3d.Platform3D
- hasDatabasePrefix(String) - Static method in class org.jmol.viewer.Viewer
- hasFocus() - Method in class org.jmol.viewer.Viewer
- hasFocus(Object) - Method in interface org.jmol.api.GenericPlatform
- hasFocus(Object) - Static method in class org.jmol.awt.Display
- hasFocus(Object) - Method in class org.jmol.awt.Platform
- hasFocus(Object) - Static method in class org.jmol.awtjs2d.Display
- hasFocus(Object) - Method in class org.jmol.awtjs2d.Platform
- hasGridPoints - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- hash - Static variable in class org.jmol.script.T
- hash_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- hashCode() - Method in class org.jmol.modelset.Atom
- hashCode() - Method in class org.jmol.script.T
- hasLocalArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- hasMeasure(int[]) - Method in class org.jmol.modelset.Trajectory
- hasMoreElements() - Method in class org.jmol.bspt.CubeIterator
-
normal iterator predicate
- hasNext() - Method in class org.jmol.adapter.smarter.AtomIterator
- hasNext() - Method in class org.jmol.adapter.smarter.BondIterator
- hasNext() - Method in class org.jmol.adapter.smarter.StructureIterator
- hasNext() - Method in interface org.jmol.api.AtomIndexIterator
- hasNext() - Method in interface org.jmol.api.JmolAdapterAtomIterator
- hasNext() - Method in class org.jmol.api.JmolAdapterBondIterator
- hasNext() - Method in class org.jmol.api.JmolAdapterStructureIterator
- hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
- hasNext() - Method in interface org.jmol.modelset.BondIterator
- hasNext() - Method in class org.jmol.modelset.BondIteratorSelected
- hasNext() - Method in class org.jmol.symmetry.UnitCellIterator
- hasNext2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- hasOAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
- hasOffset() - Method in class org.jmol.symmetry.UnitCell
- hasOuputSocket() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- hasOuputSocket() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- hasPlane() - Method in class org.jmol.jvxl.data.VolumeData
- hasRasmolHBonds - Variable in class org.jmol.modelset.Model
- hasRnaO2Prime - Variable in class org.jmol.modelsetbio.NucleicMonomer
- hasSelected - Variable in class org.jmol.viewer.Viewer
- hasSerialArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- HASSETTING - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- hasStructure - Variable in class org.jmol.modelsetbio.BioPolymer
- hasSubpattern - Variable in class org.jmol.smiles.SmilesAtom
- hasSymbol - Variable in class org.jmol.smiles.SmilesAtom
- hasSymmetry - Variable in class org.jmol.popup.JmolPopup
- hasUnitCell - Variable in class org.jmol.modelkit.ModelKit
- hasValues() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- hasVibration() - Method in class org.jmol.modelset.Atom
- hasWingPoints - Variable in class org.jmol.modelsetbio.BioPolymer
- hAtomRadius - Variable in class org.jmol.atomdata.AtomData
- hAtoms - Variable in class org.jmol.atomdata.AtomData
- have(byte[], byte) - Static method in class org.jmol.modelsetbio.Monomer
- haveAccess(Viewer.ACCESS) - Method in class org.jmol.viewer.Viewer
- haveAnisou - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- haveAromatic - Variable in class org.jmol.adapter.readers.cif.CifReader
- haveAt - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
- haveAtomFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- haveAtomLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- haveAtomMods - Variable in class org.jmol.adapter.readers.cif.MSRdr
- haveAtoms - Variable in class org.jmol.shapespecial.Dipole
- haveAtomSerials - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- haveAtropicBonds - Variable in class org.jmol.modelset.BondCollection
- haveAxis(int, V3) - Method in class org.jmol.symmetry.PointGroup
- haveBeta - Variable in class org.jmol.adapter.readers.quantum.NBOParser
- haveBFactors - Variable in class org.jmol.popup.JmolPopup
- haveBinaryArrays - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- haveBioModels - Variable in class org.jmol.modelset.ModelSet
- haveBitSetVertices - Variable in class org.jmol.shapespecial.Polyhedra
- haveBondStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
- haveBorder - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- haveBorder - Variable in class org.openscience.jmol.app.JmolApp
- haveBSClickable - Variable in class org.jmol.modelset.AtomCollection
- haveBsDisplay - Variable in class org.jmol.render.MeshRenderer
- haveBsDisplay - Variable in class org.jmol.shapesurface.PMeshWriter
- haveBSVisible - Variable in class org.jmol.modelset.AtomCollection
- haveCellWaveVector - Variable in class org.jmol.adapter.readers.cif.CifReader
- haveCharges - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- haveCharges - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- haveCharges - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- haveCharges - Variable in class org.jmol.popup.JmolPopup
- haveChirality - Variable in class org.jmol.modelset.AtomCollection
- haveCircle - Variable in class org.jmol.export._IdtfExporter
- haveCoeffMap - Variable in class org.jmol.adapter.readers.quantum.MOReader
- haveComments - Variable in class org.jmol.script.ScriptCompiler
- haveCommon(BS, BS) - Static method in class org.jmol.util.BSUtil
- haveComponents - Variable in class org.jmol.smiles.SmilesSearch
- haveCone - Variable in class org.jmol.export._IdtfExporter
- haveConsole - Variable in class org.openscience.jmol.app.JmolApp
- haveConstraints - Variable in class org.jmol.minimize.forcefield.Calculations
- haveContourData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- haveControlPointScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
- haveCylinder - Variable in class org.jmol.export._IdtfExporter
- haveCylinderIn - Variable in class org.jmol.export._IdtfExporter
- haveDisplay - Variable in class org.jmol.viewer.Viewer
- haveDisplay - Variable in class org.openscience.jmol.app.JmolApp
- haveDisplay - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- haveDocumentAccess - Variable in class org.jmol.util.GenericApplet
- haveDoubleBonds - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- haveENDIF - Variable in class org.jmol.script.ScriptCompiler
- haveEnergy - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- haveEnergy - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
- haveFileSet() - Method in class org.jmol.viewer.Viewer
- haveGlobalDummy - Variable in class org.jmol.adapter.readers.cif.CifReader
- haveHAtoms - Variable in class org.jmol.adapter.readers.cif.CifReader
- haveHeader - Variable in class org.jmol.adapter.readers.simple.MopacReader
- haveHiddenBonds - Variable in class org.jmol.modelset.BondCollection
- haveHighPrecision - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
- haveHoverCallback() - Method in class org.jmol.viewer.StatusManager
- haveHsAlready - Variable in class org.jmol.modelsetbio.BioResolver
- haveInversionCenter - Variable in class org.jmol.symmetry.PointGroup
- haveJDX - Variable in class org.jmol.viewer.Viewer
- haveLattice - Variable in class org.jmol.adapter.readers.xtal.PWmatReader
- haveLine - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
- haveM40Data - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- haveMacro - Variable in class org.jmol.script.ScriptTokenParser
- haveMacros - Variable in class org.jmol.export._PovrayExporter
- haveMagnetic - Variable in class org.jmol.adapter.readers.xtal.PWmatReader
- haveMappedSerials - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- haveMeasurements - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- haveMOData(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- haveModel - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- haveModelKit() - Method in class org.jmol.modelset.ModelSet
- haveModified - Variable in class org.jmol.modelset.MeasurementPending
- haveMolecule - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- haveMultiTouchInput - Variable in class org.jmol.viewer.ActionManager
- haveNboCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
- haveNboOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
- haveNotified - Variable in class org.jmol.thread.SpinThread
- haveNotifiedError - Variable in class org.jmol.util.GenericApplet
- haveNotifiedNaN - Variable in class org.jmol.viewer.TransformManager
- haveNucleicLadder - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- haveOccupancy - Variable in class org.jmol.adapter.readers.cif.MSRdr
- haveOneProperty - Variable in class org.jmol.jvxl.readers.AtomDataReader
- haveOperators - Variable in class org.jmol.modelkit.ModelKitPopup
- haveParameters - Variable in class org.jmol.modelsetbio.BioPolymer
- havePartialChargeFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- havePhonons - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- havePlanarContours - Variable in class org.jmol.shape.Mesh
- havePlane - Variable in class org.jmol.jvxl.readers.AtomDataReader
- havePoints - Variable in class org.jmol.quantum.MOCalculation
- havePoints - Variable in class org.jmol.quantum.NciCalculation
- havePositions - Variable in class org.jmol.adapter.readers.xtal.PWmatReader
- havePRE - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- havePrimitiveMapping - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- havePseudoAuxiliary - Variable in class org.jmol.symmetry.CIPChirality
-
do we have r or s and so will need to recalculate Mata like/unlike lists in Rule 5?
- haveQuads - Variable in class org.jmol.util.MeshSurface
- haveReadColorData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- haveReference - Variable in class org.jmol.thread.JmolThread
- haveScenes - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- haveScenes - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- haveSelected - Variable in class org.jmol.smiles.SmilesSearch
- haveSelection - Variable in class org.jmol.viewer.ActionManager
- haveSequenceNumber(int) - Static method in class org.jmol.modelset.Group
- haveSetAnisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
- haveSetStructureList - Variable in class org.jmol.viewer.GlobalSettings
- haveSmilesAtoms - Variable in class org.jmol.smiles.SmilesGenerator
- haveSpaceBeforeSquare - Variable in class org.jmol.script.ScriptMathProcessor
- haveSphere - Variable in class org.jmol.export._IdtfExporter
- haveStraightness - Variable in class org.jmol.modelset.AtomCollection
- haveString - Variable in class org.jmol.script.ScriptTokenParser
- haveStructure - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- haveSurfaceAtoms - Variable in class org.jmol.jvxl.readers.SurfaceReader
- haveTarget - Variable in class org.jmol.modelset.MeasurementPending
- haveTopo - Variable in class org.jmol.smiles.SmilesSearch
- haveTranslations - Static variable in class org.jmol.dialog.Dialog
- haveTranslucent - Variable in class org.jmol.render.EchoRenderer
- haveTranslucentObjects - Variable in class org.jmol.g3d.Graphics3D
- haveTranslucentObjects() - Method in interface org.jmol.api.JmolRendererInterface
- haveTranslucentObjects() - Method in class org.jmol.export.Export3D
- haveTranslucentObjects() - Method in class org.jmol.g3d.Graphics3D
- haveUnitCell - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- haveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- haveUnitCell - Variable in class org.jmol.adapter.writers.XtlWriter
- haveUnitCell() - Method in interface org.jmol.api.SymmetryInterface
- haveUnitCell() - Method in class org.jmol.symmetry.Symmetry
- haveUnitCells - Variable in class org.jmol.modelset.ModelSet
- haveVibration - Variable in class org.jmol.symmetry.PointGroup
- haveXMLUtil - Static variable in class org.jmol.jvxl.data.JvxlCoder
- haveXyPoints - Variable in class org.jmol.shape.Mesh
- HB - Enum in org.jmol.c
-
Enum for hydrogen bonding donor/acceptor type
- HB() - Constructor for enum org.jmol.c.HB
- HBACCEPT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- HBAMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- hBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- HBDMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- HBDONOR - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- hbond - Static variable in class org.jmol.script.T
- HBond - Class in org.jmol.modelset
- HBond(Atom, Atom, int, short, short, float) - Constructor for class org.jmol.modelset.HBond
- hbondhxdistancemaximum - Static variable in class org.jmol.script.T
- hbondHXDistanceMaximum - Variable in class org.jmol.viewer.GlobalSettings
- hbondMinRasmol - Static variable in class org.jmol.modelset.ModelSet
- hbondnodistancemaximum - Static variable in class org.jmol.script.T
- hbondNODistanceMaximum - Variable in class org.jmol.viewer.GlobalSettings
- hbondsangleminimum - Static variable in class org.jmol.script.T
- hbondsAngleMinimum - Variable in class org.jmol.viewer.GlobalSettings
- hbondsbackbone - Static variable in class org.jmol.script.T
- hbondsBackbone - Variable in class org.jmol.render.SticksRenderer
- hbondsBackbone - Variable in class org.jmol.viewer.GlobalSettings
- hbondsrasmol - Static variable in class org.jmol.script.T
- hbondsRasmol - Variable in class org.jmol.viewer.GlobalSettings
- hbondssolid - Static variable in class org.jmol.script.T
- hbondsSolid - Variable in class org.jmol.render.SticksRenderer
- hbondsSolid - Variable in class org.jmol.viewer.GlobalSettings
- HC - Static variable in class org.jmol.quantum.QS
- HC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- hCount - Variable in class org.jmol.minimize.MinAtom
- hDashes - Static variable in class org.jmol.render.FontLineShapeRenderer
- header - Variable in class org.jmol.adapter.readers.xtal.MagresReader
- header - Variable in class org.jmol.export._StlExporter
- header - Variable in class org.jmol.jvxl.readers.BCifDensityReader
- header - Variable in class org.openscience.jmol.app.HistoryFile
-
The information written to the header of the history file.
- header() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- HEADER_GAMESS_OCCUPANCIES - Variable in class org.jmol.adapter.readers.quantum.MOReader
- HEADER_GAMESS_ORIGINAL - Variable in class org.jmol.adapter.readers.quantum.MOReader
- HEADER_GAMESS_UK_MO - Variable in class org.jmol.adapter.readers.quantum.MOReader
- HEADER_NONE - Variable in class org.jmol.adapter.readers.quantum.MOReader
- headerContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- headerHeight - Static variable in class org.jmol.awtjs.swing.JDialog
- headless - Variable in class org.jmol.viewer.Viewer
-
determined by GraphicsEnvironment.isHeadless() from java -Djava.awt.headless=true disables command threading disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN
, ANIMATION ON turns SPIN into just ROTATE - headlessImageParams - Variable in class org.jmol.viewer.Viewer
- headOffsetVector - Variable in class org.jmol.renderspecial.VectorsRenderer
- headScale - Variable in class org.jmol.renderspecial.VectorsRenderer
- headWidthPixels - Variable in class org.jmol.renderspecial.DipolesRenderer
- headWidthPixels - Variable in class org.jmol.renderspecial.VectorsRenderer
- heavy_neighbor_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- heavyAtomIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- height - Variable in class org.jmol.awtjs.swing.Component
- height - Variable in class org.jmol.awtjs.swing.Dimension
- height - Variable in class org.jmol.export.Export3D
- height - Variable in class org.jmol.g3d.SphereRenderer
- height - Variable in class org.jmol.g3d.TextRenderer
- height - Variable in class org.jmol.util.GData
- height - Variable in class org.jmol.util.Rectangle
- height - Variable in class org.jmol.viewer.TransformManager
- height - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- heightOffscreen - Variable in class org.jmol.g3d.Platform3D
- heightUnitVector - Variable in class org.jmol.modelsetbio.Sheet
- helix - Static variable in class org.jmol.script.T
- Helix - Class in org.jmol.modelsetbio
- Helix(AlphaPolymer, int, int, STR) - Constructor for class org.jmol.modelsetbio.Helix
- HELIX - Enum constant in enum org.jmol.c.STR
- HELIX_CLASS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- helix310 - Static variable in class org.jmol.script.T
- HELIX310 - Enum constant in enum org.jmol.c.STR
- helixalpha - Static variable in class org.jmol.script.T
- HELIXALPHA - Enum constant in enum org.jmol.c.STR
- helixpi - Static variable in class org.jmol.script.T
- HELIXPI - Enum constant in enum org.jmol.c.STR
- helixRockets - Variable in class org.jmol.renderbio.RocketsRenderer
- helixScript - Static variable in class org.jmol.modelsetbio.BioExt
- helixstep - Static variable in class org.jmol.script.T
- helixStep - Variable in class org.jmol.viewer.GlobalSettings
- help - Static variable in class org.jmol.script.T
- helpButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- helpButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
- HelpDialog - Class in org.openscience.jmol.app.jmolpanel
- HelpDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
- HelpDialog(JFrame, String, boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
- HelpDialog(JFrame, URL) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
-
If url is null, then the default help url is taken.
- HelpDialog.PageLoader - Class in org.openscience.jmol.app.jmolpanel
-
temporary class that loads synchronously (although later than the request so that a cursor change can be done).
- helper - Variable in class org.jmol.popup.GenericPopup
- helppath - Static variable in class org.jmol.script.T
- helpPath - Variable in class org.jmol.viewer.GlobalSettings
- hemisphereOnly - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- hermite3d - Variable in class org.jmol.export.Export3D
- hermite3d - Variable in class org.jmol.g3d.Graphics3D
- hermitelevel - Static variable in class org.jmol.script.T
- hermiteLevel - Variable in class org.jmol.renderbio.BioShapeRenderer
- hermiteLevel - Variable in class org.jmol.viewer.GlobalSettings
- HermiteRenderer - Class in org.jmol.g3d
-
Implementation of hermite curves for drawing smoothed curves that pass through specified points.
- HermiteRenderer() - Constructor for class org.jmol.g3d.HermiteRenderer
- hess - Variable in class org.jmol.quantum.NciCalculation
- het() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- HETATM - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- hetero - Static variable in class org.jmol.script.T
- HETMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- hetnam() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- hi - Variable in class org.jmol.util.ColorEncoder
- hidden - Variable in class org.jmol.modelkit.ModelKitPopup
- hidden - Variable in class org.jmol.modelset.Text
- hidden - Static variable in class org.jmol.script.T
- hiddenlinesdashed - Static variable in class org.jmol.script.T
- hiddenLinesDashed - Variable in class org.jmol.viewer.GlobalSettings
- hide - Static variable in class org.jmol.script.T
- hide(ModelSet, BS, int, boolean) - Method in class org.jmol.viewer.SelectionManager
- hide_long_bonds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- hide_underscore_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- hidenameinpopup - Static variable in class org.jmol.script.T
- hideNameInPopup - Variable in class org.jmol.viewer.GlobalSettings
- hidenavigationpoint - Static variable in class org.jmol.script.T
- hideNavigationPoint - Variable in class org.jmol.viewer.GlobalSettings
- hidenotselected - Static variable in class org.jmol.script.T
- hideNotSelected - Variable in class org.jmol.viewer.SelectionManager
- hidePopup() - Method in class org.jmol.modelkit.ModelKitPopup
- HIGH - Static variable in class org.jmol.util.ColorEncoder
- highLEnabled - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- highLEnabled - Variable in class org.jmol.quantum.MOCalculation
- highlight - Static variable in class org.jmol.script.T
- highlight(BS) - Method in class org.jmol.viewer.Viewer
- highlightBond(int, int, int, int) - Method in class org.jmol.viewer.Viewer
-
from Sticks
- highresolution - Static variable in class org.jmol.script.T
- highResolutionFlag - Variable in class org.jmol.viewer.GlobalSettings
- history - Static variable in class org.jmol.script.T
- historyButton - Variable in class org.jmol.console.GenericConsole
- historyDisabled - Variable in class org.jmol.script.ScriptEval
- historyFile - Variable in class org.openscience.jmol.app.JmolApp
- historyFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- historyFile - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- historyFile - Static variable in class org.openscience.jmol.app.webexport.WebExport
- HistoryFile - Class in org.openscience.jmol.app
-
The history file contains data from previous uses of Jmol.
- HistoryFile(File, String) - Constructor for class org.openscience.jmol.app.HistoryFile
-
Creates a history file.
- historyFind(String, int) - Method in class org.jmol.viewer.Viewer
- historylevel - Static variable in class org.jmol.script.T
- histWinName - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- hkl - Static variable in class org.jmol.script.T
- hklParameter(int, Lst<P3>, boolean) - Method in class org.jmol.script.ScriptParam
- hmSymbol - Variable in class org.jmol.symmetry.SpaceGroup
- hmSymbolAbbr - Variable in class org.jmol.symmetry.SpaceGroup
- hmSymbolAbbrShort - Variable in class org.jmol.symmetry.SpaceGroup
- hmSymbolAlternative - Variable in class org.jmol.symmetry.SpaceGroup
- hmSymbolExt - Variable in class org.jmol.symmetry.SpaceGroup
- hmSymbolFull - Variable in class org.jmol.symmetry.SpaceGroup
- hNames - Variable in class org.jmol.modelsetbio.BioResolver
- hnmrPeaks - Variable in class org.jmol.popup.JmolPopup
- holdRepaint - Variable in class org.jmol.render.RepaintManager
- homeAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- HomeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction
- homePosition() - Method in class org.jmol.api.JmolViewer
- homePosition() - Method in class org.jmol.viewer.Viewer
- homePosition(boolean) - Method in class org.jmol.viewer.TransformManager
- homo - Static variable in class org.jmol.script.T
- HORIZONTAL_SPLIT - Static variable in class org.jmol.awtjs.swing.JSplitPane
- HOTPINK - Static variable in class org.jmol.util.C
- hover - Static variable in class org.jmol.script.T
- Hover - Class in org.jmol.shape
- Hover() - Constructor for class org.jmol.shape.Hover
- HOVER - Enum constant in enum org.jmol.c.CBK
- hoverable - Static variable in class org.jmol.viewer.ShapeManager
- hoverActive - Variable in class org.jmol.viewer.ActionManager
- hoverAtomIndex - Variable in class org.jmol.viewer.Viewer
- hoverdelay - Static variable in class org.jmol.script.T
- hoverDelay - Variable in class org.jmol.thread.HoverWatcherThread
- hoverDelayMs - Variable in class org.jmol.viewer.GlobalSettings
- hoverEnabled - Variable in class org.jmol.thread.JmolThread
- hoverEnabled - Variable in class org.jmol.viewer.Viewer
- hoverKey(int, int) - Method in class org.jmol.shapesurface.Isosurface
- hoverlabel - Static variable in class org.jmol.script.T
- hoverLabel - Variable in class org.jmol.viewer.Viewer
- hoverOff() - Method in class org.jmol.viewer.Viewer
- hoverOn(int, boolean) - Method in class org.jmol.viewer.Viewer
- hoverOnPt(int, int, String, String, T3) - Method in class org.jmol.viewer.Viewer
-
Hover over an arbitrary point.
- HoverRenderer - Class in org.jmol.render
- HoverRenderer() - Constructor for class org.jmol.render.HoverRenderer
- hoverText - Variable in class org.jmol.shape.Hover
- hoverText - Variable in class org.jmol.viewer.Viewer
- hoverWatcherThread - Variable in class org.jmol.viewer.ActionManager
- HoverWatcherThread - Class in org.jmol.thread
- HoverWatcherThread(ActionManager, MouseState, MouseState, Viewer) - Constructor for class org.jmol.thread.HoverWatcherThread
- HS - Static variable in class org.jmol.quantum.QS
- HS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- ht3 - Variable in class org.jmol.util.GData
- htAtomicPotentials - Variable in class org.jmol.quantum.MepCalculation
- htAtomMap - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htAtomMap - Variable in class org.jmol.modelset.ModelLoader
- htAtomMods - Variable in class org.jmol.adapter.readers.cif.MSRdr
- htAudit - Variable in class org.jmol.adapter.readers.cif.CifReader
- htBasisMap - Variable in class org.jmol.adapter.writers.QCJSONWriter
- htBiomts - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- htBondMap - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- htBondMap - Variable in class org.jmol.modelsetbio.BioResolver
- htBonds - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- htBooleanParameterFlags - Variable in class org.jmol.viewer.GlobalSettings
- htBridges - Variable in class org.jmol.dssx.DSSP
- htByOpCount - Static variable in class org.jmol.symmetry.SpaceGroup
- htCarveSets - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htCellTypes - Variable in class org.jmol.adapter.readers.cif.CifReader
- htCheckbox - Variable in class org.jmol.popup.GenericPopup
- htCriticalPoints - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- htDefinedAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htDefs - Variable in class org.jmol.export._IdtfExporter
- htEdges - Variable in class org.jmol.adapter.readers.xtal.CgdReader
- htEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- htElementMap - Static variable in class org.jmol.util.Elements
- htElementsInCurrentGroup - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- htExponents - Variable in class org.jmol.adapter.readers.quantum.DgridReader
- htFileCache - Variable in class org.jmol.script.ScriptContext
- htFont3d - Static variable in class org.jmol.g3d.TextRenderer
- htFont3dAntialias - Static variable in class org.jmol.g3d.TextRenderer
- htFormul - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- htFuncMap - Variable in class org.jmol.adapter.readers.quantum.DgridReader
- htGroup - Static variable in class org.jmol.modelsetbio.BioResolver
- htGroup1 - Variable in class org.jmol.adapter.readers.cif.CifReader
- htGroup1 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- htGroup1 - Variable in class org.jmol.modelset.ModelLoader
- htGroup1 - Static variable in class org.jmol.modelsetbio.NucleicPolymer
- htGroupBonds - Variable in class org.jmol.modelsetbio.BioResolver
- htGuiChanges - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- htHetero - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- htHetero - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- htHiddenObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htLadders - Variable in class org.jmol.dssx.DSSP
- htLanguages - Static variable in class org.jmol.i18n.GT
- htMeasures - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htMeasures - Variable in class org.jmol.smiles.SmilesParser
- htMenus - Variable in class org.jmol.popup.GenericPopup
- htMessageCallbacks - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- htMin - Variable in class org.jmol.modelset.MeasurementData
- htMin - Variable in class org.jmol.shape.Measures
- html - Variable in class org.jmol.awtjs.swing.JDialog
- html - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog
- html5Applet - Variable in class org.jmol.export.JSExporter
- html5Applet - Variable in class org.jmol.viewer.Viewer
- htmlAppletTemplate - Variable in class org.openscience.jmol.app.webexport.WebPanel
- HTMLElement - Interface in org.jmol.awtjs.swing
- htmlLabel() - Method in class org.jmol.awtjs.swing.JMenuItem
- htmlMenuOpener(String) - Method in class org.jmol.awtjs.swing.AbstractButton
- htmlName - Variable in class org.jmol.awtjs.swing.AbstractButton
- htmlName - Variable in class org.jmol.util.GenericApplet
- htmlName - Variable in class org.jmol.viewer.Viewer
- htmlPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
- HTMLWindowEvent - Interface in org.jmol.awtjs.swing
-
The window.Event in HTML5 See SwingController.
- htModelAtomMap - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- htModels - Variable in class org.jmol.shapesurface.MolecularOrbital
- htModulation - Variable in class org.jmol.adapter.readers.cif.MSRdr
- htMolIds - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- htMOs - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
- htNested - Variable in class org.jmol.smiles.SmilesSearch
- htNodes - Variable in class org.jmol.export._IdtfExporter
- htNonbooleanParameterValues - Variable in class org.jmol.viewer.GlobalSettings
- htObjectAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htObjectGroups - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htObjects - Variable in class org.jmol.export.JSExporter
- htObjects - Variable in class org.jmol.shape.MeshCollection
- htObjectSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htOxStates - Variable in class org.jmol.adapter.readers.cif.CifReader
- htParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- htParams - Variable in class org.jmol.io.DOMReader
- htParams - Variable in class org.jmol.io.FileReader
- htParams - Variable in class org.jmol.io.FilesReader
- htParams - Variable in class org.jmol.util.GenericApplet
- htPathPoints - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Rule 1b hash table that maintains distance of the associated nonduplicated atom node
- htPdbBondInfo - Static variable in class org.jmol.modelsetbio.BioResolver
- htPeaks - Variable in class org.jmol.modelset.ModelSet
- htPropertyFlagsRemoved - Variable in class org.jmol.viewer.GlobalSettings
- htPts - Variable in class org.jmol.jvxl.calc.MarchingSquares
- htRegistry - Static variable in class org.jmol.util.GenericApplet
- htRings - Variable in class org.jmol.smiles.SmilesGenerator
- htRingsSequence - Variable in class org.jmol.smiles.SmilesGenerator
- htSites - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- htSites - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- htSlaterIDs - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- htSources - Variable in class org.jmol.awt.AwtPopupHelper
- htSpacefill - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htSpecialAtoms - Static variable in class org.jmol.modelsetbio.BioResolver
- htSpecies - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- htSpheresRendered - Variable in class org.jmol.export._VrmlExporter
- htSpheresRendered - Variable in class org.jmol.export.JSExporter
- htStateSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- htSubsystems - Variable in class org.jmol.adapter.readers.cif.MSRdr
- htSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- htTiming - Static variable in class org.jmol.util.Logger
- htTracker - Variable in class org.jmol.symmetry.CIPDataTracker
-
a table to track decision making when only one atom is selected for calculation
- htUij - Variable in class org.jmol.util.ModulationSet
-
current value of anisotropic parameter modulation
- htUserFunctions - Variable in class org.jmol.script.ScriptTokenParser
- htUserVariables - Variable in class org.jmol.viewer.GlobalSettings
- htVertex - Static variable in class org.jmol.util.Geodesic
- htVertices - Variable in class org.jmol.jvxl.readers.Ras3DReader
- hType - Variable in class org.jmol.minimize.forcefield.AtomType
- HUGE - Static variable in class org.jmol.util.GData
- HYDRO - Enum constant in enum org.jmol.c.VDW
- hydrogen - Static variable in class org.jmol.script.T
- hydrogenAtomCount - Variable in class org.jmol.atomdata.AtomData
- hydrogenAtomPsi(P3) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- hydrogenCount - Variable in class org.jmol.modelset.Model
- hydrogensAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- hydrophobicities - Variable in class org.jmol.modelset.AtomCollection
- hydrophobicities - Static variable in class org.jmol.util.Elements
- hydrophobicity - Static variable in class org.jmol.script.T
- hyperChemLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- HyperChemReader - Class in org.jmol.adapter.readers.simple
-
Support for .hin, HyperChem's native file format.
- HyperChemReader() - Constructor for class org.jmol.adapter.readers.simple.HyperChemReader
- hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
- hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
I
- i - Variable in class org.jmol.quantum.NMRNoeMatrix
- i - Variable in class org.jmol.util.Point3fi
-
index in full collection
- i(int) - Static method in class org.jmol.script.T
- i(String, int) - Static method in class org.jmol.i18n.GT
- i0 - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
base atom index to be added to any atom bitsets
- i0 - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
- i0 - Variable in class org.jmol.shapesurface.PMeshWriter
- ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
- ia - Variable in class org.jmol.minimize.forcefield.Calculation
- ia - Variable in class org.jmol.minimize.forcefield.Calculations
- iA - Variable in class org.jmol.util.MeshSurface
- iAddGridPoints - Variable in class org.jmol.jvxl.readers.Parameters
- iatom - Variable in class org.jmol.adapter.smarter.AtomIterator
- iAtom - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- iAtom - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
- iatom0 - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- iatom0 - Variable in class org.jmol.modelkit.ModelKit
- iAtomSurface - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
- iAtomSurface - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
- ib - Variable in class org.jmol.minimize.forcefield.Calculation
- ib - Variable in class org.jmol.minimize.forcefield.Calculations
- iB - Variable in class org.jmol.util.MeshSurface
- ibond - Variable in class org.jmol.adapter.smarter.BondIterator
- iBond - Variable in class org.jmol.modelset.BondIteratorSelected
- iBrace - Variable in class org.jmol.script.ScriptCompiler
- ic - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
- ic - Variable in class org.jmol.minimize.forcefield.Calculation
- ic - Variable in class org.jmol.minimize.forcefield.Calculations
- iC - Variable in class org.jmol.util.MeshSurface
- IC - Static variable in class org.jmol.quantum.QS
- IC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- iChain - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
- iChain - Variable in class org.jmol.modelset.ModelLoader
- ichBrace - Variable in class org.jmol.script.ScriptCompiler
- ichCommand - Variable in class org.jmol.script.ScriptFlowContext
- ichComment - Variable in class org.jmol.script.ScriptTokenParser
- ichCurrentCommand - Variable in class org.jmol.script.ScriptTokenParser
- ichEnd - Variable in class org.jmol.script.ScriptTokenParser
- ichToken - Variable in class org.jmol.script.ScriptTokenParser
- iCommand - Variable in class org.jmol.script.ScriptTokenParser
- iCommandError - Variable in class org.jmol.script.ScriptContext
- iCommandError - Variable in class org.jmol.script.ScriptError
- icon - Variable in class org.jmol.awtjs.swing.AbstractButton
- iCutout - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- id - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- id - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- id - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- id - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- id - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- id - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- id - Variable in class org.jmol.awtjs.swing.ButtonGroup
- id - Variable in class org.jmol.awtjs.swing.Component
- id - Variable in enum org.jmol.c.PAL
- id - Variable in enum org.jmol.c.STR
- id - Variable in class org.jmol.export._MayaExporter
- id - Variable in class org.jmol.minimize.forcefield.Calculation
- id - Variable in class org.jmol.minimize.forcefield.Calculations
- id - Variable in class org.jmol.modelset.TickInfo
- id - Variable in class org.jmol.modelsetbio.ProteinStructure
- id - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- id - Variable in class org.jmol.script.ScriptContext
- id - Static variable in class org.jmol.script.T
- id - Variable in enum org.jmol.shapespecial.Draw.EnumDrawType
- id - Variable in class org.jmol.shapespecial.Ellipsoid
- id - Variable in class org.jmol.shapespecial.Polyhedron
- id - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
unique ID for this CIPAtom for debugging only
- id - Variable in class org.jmol.util.BZone
- id - Variable in class org.jmol.util.JmolAudio
- id - Variable in class org.jmol.util.MeshCapper.CapVertex
-
for debugging
- id - Variable in class org.jmol.util.ModulationSet
-
an identifier for this modulation
- id - Variable in class org.jmol.util.Tensor
- id - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- iD - Variable in class org.jmol.util.MeshSlicer
- ID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ID - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- ID - Static variable in class org.jmol.shapespecial.Ellipsoid
- ID_ALL - Static variable in class org.jmol.modelset.Atom
- ID_CHIME - Static variable in class org.jmol.modelset.Atom
- ID_U - Static variable in class org.jmol.modelset.Atom
- ID_XTAL - Static variable in class org.jmol.modelset.Atom
- iData - Variable in class org.jmol.minimize.forcefield.Calculation
- idCount - Static variable in class org.jmol.util.JmolAudio
- ident - Variable in class org.jmol.script.ScriptCompiler
- ident - Variable in class org.jmol.script.ScriptFlowContext
- identifier - Static variable in class org.jmol.script.T
- identify - Static variable in class org.jmol.script.T
- identLC - Variable in class org.jmol.script.ScriptCompiler
- idFontFace - Variable in class org.jmol.util.Font
- idFontStyle - Variable in class org.jmol.util.Font
- idle_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ids - Static variable in class org.jmol.modelsetbio.ProteinStructure
- idSpherical - Static variable in class org.jmol.quantum.QS
- idx - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- idx - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- idx - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- idx - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- iE - Variable in class org.jmol.util.MeshSlicer
- ifcmd - Static variable in class org.jmol.script.T
- iFirstAtom - Variable in class org.jmol.modelset.MeasurementData
- ifPt - Variable in class org.jmol.script.ScriptMathProcessor
- ifStack - Variable in class org.jmol.script.ScriptMathProcessor
- ignore - Static variable in class org.jmol.script.T
- IGNORE - Static variable in class org.jmol.symmetry.CIPChirality
- ignore_case - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ignore_pdb_segi - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ignoreApplicationBundle - Static variable in class org.jmol.i18n.GT
- ignoreApplicationBundle() - Static method in class org.jmol.i18n.GT
- ignoreAtomClass - Variable in class org.jmol.smiles.SmilesSearch
- ignoreElement - Variable in class org.jmol.smiles.SmilesSearch
- ignoreError - Variable in class org.jmol.script.ScriptError
- ignoreFileSpaceGroupName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ignoreFileSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ignoreFileUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ignoreMOs - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- ignoreStereochemistry - Variable in class org.jmol.smiles.SmilesParser
- ignoreStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
- ignoreStructure - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- iGroup - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
- ihalf - Variable in class org.jmol.util.ColorEncoder
- iHaveBitSets - Variable in class org.jmol.shapesurface.Isosurface
- iHaveCenterBitSet - Variable in class org.jmol.shapespecial.Polyhedra
- iHaveCoefMaps - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- iHaveDesiredModel - Variable in class org.jmol.adapter.readers.cif.CifReader
- iHaveDesiredModel - Variable in class org.jmol.adapter.readers.xtal.OptimadeReader
- iHaveFractionalCoordinates - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- iHaveModelIndex - Variable in class org.jmol.shapesurface.Isosurface
- iHaveModelStatement - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- iHaveNewDir - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- iHaveQuotedString - Variable in class org.jmol.script.ScriptCompiler
- iHaveSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- iHaveTwoEnds - Variable in class org.jmol.shapespecial.Dipoles
- iHaveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- iHideBackground - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- iHypervalent - Variable in class org.jmol.smiles.SmilesGenerator
- ijkToPoint3f(int, P3, int, int) - Static method in class org.jmol.util.SimpleUnitCell
-
Expanded cell notation: 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to +499
- iList - Variable in class org.jmol.navigate.Navigator
- image - Variable in class org.jmol.awt.AwtClipboard
-
The image to transfer into the clipboard.
- image - Variable in class org.jmol.console.ImageDialog
- image - Variable in class org.jmol.modelset.Text
- image - Static variable in class org.jmol.script.T
- image() - Method in class org.jmol.scriptext.CmdExt
- Image - Class in org.jmol.awt
-
methods required by Jmol that access java.awt.Image private to org.jmol.awt
- Image - Class in org.jmol.awtjs2d
-
methods required by Jmol that access java.awt.Image private to org.jmol.awt
- Image() - Constructor for class org.jmol.awt.Image
- Image() - Constructor for class org.jmol.awtjs2d.Image
- IMAGE - Enum constant in enum org.jmol.c.CBK
- image_copy_always - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- image_dots_per_inch - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- IMAGE_OR_SCENE - Static variable in class org.jmol.viewer.JC
- IMAGE_TYPES - Static variable in class org.jmol.viewer.JC
- ImageCanvas() - Constructor for class org.jmol.console.ImageDialog.ImageCanvas
- imageChoices - Variable in class org.jmol.dialog.Dialog
- imageChoices - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- imageChooser - Static variable in class org.jmol.dialog.Dialog
- ImageDialog - Class in org.jmol.console
- ImageDialog(Viewer, String, Map<String, GenericImageDialog>) - Constructor for class org.jmol.console.ImageDialog
- ImageDialog.ImageCanvas - Class in org.jmol.console
- imageExtensions - Variable in class org.jmol.dialog.Dialog
- imageExtensions - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- imageFontScaling - Variable in class org.jmol.render.FontLineShapeRenderer
- imageFontScaling - Variable in class org.jmol.render.MeshRenderer
- imageFontScaling - Variable in class org.jmol.viewer.Viewer
- imageMap - Variable in class org.jmol.console.ImageDialog
- imageMap - Variable in class org.jmol.viewer.StatusManager
- imageScale - Variable in class org.jmol.modelset.Text
- imageSizeChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Called when the ImageSize check box is modified
- imageSizeHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- imageSizeRatioBox - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- imageSizeRatioCombo - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- imageSizeTextHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- imageSizeTextWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- imageSizeWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- imagestate - Static variable in class org.jmol.script.T
- imageState - Variable in class org.jmol.viewer.GlobalSettings
- imageType - Variable in class org.jmol.dialog.Dialog
- imageType - Variable in class org.jmol.viewer.StatusManager
- imageType - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- imap - Variable in class org.jmol.shapesurface.PMeshWriter
- imaxp - Variable in class org.openscience.jmol.app.janocchio.PopulationDisplay
- imesh - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- imesh - Variable in class org.jmol.shapesurface.PMeshWriter
- imgHeight - Variable in class org.openscience.jmol.app.jmolpanel.Splash
- imgWidth - Variable in class org.openscience.jmol.app.jmolpanel.Splash
- iMo0 - Variable in class org.jmol.adapter.readers.quantum.MOReader
- iModel - Variable in class org.jmol.modelset.ModelLoader
- iModelMO - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- iMolecule - Variable in class org.jmol.quantum.QMAtom
- implicitHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
- implicitString - Variable in class org.jmol.script.ScriptCompiler
- implicitStringCommand - Static variable in class org.jmol.script.T
- importData(JComponent, Transferable) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- in - Static variable in class org.jmol.script.T
- IN_JMOL - Static variable in class org.openscience.jmol.app.webexport.WebExport
- inchi - Static variable in class org.jmol.awt.Platform
- inchi - Static variable in class org.jmol.awtjs2d.Platform
- inchi - Static variable in class org.jmol.script.T
- InChIJNI - Class in org.jmol.inchi
- InChIJNI() - Constructor for class org.jmol.inchi.InChIJNI
- InChIJS - Class in org.jmol.inchi
-
This class adapts Richard Apodaca's 2020 molfile-to-inchi LLVM-derived Web Assembly implementation of IUPAC InChI v.
- InChIJS() - Constructor for class org.jmol.inchi.InChIJS
- inchikey - Static variable in class org.jmol.script.T
- includeAllRelatedFrames(BS) - Method in class org.jmol.modelset.ModelSet
- includes(int, int) - Static method in class org.jmol.viewer.binding.Binding
- includeValueNaN - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- incompleteCmd - Variable in class org.jmol.console.GenericConsole
- increment - Static variable in class org.jmol.script.T
- increment(int) - Method in class org.jmol.script.SV
- incrementLineCount(String) - Method in class org.jmol.script.ScriptCompiler
- incrementModel(int) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- inDefinedStateBlock - Variable in class org.jmol.modelset.StateScript
- indent - Variable in class org.jmol.util.JSONWriter
- INDENT - Static variable in class org.jmol.shapecgo.CGOMesh
- index - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
- index - Variable in class org.jmol.adapter.smarter.Atom
- index - Variable in class org.jmol.bspt.Bspt
- index - Variable in class org.jmol.minimize.MinAtom
- index - Variable in class org.jmol.minimize.MinBond
- index - Variable in class org.jmol.modelset.Measurement
- index - Variable in class org.jmol.quantum.QMAtom
- index - Variable in class org.jmol.quantum.SlaterData
- index - Variable in class org.jmol.script.SV
- index - Variable in class org.jmol.shape.Mesh
- index - Variable in class org.jmol.smiles.SmilesAtom
- index - Variable in class org.jmol.smiles.SmilesMeasure
- index - Variable in class org.jmol.symmetry.PointGroup.Operation
- index - Variable in class org.jmol.symmetry.SpaceGroup
- index - Variable in class org.jmol.symmetry.SpaceGroupFinder.SGAtom
- index - Variable in class org.jmol.thread.SpinThread
- index - Variable in class org.jmol.util.BZone
- index - Variable in class org.jmol.util.Edge
- index - Variable in class org.jmol.viewer.MotionPoint
- indexes - Variable in class org.jmol.minimize.MMConstraint
- indexes - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.
- indexI - Variable in class org.jmol.geodesic.EnvelopeCalculation
- indexInFrame(Atom) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- indexInModel - Variable in class org.jmol.util.JmolMolecule
- indexLower(float, int) - Method in class org.jmol.jvxl.data.VolumeData
-
periodic grids should have val[0] == val[xMax] voxelCount: 1....2....3....4....5 xMax/index: 0....1....2....3....4....
- indexUpper(float, int, int) - Method in class org.jmol.jvxl.data.VolumeData
- indicatedModelIndex - Variable in class org.jmol.shapecgo.CGO
- indicatedModelIndex - Variable in class org.jmol.shapespecial.Draw
- indices - Variable in class org.jmol.smiles.SmilesMeasure
- iNested - Variable in class org.jmol.smiles.SmilesAtom
- iNext - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- iNext - Variable in class org.jmol.renderbio.BioShapeRenderer
- iNext2 - Variable in class org.jmol.renderbio.BioShapeRenderer
- iNext3 - Variable in class org.jmol.renderbio.BioShapeRenderer
- info - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- info - Variable in class org.jmol.atomdata.RadiusData
- info - Variable in class org.jmol.awtjs.swing.JComboBox
- info - Variable in class org.jmol.modelsetbio.BasePair
- info - Static variable in class org.jmol.script.T
- info - Variable in class org.jmol.shapespecial.Ellipsoid
- info - Variable in class org.jmol.shapespecial.Polyhedra
- info - Variable in class org.jmol.shapespecial.Polyhedron
- info - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- info - Variable in class org.jmol.symmetry.PointGroup
- info - Variable in class org.jmol.symmetry.SpaceGroup
- info - Variable in class org.jmol.symmetry.SymmetryOperation
- info - Variable in class org.openscience.jmol.app.JmolApp
- info() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- info() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- info(String) - Method in class org.jmol.util.DefaultLogger
- info(String) - Static method in class org.jmol.util.Logger
-
og* Writes a log at INFO level.
- info(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at INFO level.
- INFO_A - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_ALPHA - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_B - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_BETA - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_C - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_DIMENSIONS - Static variable in class org.jmol.util.SimpleUnitCell
- INFO_GAMMA - Static variable in class org.jmol.util.SimpleUnitCell
- infofontsize - Static variable in class org.jmol.script.T
- infoFontSize - Variable in class org.jmol.viewer.GlobalSettings
- infoLabel - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- infoList - Static variable in class org.jmol.util.Tensor
- infoStr - Variable in class org.jmol.symmetry.SymmetryInfo
- inFront - Variable in class org.jmol.modelset.Measurement
- inGreyscaleMode - Variable in class org.jmol.util.GData
- INHERIT - Static variable in class org.jmol.util.ColorEncoder
- INHERIT_ALL - Static variable in class org.jmol.util.C
- INHERIT_COLOR - Static variable in class org.jmol.util.C
- inInput - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
- init() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- init() - Method in class org.jmol.symmetry.CIPData
-
initializer -- called also by CIPDataSmiles
- init() - Method in class org.openscience.jmol.app.janocchio.Nmr
- init(boolean) - Method in class org.jmol.symmetry.SpaceGroup
- init(float[]) - Method in class org.jmol.util.SimpleUnitCell
- init(int, String, String, short, short, boolean) - Method in class org.jmol.shapespecial.Dipole
- init(Object) - Method in class org.jmol.scriptext.MathExt
- init(Object) - Method in class org.jmol.scriptext.ScriptExt
- init(Object) - Method in class org.jmol.scriptext.SmilesExt
- init(Object) - Method in class org.jmol.util.GenericApplet
- init(String, Object, String, SC) - Method in interface org.jmol.api.SC
- init(String, Object, String, SC) - Method in class org.jmol.awt.AwtSwingComponent
- init(String, Object, String, SC) - Method in class org.jmol.awtjs.swing.AbstractButton
- init(String, Viewer, Lst<Object>) - Method in class org.jmol.modelset.MeasurementData
- init(URL, String) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMepReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMlpReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMOReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoPlaneReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.SurfaceReader
-
implemented in SurfaceFileReader and
- init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.VolumeDataReader
- INIT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- INIT - Static variable in class org.jmol.thread.JmolThread
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.ApbsReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.BCifDensityReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.CastepDensityReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.CubeReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.EfvetReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JaguarReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JvxlReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.KinemageReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MapFileReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MrcBinaryReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MsmsReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.NffReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.ObjReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PltFormattedReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Pmesh4Reader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PmeshReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Ras3DReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.UhbdReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.VaspChgcarReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.XplorReader
- init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.XsfReader
- init2JXR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- init2MFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MapFileReader
- init2PFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PolygonFileReader
- init2PR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PmeshReader
- init2PR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Ras3DReader
- init2SFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- init2VFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- initADR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.AtomDataReader
- initApplication() - Method in class org.jmol.util.GenericApplet
- initArrays(int) - Method in class org.jmol.quantum.NMRNoeMatrix
-
create an empty atom list for subsequent population with atoms
- initBS() - Method in class org.jmol.renderbio.BioMeshRenderer
- initCGO() - Method in class org.jmol.shapecgo.CGO
- initCML() - Method in class org.jmol.adapter.readers.xml.XmlReader
- initComponents() - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
-
This method is called from within the constructor to initialize the form.
- initComponents() - Method in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
-
This method is called from within the constructor to initialize the form.
- initComponents() - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
-
This method is called from within the constructor to initialize the form.
- initComponents() - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
-
This method is called from within the constructor to initialize the form.
- initDraw() - Method in class org.jmol.shapespecial.Draw
- initEllipsoids(Object) - Method in class org.jmol.shapespecial.Ellipsoids
- initialFile - Variable in class org.jmol.dialog.Dialog
- initialize - Static variable in class org.jmol.script.T
- initialize() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initialize() - Method in class org.jmol.jvxl.readers.Parameters
- initialize() - Method in class org.jmol.shapebio.BioShapeCollection
- initialize() - Method in class org.jmol.shapespecial.Dots
- initialize(boolean, boolean) - Method in class org.jmol.viewer.Viewer
- initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.MOCalculation
- initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
- initialize(int, P3[], BS) - Method in class org.jmol.bspt.Bspf
- initialize(int, T3[], P4) - Method in class org.jmol.shape.Mesh
- initialize(String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- initialize(T3, float, boolean) - Method in class org.jmol.bspt.CubeIterator
-
initialize to return all points within the sphere defined by center and radius
- initialize(BasisFunctionReader, String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- initialize(AtomSetCollectionReader, int) - Method in class org.jmol.adapter.readers.cif.MSRdr
- initialize(AtomSetCollectionReader, int) - Method in interface org.jmol.adapter.smarter.MSInterface
- initialize(Bspf, BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.AtomIteratorWithinModel
-
############## ITERATOR SHOULD BE RELEASED #################
- initialize(ShapeRenderer, BioShape, int) - Method in class org.jmol.renderbio.BioMeshRenderer
- initialize(Node[], int, int, BS, int, int) - Static method in class org.jmol.util.JmolMolecule
- initialize(Viewer, GenericPlatform) - Method in class org.jmol.g3d.Graphics3D
- initialize(Viewer, GenericPlatform) - Method in class org.jmol.util.GData
- initialize(Viewer, PopupResource, String) - Method in class org.jmol.popup.JmolGenericPopup
- initialize0(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
- initializeAnnotation(SV, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
- initializeAnnotation(SV, int, int) - Method in class org.jmol.dssx.AnnotationParser
-
We create a main list of mappings, where each mapping has _atoms and _path
- initializeAtomBondModelCounts(int) - Method in class org.jmol.modelset.ModelLoader
- initializeBonding() - Method in class org.jmol.modelset.ModelLoader
- initializeBspf() - Method in class org.jmol.modelset.ModelSet
- initializeBspt(int) - Method in class org.jmol.modelset.ModelSet
- initializeCartesianToFractional() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initializeEigen() - Method in class org.jmol.quantum.NciCalculation
- initializeExporter(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
- initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.Export3D
- initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
- initializeForModel() - Method in class org.jmol.modelkit.ModelKit
- initializeHydrogenAddition() - Method in class org.jmol.modelsetbio.BioResolver
- initializeInfo(String, Map<String, Object>) - Method in class org.jmol.modelset.ModelLoader
- initializeIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- initializeIsosurface() - Method in class org.jmol.shapesurface.Isosurface
- initializeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
- initializeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
- initializeModel(boolean) - Method in class org.jmol.viewer.Viewer
- initializeMSCIF() - Method in class org.jmol.adapter.readers.cif.CifReader
- initializeOnePoint() - Method in class org.jmol.quantum.NciCalculation
- initializeOnePoint() - Method in class org.jmol.quantum.QuantumCalculation
- initializeOnePointQC() - Method in class org.jmol.quantum.QuantumCalculation
- initializeOrientation(M3) - Method in interface org.jmol.api.SymmetryInterface
- initializeOrientation(M3) - Method in class org.jmol.symmetry.Symmetry
- initializeOutput(Viewer, double, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
- initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.export.Export3D
- initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
- initializeOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.___Exporter
- initializeOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._ObjExporter
- initializeOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._TachyonExporter
- initializePointers(int) - Method in class org.jmol.viewer.AnimationManager
- initializePolymer(BioShape) - Method in class org.jmol.renderbio.BioShapeRenderer
- initializeProperties() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- initializeReader() - Method in class org.jmol.adapter.readers.cif.CifReader
- initializeReader() - Method in class org.jmol.adapter.readers.molxyz.Mol3DReader
- initializeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.GromacsReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.MdCrdReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
- initializeReader() - Method in class org.jmol.adapter.readers.more.Mol2Reader
- initializeReader() - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
- initializeReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- initializeReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianWfnReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.MOReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- initializeReader() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.CubeReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.FAHReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.JmeReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.JSONReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacReader
- initializeReader() - Method in class org.jmol.adapter.readers.simple.OrcaReader
- initializeReader() - Method in class org.jmol.adapter.readers.spartan.OdysseyReader
- initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanReader
- initializeReader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- initializeReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
not sure how to work with symmetry here...
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
- initializeReader() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
- initializeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initializeShape(Viewer, ModelSet, int) - Method in class org.jmol.shape.Shape
- initializeSurfaceData() - Method in class org.jmol.jvxl.readers.VolumeFileReader
- initializeSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initializeSymmetryOptions() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initializeTrajectoryFile() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- initializeUnitCellAndSymmetry() - Method in class org.jmol.modelset.ModelLoader
- initializeVolumetricData() - Method in class org.jmol.jvxl.readers.SurfaceReader
- initIFR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- initIMR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMepReader
- initIsosurface(int) - Method in class org.jmol.scriptext.IsoExt
- initModelSet() - Method in class org.jmol.shape.AtomShape
- initModelSet() - Method in class org.jmol.shape.Measures
- initModelSet() - Method in class org.jmol.shape.Shape
- initModelSet() - Method in class org.jmol.shape.TextShape
- initModelSet() - Method in class org.jmol.shapebio.BioShapeCollection
- initModelSet() - Method in class org.jmol.shapespecial.Vectors
- initModForStructure(int) - Method in class org.jmol.adapter.readers.cif.MSRdr
- initOptions() - Method in class org.jmol.util.GenericApplet
- initOrientation(M3) - Method in class org.jmol.symmetry.UnitCell
- initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.___Exporter
- initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.__RayTracerExporter
- initPlanes() - Method in class org.jmol.jvxl.readers.SurfaceReader
- initRenderer() - Method in class org.jmol.render.AxesRenderer
- initRenderer() - Method in class org.jmol.render.BbcageRenderer
- initRenderer() - Method in class org.jmol.render.MeasuresRenderer
- initRenderer() - Method in class org.jmol.render.ShapeRenderer
- initRenderer() - Method in class org.jmol.render.UccageRenderer
- initRenderer() - Method in class org.jmol.renderspecial.DotsRenderer
- initShape() - Method in class org.jmol.shape.AtomShape
- initShape() - Method in class org.jmol.shape.Axes
- initShape() - Method in class org.jmol.shape.Bbcage
- initShape() - Method in class org.jmol.shape.Echo
- initShape() - Method in class org.jmol.shape.FontLineShape
- initShape() - Method in class org.jmol.shape.Frank
- initShape() - Method in class org.jmol.shape.Hover
- initShape() - Method in class org.jmol.shape.Labels
- initShape() - Method in class org.jmol.shape.Measures
- initShape() - Method in class org.jmol.shape.MeshCollection
- initShape() - Method in class org.jmol.shape.Shape
- initShape() - Method in class org.jmol.shape.Sticks
- initShape() - Method in class org.jmol.shape.Uccage
- initShape() - Method in class org.jmol.shapebio.Backbone
- initShape() - Method in class org.jmol.shapebio.BioShapeCollection
- initShape() - Method in class org.jmol.shapebio.Cartoon
- initShape() - Method in class org.jmol.shapebio.MeshRibbon
- initShape() - Method in class org.jmol.shapebio.Rockets
- initShape() - Method in class org.jmol.shapebio.Trace
- initShape() - Method in class org.jmol.shapespecial.Dipoles
- initShape() - Method in class org.jmol.shapespecial.Dots
- initShape() - Method in class org.jmol.shapespecial.Draw
- initShape() - Method in class org.jmol.shapespecial.Ellipsoids
- initShape() - Method in class org.jmol.shapespecial.GeoSurface
- initShape() - Method in class org.jmol.shapesurface.Contact
- initShape() - Method in class org.jmol.shapesurface.Isosurface
- initShape() - Method in class org.jmol.shapesurface.LcaoCartoon
- initShape() - Method in class org.jmol.shapesurface.MolecularOrbital
- initShape() - Method in class org.jmol.shapesurface.NBO
- initShape() - Method in class org.jmol.shapesurface.Plot3D
- initShape() - Method in class org.jmol.shapesurface.Pmesh
- initSlice() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- initSR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.SurfaceReader
- initState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- initState() - Method in class org.jmol.shape.Halos
- initState() - Method in class org.jmol.shapesurface.Isosurface
- initSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
- initSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- initSwing(String, PopupResource, Object, boolean, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
- initUnitcellVertices() - Method in class org.jmol.symmetry.UnitCell
- initVariables() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- initVars() - Method in class org.jmol.export.__RayTracerExporter
- initVDR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.VolumeDataReader
- inline - Static variable in class org.jmol.script.T
- inlineNewlineChar - Variable in class org.jmol.viewer.GlobalSettings
- inMotion - Variable in class org.jmol.viewer.Viewer
- inMovie - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- inNames - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- inp - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- inPath - Variable in class org.jmol.awtjs2d.JsG2D
- input - Variable in class org.jmol.console.GenericConsole
- inputCode - Variable in class org.jmol.symmetry.HallRotationTerm
- inputContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- inputFileName - Variable in class org.jmol.dialog.Dialog
- inputFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- inputOnly - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- inputOnly - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
- inputOnly - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- inputOnly - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- InputReader - Class in org.jmol.adapter.readers.simple
- InputReader() - Constructor for class org.jmol.adapter.readers.simple.InputReader
- InputScannerThread - Class in org.openscience.jmol.app
- InputScannerThread(JmolViewer, boolean) - Constructor for class org.openscience.jmol.app.InputScannerThread
- inRange(int, int, int) - Method in class org.jmol.viewer.MouseState
- INS_CODE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- inscode - Static variable in class org.jmol.script.T
- insCode - Variable in class org.jmol.smiles.SmilesAtom
- INSCODE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- insert(SC, int) - Method in interface org.jmol.api.SC
- insert(SC, int) - Method in class org.jmol.awt.AwtSwingComponent
- insert(SC, int) - Method in class org.jmol.awtjs.swing.AbstractButton
- insertComponent(Component, int) - Method in class org.jmol.awtjs.swing.Container
- insertedCommand - Variable in class org.jmol.viewer.Viewer
- insertion - Static variable in class org.jmol.script.T
- INSERTION - Enum constant in enum org.jmol.c.PAL
- INSERTION_CODE_MASK - Static variable in class org.jmol.modelset.Group
- insertionCode - Variable in class org.jmol.adapter.smarter.Atom
- insertionCount - Variable in class org.jmol.modelset.Model
- insertString(int, String, Object) - Method in interface org.jmol.awtjs.swing.Document
- insertString(int, String, Object) - Method in class org.jmol.awtjs.swing.JTextPane
- insertString(int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- insets - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- Insets - Class in org.jmol.awtjs.swing
- Insets(int, int, int, int) - Constructor for class org.jmol.awtjs.swing.Insets
- insideMaskTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- insideout - Static variable in class org.jmol.script.T
- insideOut - Variable in class org.jmol.jvxl.data.JvxlData
- insideOut - Variable in class org.jmol.jvxl.readers.Parameters
- insideOut - Variable in class org.jmol.shape.Mesh
- inSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- INSOCKET - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- instance - Static variable in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- instance - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- InstanceCellRenderer() - Constructor for class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
- instanceList - Variable in class org.openscience.jmol.app.webexport.WebPanel
- INT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- Int2IntHash - Class in org.jmol.util
- Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
- Int2IntHashEntry - Class in org.jmol.util
- Int2IntHashEntry(int, int, Int2IntHashEntry) - Constructor for class org.jmol.util.Int2IntHashEntry
- intAnimThread - Variable in class org.jmol.viewer.AnimationManager
- intAsFloat - Variable in class org.jmol.modelset.LabelToken
- intAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- integer - Static variable in class org.jmol.script.T
- integerOutOfRange(int, int) - Method in class org.jmol.script.ScriptError
- integrateSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
- integration - Variable in class org.jmol.jvxl.data.JvxlData
- integration - Variable in class org.jmol.quantum.QuantumCalculation
- integrationKeyMap - Static variable in class org.jmol.adapter.writers.QCJSONWriter
- intenseFraction - Variable in class org.jmol.util.Shader
- INTERACTION_FACTOR - Static variable in class org.jmol.util.Tensor
- interactionTensors - Variable in class org.jmol.adapter.readers.xtal.MagresReader
- intercept(MarchingSquares.Triangle, int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- interestingAminoAtomIDs - Static variable in class org.jmol.modelsetbio.AminoMonomer
- interestingNucleicAtomIDs - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- Interface - Class in org.jmol.api
- Interface() - Constructor for class org.jmol.api.Interface
- interior - Static variable in class org.jmol.script.T
- intermolecular - Static variable in class org.jmol.script.T
- internal - Static variable in class org.jmol.script.T
- internal_feedback - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- internal_gui - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- internal_gui_control_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- internal_gui_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- internal_gui_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- internal_prompt - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- internalRotationAngle - Variable in class org.jmol.viewer.TransformManager
- internalRotationAxis - Variable in class org.jmol.viewer.TransformManager
- internalRotationCenter - Variable in class org.jmol.viewer.TransformManager
- internalSlab - Variable in class org.jmol.viewer.TransformManager
- internalTranslation - Variable in class org.jmol.viewer.TransformManager
- interpolate(int, int, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
- interpolateFraction(T3, T3, float, float, float, int) - Method in class org.jmol.util.MeshSlicer
- interpolatePoint(T3, T3, float, float, float, float, int) - Method in class org.jmol.util.MeshSlicer
- interpolatePrecisely(int, int, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
- interpolateSphere(T3, T3, float, float, double, float, float, int) - Method in class org.jmol.util.MeshSlicer
- interpolateX(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.CapVertex
-
Get interpolated x for the scan line intersection with an edge.
- interrupt() - Method in interface org.jmol.api.JmolNavigatorInterface
- interrupt() - Method in class org.jmol.thread.AnimationThread
- interrupt() - Method in class org.jmol.thread.JmolThread
- interrupt() - Method in class org.jmol.thread.MoveToThread
- interruptQueueThreads() - Method in class org.jmol.script.ScriptManager
- intersectID - Variable in class org.jmol.shapespecial.Draw
- intersection - Variable in class org.jmol.jvxl.readers.Parameters
- intersection - Static variable in class org.jmol.script.T
- intersectLine(P3[], int, P3, V3) - Method in class org.jmol.util.Triangulator
- intersectPlane(P4, T3[], int) - Method in class org.jmol.util.Triangulator
-
a generic cell - plane intersector -- used for finding the plane through a not static so as to allow JavaScript to not load it as core.
- intlTableNo - Variable in class org.jmol.symmetry.SymmetryInfo
- intlTableNumber - Variable in class org.jmol.symmetry.SpaceGroup
- intlTableNumberExt - Variable in class org.jmol.symmetry.SpaceGroup
- intlTableNumberFull - Variable in class org.jmol.symmetry.SpaceGroup
- intparam - Static variable in class org.jmol.script.T
- intParameter(int) - Method in class org.jmol.script.ScriptParam
- intParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- intParameterRange(int, int, int) - Method in class org.jmol.script.ScriptParam
- intPeek() - Method in class org.jmol.script.ScriptTokenParser
- intproperty - Static variable in class org.jmol.script.T
- intramolecular - Variable in class org.jmol.modelset.MeasurementData
- intramolecular - Static variable in class org.jmol.script.T
- intramolecular - Variable in class org.jmol.shape.Measures
- intThread - Variable in class org.jmol.thread.AnimationThread
- intValue - Variable in class org.jmol.script.T
- INVALID_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- invalidatedVertexCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- invalidateMesh - Variable in class org.jmol.renderbio.BioShapeRenderer
- invalidatePolygons() - Method in class org.jmol.util.MeshSurface
- invalidateSheets - Variable in class org.jmol.renderbio.BioShapeRenderer
- invalidateSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
- invalidateTriangles() - Method in interface org.jmol.jvxl.api.MeshDataServer
- invalidateTriangles() - Method in class org.jmol.shapesurface.Isosurface
- invalidateVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
- invalidControl - Variable in class org.jmol.modelsetbio.BioPolymer
- invalidLead - Variable in class org.jmol.modelsetbio.BioPolymer
- InvalidSmilesException - Exception in org.jmol.smiles
-
Exception thrown for invalid SMILES String
- InvalidSmilesException(String) - Constructor for exception org.jmol.smiles.InvalidSmilesException
-
Constructs a
InvalidSmilesException
with a detail message. - invArg() - Method in class org.jmol.script.ScriptError
- invArg() - Method in class org.jmol.scriptext.ScriptExt
- inverseMatrix - Variable in class org.jmol.jvxl.data.VolumeData
- inverseNormixes - Static variable in class org.jmol.util.Normix
- invertAtomCoord(P3, P4, BS, int, boolean) - Method in class org.jmol.viewer.Viewer
- invertInPlace(BS, int) - Static method in class org.jmol.util.BSUtil
-
inverts the bitset bits 0 through n-1, and returns a reference to the modified bitset
- invertNormixes() - Method in class org.jmol.shape.Mesh
- invertSelected - Static variable in class org.jmol.script.T
- invertSelected() - Method in class org.jmol.scriptext.CmdExt
- invertSelected(P3, P4, int, BS) - Method in class org.jmol.modelset.ModelSet
-
Carries out a stereochemical inversion through a point, across a plane, or at a chirality center.
- invertSelected(P3, P4, int, BS) - Method in class org.jmol.viewer.Viewer
- invertSelection() - Method in class org.jmol.viewer.SelectionManager
- invertStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
- invMatrix - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- invPO() - Method in class org.jmol.scriptext.ScriptExt
- iObj - Variable in class org.jmol.export._IdtfExporter
- iObj - Variable in class org.jmol.export.UseTable
- iop - Variable in class org.jmol.util.ModulationSet
-
the symmetry operation used to generate this atom
- iopLast - Variable in class org.jmol.adapter.readers.cif.MSRdr
- ipadx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- ipady - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- iPlaneNCI - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- iPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
- iProcess - Static variable in class org.jmol.script.ScriptEval
- ipt - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- ipt - Variable in class org.jmol.symmetry.UnitCellIterator
- ipt - Variable in class org.jmol.util.MeshCapper.CapVertex
-
external reference
- is(int) - Method in class org.jmol.modelset.Bond
- is(MouseState) - Method in class org.jmol.viewer.MouseState
- IS - Static variable in class org.jmol.quantum.QS
- IS_APPEND - Static variable in interface org.jmol.api.JmolScriptManager
- IS_HETERO_FLAG - Static variable in class org.jmol.modelset.Atom
- IS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- IS_POINTMAPPABLE - Static variable in class org.jmol.jvxl.readers.Parameters
- IS_SILENT - Static variable in class org.jmol.jvxl.readers.Parameters
- IS_SLABBABLE - Static variable in class org.jmol.jvxl.readers.Parameters
- IS_SOLVENTTYPE - Static variable in class org.jmol.jvxl.readers.Parameters
- is2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- is2D - Variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- is2D - Variable in class org.jmol.modelset.ModelLoader
- is2D - Variable in class org.jmol.rendercgo.CGORenderer
- is2D - Variable in class org.jmol.smiles.SmilesGenerator
- is2DPercent - Variable in class org.jmol.rendercgo.CGORenderer
- is3D - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- is47File - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- is4D - Variable in class org.jmol.viewer.TransformManager4D
- isActive - Variable in class org.jmol.shape.AtomShape
- isActive - Variable in class org.jmol.shapebio.BioShapeCollection
- isActive() - Method in class org.jmol.shapespecial.Ellipsoids
- isActiveLevel(int) - Static method in class org.jmol.util.Logger
-
Tells if a logging level is active.
- isAdded(int) - Method in class org.jmol.modelset.Group
- isAdjacentSp2(Atom) - Method in class org.jmol.modelset.AtomCollection
- isAFLOW - Variable in class org.jmol.adapter.readers.cif.CifReader
- isAligned(T3, T3, T3) - Method in class org.jmol.smiles.PolyhedronStereoSorter
-
check alignment, within 10 degrees is considered aligned.
- isAlkene - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
is one atom of a double bond
- isAlkeneAtom2 - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
a flag used in Rule 3 to indicate the second carbon of a double bond
- isAll - Variable in class org.jmol.modelset.MeasurementData
- isAll - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- isAll - Variable in class org.jmol.shape.TextShape
- isAllQ - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- isAlphaMonomer() - Method in class org.jmol.modelsetbio.AlphaMonomer
- isAltKeyReleased - Variable in class org.jmol.viewer.ActionManager
- isAltLoc(char, String) - Method in class org.jmol.modelset.AtomCollection
- isAmide - Variable in class org.jmol.minimize.MinBond
- isAminoMonomer() - Method in class org.jmol.modelsetbio.AminoMonomer
- isAND - Variable in class org.jmol.smiles.SmilesAtom
- isAngstroms - Variable in class org.jmol.adapter.readers.simple.CubeReader
- isAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
- isAngstroms - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- isAnisotropic - Variable in class org.jmol.jvxl.readers.Parameters
- isAnisotropic - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isAntialiased - Variable in class org.jmol.render.HalosRenderer
- isAntialiased - Variable in class org.jmol.render.SticksRenderer
- isAntialiased() - Method in interface org.jmol.api.JmolGraphicsInterface
- isAntialiased() - Method in class org.jmol.export.Export3D
-
is full scene / oversampling antialiasing in effect
- isAntialiased() - Method in class org.jmol.util.GData
-
is full scene / oversampling antialiasing in effect
- isAntiparallel - Variable in class org.jmol.dssx.Bridge
- isAppend - Variable in class org.jmol.io.FileReader
- isAppend - Variable in class org.jmol.io.FilesReader
- isAppendSelected() - Method in class org.jmol.dialog.FilePreview
- isApplet - Variable in class org.jmol.popup.GenericPopup
- isApplet - Variable in class org.jmol.viewer.Viewer
- isApplet - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- isApprox(V3d, V3d, double) - Static method in class org.jmol.minimize.Util
- isArc - Variable in class org.jmol.shapespecial.Draw
- isaromatic - Static variable in class org.jmol.script.T
- isAromatic - Variable in class org.jmol.minimize.MinBond
- isAromatic - Variable in class org.jmol.smiles.SmilesAtom
- isAromatic() - Method in class org.jmol.modelset.Bond
- isAromaticBond(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- isArray(Object) - Static method in class org.jmol.script.SV
-
Must be updated if getVariable is updated!
- isArrayItem - Variable in class org.jmol.script.ScriptMathProcessor
- isArrayParameter(int) - Method in class org.jmol.script.ScriptParam
- isArrow - Variable in class org.jmol.shapespecial.Draw
- isAssignment - Variable in class org.jmol.script.ScriptMathProcessor
- isASV(Object) - Static method in class org.jmol.script.SV
- isAtEnd() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- isAtomExpression(int) - Method in class org.jmol.script.ScriptEval
- isAtomHidden(int) - Method in class org.jmol.modelset.AtomCollection
- isAtomNameMatch(Atom, String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
- isAtomPDB(int) - Method in class org.jmol.modelset.ModelSet
- isAtoms - Variable in class org.jmol.symmetry.PointGroup
- isAtomSelected(int) - Method in class org.jmol.viewer.SelectionManager
- isAtropism(int) - Static method in class org.jmol.util.Edge
- isAuto - Variable in class org.jmol.shapespecial.Polyhedra
- isAux - Variable in class org.jmol.symmetry.CIPChirality
-
are we in the midst of auxiliary center creation?
- isAV(Object) - Static method in class org.jmol.util.Escape
- isBarb - Variable in class org.jmol.shapespecial.Draw
- isBarb - Variable in class org.jmol.shapespecial.DrawMesh
- isBbcageDefault - Variable in class org.jmol.modelset.ModelSet
- isBCSfile - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
- isBiColor - Variable in enum org.jmol.c.STER
- isBiColor() - Method in enum org.jmol.c.STER
- isBicolorMap - Variable in class org.jmol.jvxl.data.JvxlData
- isBicolorMap - Variable in class org.jmol.jvxl.readers.Parameters
- isBicolorMap - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- isBilbao - Variable in class org.jmol.symmetry.SpaceGroup
- isBinary - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isBinary - Variable in class org.jmol.jvxl.readers.PmeshReader
- isBinary - Variable in class org.jmol.shapesurface.PMeshWriter
- isBio - Variable in class org.jmol.symmetry.SpaceGroup
- isBio - Variable in class org.jmol.symmetry.Symmetry
- isBio - Variable in class org.jmol.symmetry.SymmetryOperation
- isBio() - Method in interface org.jmol.api.SymmetryInterface
- isBio() - Method in class org.jmol.symmetry.Symmetry
- isBioAtom - Variable in class org.jmol.smiles.SmilesAtom
- isBioAtomWild - Variable in class org.jmol.smiles.SmilesAtom
- isBioModel - Variable in class org.jmol.modelset.Model
- isbiomol - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- isBiomolecule - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- isBioResidue - Variable in class org.jmol.smiles.SmilesAtom
- isBioSequence - Variable in class org.jmol.smiles.SmilesParser
- isBioShape - Variable in class org.jmol.shape.Shape
- isBold - Variable in class org.jmol.util.Font
- isBond - Variable in class org.jmol.shapespecial.Dipoles
- isBondable(float, float, float, float, float) - Method in class org.jmol.modelset.ModelSet
- isBondDipole(int) - Method in class org.jmol.shapespecial.Dipoles
- isBonded(Atom) - Method in class org.jmol.modelset.Atom
- isBondedCorrectly(int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
- isBondedCorrectlyRange(int, int, int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
- isBondSet - Variable in class org.jmol.script.ScriptParam
- isBondType() - Method in class org.jmol.shapespecial.Dipole
- isBondType(char, boolean, boolean) - Static method in class org.jmol.smiles.SmilesBond
- isBound(int, int) - Method in class org.jmol.viewer.binding.Binding
- isBound(int, int) - Method in class org.jmol.viewer.Viewer
- isBreakableContext(int) - Static method in class org.jmol.script.ScriptCompiler
- isBXSF - Variable in class org.jmol.jvxl.readers.XsfReader
- isCA2(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isCarbohydrate - Variable in class org.jmol.renderbio.BioShapeRenderer
- isCarbohydrate() - Method in class org.jmol.modelset.Group
- isCarbohydrate() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
- isCartesian - Variable in class org.jmol.export.Export3D
- isCartesian - Variable in class org.jmol.render.SticksRenderer
- isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
- isCartoonsSelected() - Method in class org.jmol.dialog.FilePreview
- isCavity - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- isCavity - Variable in class org.jmol.jvxl.readers.Parameters
- isCell - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- isCellEditable(int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- isCellEditable(int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- isCellEditable(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- isCellEditable(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
- isCenteringOp - Variable in class org.jmol.symmetry.SymmetryOperation
- isCenterParameter(int) - Method in class org.jmol.script.ScriptParam
- isCentrosymmetric - Variable in class org.jmol.symmetry.HallInfo
- isChain - Variable in class org.jmol.smiles.SmilesBond
- isCheckOnly - Variable in class org.jmol.script.ScriptCompiler
- isChiralPath - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
a check for downstream chirality
- isCircle - Variable in class org.jmol.shapespecial.Draw
- isCis(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPData
-
Check cis vs.
- isCis(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPDataSmiles
-
Check cis vs.
- isClickable() - Method in class org.jmol.modelset.Atom
- isClipped(int, int) - Method in class org.jmol.export.Export3D
- isClipped(int, int) - Method in class org.jmol.util.GData
- isClipped(int, int, int) - Method in class org.jmol.export.Export3D
- isClipped3(int, int, int) - Method in class org.jmol.util.GData
- isClippedXY(int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
- isClippedXY(int, int, int) - Method in class org.jmol.export.Export3D
- isClippedXY(int, int, int) - Method in class org.jmol.util.GData
- isClippedZ(int) - Method in class org.jmol.util.GData
- isClosedFace - Variable in class org.jmol.jvxl.readers.PmeshReader
- isCmdf - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
- isCmdLine_C_Option - Variable in class org.jmol.script.ScriptEval
- isCmdLine_c_or_C_Option - Variable in class org.jmol.script.ScriptEval
- isColixColorInherited(short) - Static method in class org.jmol.util.C
- isColixLastAvailable(short) - Static method in class org.jmol.util.C
- isColixTranslucent(short) - Static method in class org.jmol.util.C
- isCollapsed - Variable in class org.jmol.shapespecial.Polyhedra
- isColorExplicit - Variable in class org.jmol.shapesurface.Isosurface
- isColorIndex - Variable in class org.jmol.util.ColorEncoder
- isColorParam(int) - Method in class org.jmol.script.ScriptParam
- isColorReversed - Variable in class org.jmol.jvxl.data.JvxlData
- isColorReversed - Variable in class org.jmol.jvxl.readers.Parameters
- isColorSolid - Variable in class org.jmol.util.MeshSurface
- isCommaAsOrAllowed - Variable in class org.jmol.script.ScriptTokenParser
- isCommandDisplayable(int) - Method in class org.jmol.script.ScriptEval
-
provides support for the script editor
- isCommensurate - Variable in class org.jmol.adapter.readers.cif.MSRdr
- isCommensurate - Variable in class org.jmol.util.ModulationSet
-
commensurate modulations cannot be "undone" and they cannot be turned off
- isComment - Variable in class org.jmol.script.ScriptCompiler
- isComplete - Variable in class org.jmol.script.ScriptContext
- isCompoundDocument - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- isConcatenated - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isConnect() - Method in class org.jmol.modelset.StateScript
- isConnected(Atom[], int) - Method in class org.jmol.modelset.Measurement
- isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AlphaMonomer
- isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AminoMonomer
- isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
- isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.Monomer
- isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.NucleicMonomer
- isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isConnectedPrevious() - Method in class org.jmol.modelset.Group
- isConnectedPrevious() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
- isConnectedPrevious() - Method in class org.jmol.modelsetbio.Monomer
- isConnection - Variable in class org.jmol.smiles.SmilesBond
- isConnectStateBug - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- isContainedIn(BS) - Method in class org.jmol.modelset.Model
- isContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
- isContoured - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isContoured - Variable in class org.jmol.jvxl.data.JvxlData
- isContoured - Variable in class org.jmol.jvxl.readers.Parameters
- isCore - Variable in class org.jmol.quantum.SlaterData
- isCourseGrained - Variable in class org.jmol.adapter.readers.cif.CifReader
- isCourseGrained - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- isCovalent() - Method in class org.jmol.modelset.Bond
- isCovalent() - Method in class org.jmol.smiles.SmilesBond
- isCovalent() - Method in class org.jmol.util.Edge
- isCovalent() - Method in interface org.jmol.util.SimpleEdge
- isCovalentlyBonded(Atom) - Method in class org.jmol.modelset.Atom
- iscroll - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- isCrossed - Variable in class org.jmol.shapespecial.Draw
- isCrossLinked(Group) - Method in class org.jmol.modelset.Group
- isCrossLinked(Group) - Method in class org.jmol.modelsetbio.Monomer
- isCrossLinked(Group) - Method in class org.jmol.modelsetbio.NucleicMonomer
- isCrossLinked(Node) - Method in class org.jmol.modelset.Atom
- isCrossLinked(Node) - Method in class org.jmol.smiles.SmilesAtom
- isCrossLinked(Node) - Method in interface org.jmol.util.Node
- iScrPt - Variable in class org.jmol.viewer.TransformManager
- isCursorOnTopOf(int, int, int, Atom) - Method in class org.jmol.modelset.Atom
- isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.AtomCollection
-
used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability
- isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.Group
- isCurve - Variable in class org.jmol.shapespecial.Draw
- isCutoffAbsolute - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isCutoffAbsolute - Variable in class org.jmol.jvxl.data.JvxlData
- isCutoffAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
- isCyclic - Variable in class org.jmol.renderbio.BioShapeRenderer
- isCyclic() - Method in class org.jmol.modelsetbio.BioPolymer
- isCylinder - Variable in class org.jmol.shapespecial.Draw
- isDatabaseCode(char) - Static method in class org.jmol.viewer.Viewer
- isDataFlavorSupported(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
- isDataFlavorSupported(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
- isDataFrame - Variable in class org.jmol.renderbio.BackboneRenderer
- isDataOnly - Variable in class org.openscience.jmol.app.JmolApp
- isDebug - Variable in class org.jmol.export._StlExporter
- isDecimal(SV) - Method in class org.jmol.script.ScriptMathProcessor
- isDefaultColorRasmol - Variable in class org.jmol.viewer.ColorManager
- isDefined() - Method in class org.jmol.smiles.SmilesAtom
- isDeleted() - Method in class org.jmol.modelset.Atom
- isDeleted() - Method in class org.jmol.smiles.SmilesAtom
- isDeleted() - Method in interface org.jmol.util.Node
- isDeleted(Atom) - Static method in class org.jmol.modelset.AtomCollection
- isDensityRange - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isDiaxial(SimpleNode, SimpleNode, SimpleNode, SimpleNode, VTemp, float) - Static method in class org.jmol.smiles.SmilesStereo
- isDiff - Variable in class org.jmol.jvxl.readers.BCifDensityReader
- isDirectedTowardsCamera(short) - Method in class org.jmol.util.GData
- isDirectory() - Method in interface org.jmol.api.GenericFileInterface
- isDirectory() - Method in class org.jmol.awtjs2d.JSFile
- isDisplayWithinNot - Variable in class org.jmol.shape.MeshCollection
- isDna() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isDna() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isDna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isDnaByID() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isDone - Variable in class org.jmol.thread.SpinThread
- isDotDot - Variable in class org.jmol.script.ScriptCompiler
- isDraggedIsShiftDown() - Method in class org.jmol.viewer.ActionManager
- isDrawOrLabelAction(int) - Method in class org.jmol.viewer.ActionManager
- isDrawPolygon - Variable in class org.jmol.util.MeshSurface
- isDrawType(String, int, float) - Method in class org.jmol.symmetry.PointGroup
- isDSSP1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isDSSP2 - Variable in class org.jmol.dssx.DSSP
- isDssrSet - Variable in class org.jmol.modelsetbio.NucleicPolymer
- isDuplicate - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
a flag to indicate atom that is a duplicate, either due to ring closure or multiple bonding -- element number and mass, but no substituents; slightly lower in priority than standard atoms.
- isE_fr_energy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- isE_wo_entrp - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- isEccentric - Variable in class org.jmol.jvxl.readers.Parameters
- isEccentric - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isEcho - Variable in class org.jmol.modelset.Text
- isEdge(int, int) - Method in class org.jmol.util.MeshCapper
- isEditor - Variable in class org.jmol.script.ScriptContext
- isEditor - Variable in class org.jmol.script.ScriptEval
- isEditorScript - Variable in class org.jmol.script.ScriptContext
- isElectronDensityCalc - Variable in class org.jmol.jvxl.readers.IsoMOReader
- isElement(int, int) - Static method in class org.jmol.util.Elements
- isEmbeddable(String) - Static method in class org.jmol.viewer.FileManager
-
Check to see if it is possible that this file has been embedded by Jmol using JC.EMBEDDED_SCRIPT_TAG.
- isEmbedded - Variable in class org.jmol.script.ScriptEval
- isEmbeddedExpression - Variable in class org.jmol.script.ScriptTokenParser
- isEmpty() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- isEnabled() - Method in interface org.jmol.api.JmolModulationSet
- isEnabled() - Method in interface org.jmol.api.SC
- isEnabled() - Method in class org.jmol.awt.AwtSwingComponent
- isEnabled() - Method in class org.jmol.awtjs.swing.Component
- isEnabled() - Method in class org.jmol.util.ModulationSet
- isEndOfCommand - Variable in class org.jmol.script.ScriptCompiler
- isEqual(PointGroup) - Method in class org.jmol.symmetry.PointGroup
- isEqualD(T3, T3, double) - Static method in class org.jmol.adapter.readers.cif.TopoCifParser
- isEquiv(Tensor) - Method in class org.jmol.util.Tensor
- isError - Variable in exception org.jmol.script.ScriptException
- isError - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- isError() - Method in class org.jmol.script.ScriptTokenParser
- iSet - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- isEvenEne - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
alkene or even cumulene, so chirality will be EZ, not MP
- isExecuting() - Method in interface org.jmol.api.JmolScriptEvaluator
- isExecuting() - Method in class org.jmol.script.ScriptEval
- isExplicitOnly(SimpleNode) - Method in class org.jmol.smiles.SmilesGenerator
- isExport - Variable in class org.jmol.render.ShapeRenderer
- isExpressionNext() - Method in class org.jmol.script.ScriptTokenParser
- isFinalized - Variable in class org.jmol.adapter.readers.cif.Subsystem
- isFinalized - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- isFinalized - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- isFinalized - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isFinalized - Variable in class org.jmol.symmetry.SymmetryOperation
- isFinite(double) - Static method in class org.jmol.minimize.Util
- isFirst - Variable in class org.jmol.smiles.SmilesAtom
-
true if this atom is the first SMILES atom or first after a .
- isFirst - Variable in class org.jmol.thread.AnimationThread
- isFirstJob - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- isFirstRow(SimpleNode) - Static method in class org.jmol.symmetry.CIPChirality
-
Check if an atom is 1st row.
- isFixed - Variable in class org.jmol.shape.MeshCollection
- isFixed - Variable in class org.jmol.shapespecial.DrawMesh
- isFloat(String) - Static method in class org.jmol.adapter.smarter.Resolver
- isFloatInfo(String) - Static method in class org.jmol.util.Tensor
- isFloatParameter(int) - Method in class org.jmol.script.ScriptParam
- isFloatParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- isFlowIfContextOK(ScriptFlowContext) - Method in class org.jmol.script.ScriptCompiler
-
check for proper sequence: if...[any number of elseif]...[zero or one else]...[endif]
- isFractional - Variable in class org.jmol.adapter.readers.xtal.AimsReader
- isFractional - Variable in class org.jmol.modelset.Trajectory
- isFromPreviousTo(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
-
Check to see if this is the bond to the previous atom
- isFront(P3, P3, P3) - Static method in class org.jmol.g3d.HermiteRenderer
- isFull - Variable in class org.jmol.shapespecial.Polyhedra
- isFullSceneAntialiasingEnabled - Variable in class org.jmol.g3d.Graphics3D
- isFullyLit - Variable in class org.jmol.shapespecial.Polyhedron
- isFullyLit() - Method in class org.jmol.jvxl.readers.Parameters
- isFuncReturn - Variable in class org.jmol.script.ScriptEval
- isFunction - Variable in class org.jmol.script.ScriptContext
- isFunction(String) - Method in class org.jmol.script.ScriptExpr
- isFunction(String) - Method in class org.jmol.viewer.Viewer
- isGesture - Variable in class org.jmol.thread.SpinThread
- isGhostPass - Variable in class org.jmol.render.MeshRenderer
- isGreaterOnly - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- isGuanine() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isGUI - Variable in class org.jmol.script.ScriptEval
- isH - Variable in class org.jmol.awtjs.swing.JSplitPane
- isHbonded(int, int, int, int, int[][][][]) - Method in class org.jmol.dssx.DSSP
- isHeader - Variable in class org.jmol.adapter.readers.simple.InputReader
- isHeadless() - Method in interface org.jmol.api.GenericPlatform
- isHeadless() - Method in class org.jmol.awt.Platform
- isHeadless() - Method in class org.jmol.awtjs2d.Platform
- isHelix() - Method in class org.jmol.modelsetbio.AlphaMonomer
- isHelix() - Method in class org.jmol.modelsetbio.Monomer
- isHelix(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
- isHetero - Variable in class org.jmol.adapter.smarter.Atom
- isHetero() - Method in class org.jmol.modelset.Atom
- isHetero(String) - Method in class org.jmol.modelsetbio.BioResolver
-
MMCif, Gromacs, MdTop, Mol2 readers only
- isHidden - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- isHidden - Variable in class org.jmol.modelset.Measurement
- isHidden() - Method in class org.jmol.modelkit.ModelKit
- isHighPrecision - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
- isHighRes - Variable in class org.jmol.renderbio.BioShapeRenderer
- isHover - Variable in class org.jmol.shape.TextShape
- iShowNormals - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- iShowSolid - Variable in class org.jmol.renderspecial.DotsRenderer
- isHydrogen() - Method in class org.jmol.modelset.Bond
- isHydrogen() - Method in class org.jmol.smiles.SmilesBond
- isHydrogen() - Method in class org.jmol.util.Edge
- isIDcmd(int) - Static method in class org.jmol.script.T
-
commands that allow implicit ID as first parameter
- isImproper - Variable in class org.jmol.symmetry.HallRotationTerm
- isInchiOpposite(int, int, int, int) - Method in class org.jmol.inchi.InChIJNI
- isInDisplayRange(int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
- isInDisplayRange(int, int) - Method in class org.jmol.export.Export3D
- isInDisplayRange(int, int) - Method in class org.jmol.util.GData
- isInitializedIndex(int) - Method in class org.jmol.bspt.Bspf
- isInPosition(V3, float) - Method in class org.jmol.viewer.TransformManager
- isInputFirst - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- isInRange(RadiusData, float) - Method in class org.jmol.modelset.Measurement
- isInRange(Atom, Atom, float, float, boolean, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
-
Consider the min/max option for CONNECT
- isInSelectionSubset(int) - Method in class org.jmol.viewer.SelectionManager
- isInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isInside(float, float, boolean) - Static method in class org.jmol.jvxl.calc.MarchingCubes
- isInsideOut() - Method in class org.jmol.jvxl.readers.Parameters
- isInt(float) - Static method in class org.jmol.adapter.readers.xtal.CastepReader
- isInt(String) - Static method in class org.jmol.adapter.smarter.Resolver
- isIntramolecular(Atom[], int) - Method in class org.jmol.modelset.Measurement
- isInvalid - Variable in class org.jmol.g3d.TextRenderer
- isInvertible(int) - Static method in class org.jmol.minimize.forcefield.CalculationsUFF
- isInvertible(MinAtom) - Static method in class org.jmol.minimize.forcefield.CalculationsMMFF
- isIsotropic - Variable in class org.jmol.util.Tensor
- isItalic - Variable in class org.jmol.util.Font
- isJmolDataFrame - Variable in class org.jmol.modelset.Model
- isJmolDataFrame() - Method in class org.jmol.viewer.Viewer
- isJmolDataFrameForAtom(Atom) - Method in class org.jmol.modelset.ModelSet
- isJmolDataFrameForModel(int) - Method in class org.jmol.modelset.ModelSet
- isJmolType(String) - Static method in class org.jmol.viewer.FileManager
-
Check to see if this is a Jmol WRITE file type that might be or have attached a ZIP collection .
- isJmolVariable(String) - Method in class org.jmol.viewer.GlobalSettings
- isJmolZformat - Variable in class org.jmol.adapter.readers.simple.InputReader
- isJNLP - Variable in class org.jmol.viewer.Viewer
- isJPEG - Variable in class org.jmol.dialog.Dialog.QualityListener
- isJS - Variable in class org.jmol.popup.GenericPopup
- isJS - Variable in class org.jmol.script.ScriptEval
- isJS - Variable in class org.jmol.thread.JmolThread
- isJS - Static variable in class org.jmol.util.GenericApplet
- isJS - Static variable in class org.jmol.viewer.Viewer
- isJSNoAWT - Variable in class org.jmol.viewer.Viewer
- isJSThread - Variable in class org.jmol.script.ScriptContext
- isJvxl - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isJvxlPrecisionColor - Variable in class org.jmol.jvxl.data.JvxlData
- isKekuleAmbiguous - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
is an atom that is involved in more than one Kekule form
- iskiosk - Static variable in class org.jmol.script.T
- isKiosk - Variable in class org.jmol.viewer.Viewer
- isKiosk - Variable in class org.openscience.jmol.app.JmolApp
- isKiosk() - Method in class org.jmol.viewer.Viewer
- isKnownPDBGroup(String, int) - Method in class org.jmol.modelsetbio.BioResolver
- isLabelPropertyTok(int) - Static method in class org.jmol.modelset.LabelToken
- isLastFrame - Variable in class org.jmol.popup.JmolPopup
- isLastModel(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
after reading a model, Q: Is this the last model?
- isLeadAtom - Variable in class org.jmol.smiles.SmilesAtom
- isLeadAtom() - Method in class org.jmol.modelset.Atom
- isLeadAtom() - Method in class org.jmol.smiles.SmilesAtom
- isLeadAtom() - Method in interface org.jmol.util.Node
- isLeadAtom(int) - Method in class org.jmol.modelset.Group
- isLeadAtom(int) - Method in class org.jmol.modelsetbio.Monomer
- isLegacyModelType - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- isLegendre - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- isLigand - Variable in class org.jmol.adapter.readers.cif.CifReader
- isLigandBondBug - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- isLike(SV, SV) - Static method in class org.jmol.script.SV
-
a LIKE "x" a is a string and equals x a LIKE "*x" a is a string and ends with x a LIKE "x*" a is a string and starts with x a LIKE "*x*" a is a string and contains x
- isLine - Variable in class org.jmol.shapespecial.Draw
- isLinear(int) - Method in class org.jmol.minimize.forcefield.Calculations
- isLinear(int) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
- isLinear(T3[]) - Method in class org.jmol.symmetry.PointGroup
- isLinear(MinAtom) - Static method in class org.jmol.minimize.MinAtom
- isLineContinuation(int, boolean) - Method in class org.jmol.script.ScriptCompiler
- isLoadOption(int) - Method in class org.jmol.script.ScriptEval
- isLonePair - Variable in class org.jmol.shapesurface.LcaoCartoon
- isLongMode - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- isLoop - Variable in class org.jmol.adapter.readers.cif.CifReader
- isM3D - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
- isMac - Static variable in class org.jmol.dialog.Dialog
- isMagCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
- isMapped - Variable in class org.jmol.jvxl.readers.Parameters
- isMapped - Variable in class org.jmol.rendercgo.CGORenderer
- isMatch(String) - Method in class org.jmol.shapespecial.Polyhedra
- isMathExpressionCommand - Variable in class org.jmol.script.ScriptTokenParser
- isMeasure - Variable in class org.jmol.modelset.Text
- isMenu(String) - Method in class org.jmol.script.ScriptEval
- isMenuItem(Object) - Method in class org.jmol.console.GenericConsole
- isMenuItem(Object) - Method in class org.jmol.console.JmolConsole
- isMenuItem(Object) - Method in class org.jmol.consolejs.AppletConsole
- isMerged - Variable in class org.jmol.util.MeshSurface
- isMesh - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- isMesh - Variable in class org.jmol.shapebio.Strands
- isMin(Map<String, Integer>) - Method in class org.jmol.modelset.Measurement
- isMixed(Matrix) - Method in class org.jmol.adapter.readers.cif.Subsystem
- isMMCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
- isModel2D(BS) - Method in class org.jmol.viewer.Viewer
- isModelConnected - Variable in class org.jmol.jvxl.data.JvxlData
- isModelConnected - Variable in class org.jmol.jvxl.readers.Parameters
- isModelConnected - Variable in class org.jmol.shape.Mesh
- isModelKit - Variable in class org.jmol.modelset.Model
- isModelKitOpen() - Method in class org.jmol.viewer.Viewer
- isModelkitPickingActive() - Method in class org.jmol.viewer.Viewer
- isModelKitPickingRotateBond() - Method in class org.jmol.viewer.Viewer
- isModelPDB(int) - Method in class org.jmol.viewer.Viewer
- isModulated - Variable in class org.jmol.util.Tensor
- isModulated(int) - Method in class org.jmol.modelset.AtomCollection
- isMOL2D - Variable in class org.jmol.modelset.ModelLoader
- isMolecular - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isMolecular - Variable in class org.jmol.shapesurface.LcaoCartoon
- isMonomerSelected(int) - Method in class org.jmol.modelsetbio.BioPolymer
- isMopac - Variable in class org.jmol.adapter.readers.simple.InputReader
- isMouseDown - Variable in class org.jmol.awt.Mouse
- isMouseDown - Variable in class org.jmol.awtjs2d.Mouse
- isMove - Variable in class org.jmol.thread.MoveToThread
- isMovie - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- isMovie - Variable in class org.jmol.viewer.AnimationManager
- isMTClient() - Method in class org.jmol.viewer.ActionManager
- isMTServer() - Method in class org.jmol.viewer.ActionManager
- isMultiCell - Variable in class org.jmol.symmetry.SymmetryInfo
- isMultiConfiguration - Variable in class org.jmol.popup.JmolPopup
- isMultiFrame - Variable in class org.jmol.popup.JmolPopup
- isMultiModel - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- isMultiTouch - Variable in class org.jmol.viewer.ActionManager
- isMultiTouchClient - Variable in class org.jmol.viewer.ActionManager
- isMultiTouchServer - Variable in class org.jmol.viewer.ActionManager
- isMutate - Variable in class org.jmol.modelset.ModelLoader
- isMutated - Variable in class org.jmol.modelsetbio.BioModel
- isNaN() - Method in class org.jmol.script.SV
- isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
- isNav - Variable in class org.jmol.thread.SpinThread
- isNavigating() - Method in class org.jmol.viewer.TransformManager
- isNavigationMode - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- isNavTo - Variable in class org.jmol.navigate.Navigator
- isNci - Variable in class org.jmol.jvxl.readers.IsoMOReader
- isNear(double, double) - Static method in class org.jmol.minimize.Util
- isNear3(double, double, double) - Static method in class org.jmol.minimize.Util
- isNearPlane(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
- isNearZero(double) - Static method in class org.jmol.minimize.Util
- isNearZero2(double, double) - Static method in class org.jmol.minimize.Util
- isNegDisorder - Variable in class org.jmol.adapter.smarter.Atom
- isNegligible(double, double) - Static method in class org.jmol.minimize.Util
- isNegligible3(double, double, double) - Static method in class org.jmol.minimize.Util
- isNewChain - Variable in class org.jmol.modelset.ModelLoader
- isNewFormat - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- isNewSet - Variable in class org.jmol.script.ScriptTokenParser
- isNext(String) - Method in class org.jmol.jvxl.readers.XmlReader
- isNonzero() - Method in class org.jmol.util.ModulationSet
- isNonzero() - Method in class org.jmol.util.Vibration
- isNormalized - Variable in class org.jmol.smiles.SmilesSearch
- isNot - Variable in class org.jmol.smiles.SmilesBond
- isNot - Variable in class org.jmol.smiles.SmilesMeasure
- isNot - Variable in class org.jmol.smiles.SmilesStereo
- isNotCentroid(P3, int, int[], boolean) - Method in class org.jmol.symmetry.Symmetry
- isNotInRange(float) - Method in class org.jmol.viewer.AnimationManager
- isNucleic - Variable in class org.jmol.renderbio.BioShapeRenderer
- isNucleic() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isNucleic() - Method in class org.jmol.modelsetbio.BioPolymer
- isNucleic() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isNucleic() - Method in class org.jmol.smiles.SmilesAtom
- isNucleicMonomer() - Method in class org.jmol.modelset.Group
- isNucleicMonomer() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isNull(String) - Method in class org.jmol.adapter.readers.cif.CifReader
- isNumericAndNonZero() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- isOccupied() - Method in class org.jmol.modelset.Atom
- isoExt - Variable in class org.jmol.script.ScriptExpr
- IsoExt - Class in org.jmol.scriptext
- IsoExt() - Constructor for class org.jmol.scriptext.IsoExt
- isOffsetAbsolute(int) - Static method in class org.jmol.viewer.JC
- IsoFxyReader - Class in org.jmol.jvxl.readers
- IsoFxyReader() - Constructor for class org.jmol.jvxl.readers.IsoFxyReader
- IsoFxyzReader - Class in org.jmol.jvxl.readers
- IsoFxyzReader() - Constructor for class org.jmol.jvxl.readers.IsoFxyzReader
- IsoIntersectAtomReader - Class in org.jmol.jvxl.readers
- IsoIntersectAtomReader() - Constructor for class org.jmol.jvxl.readers.IsoIntersectAtomReader
- IsoIntersectGridReader - Class in org.jmol.jvxl.readers
-
A class to read a linear combination of cube file data.
- IsoIntersectGridReader() - Constructor for class org.jmol.jvxl.readers.IsoIntersectGridReader
- IsoIntersectReader - Class in org.jmol.jvxl.readers
- IsoIntersectReader() - Constructor for class org.jmol.jvxl.readers.IsoIntersectReader
- isOK - Variable in class org.jmol.smiles.SmilesRing
- IsoMepReader - Class in org.jmol.jvxl.readers
- IsoMepReader() - Constructor for class org.jmol.jvxl.readers.IsoMepReader
- isomesh_auto_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- isomeshes - Variable in class org.jmol.shapesurface.Isosurface
- IsoMlpReader - Class in org.jmol.jvxl.readers
- IsoMlpReader() - Constructor for class org.jmol.jvxl.readers.IsoMlpReader
- IsoMOReader - Class in org.jmol.jvxl.readers
- IsoMOReader() - Constructor for class org.jmol.jvxl.readers.IsoMOReader
- isOn - Variable in class org.jmol.shapespecial.Ellipsoid
- isOn - Variable in class org.jmol.util.CommandHistory
- isOpenShell - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- isOpenShell() - Method in class org.jmol.adapter.readers.quantum.NBOParser
- isOpFunc(T) - Static method in class org.jmol.script.ScriptMathProcessor
- IsoPlaneReader - Class in org.jmol.jvxl.readers
- IsoPlaneReader() - Constructor for class org.jmol.jvxl.readers.IsoPlaneReader
- isoPointIndexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isOrderH(int) - Static method in class org.jmol.util.Edge
- isOrderly - Variable in class org.jmol.modelset.Model
-
a flag that, when false, indicates that the model has atoms in different regions of the Atom[] array
- isOrthographic - Variable in class org.jmol.g3d.PrecisionRenderer
- IsoShapeReader - Class in org.jmol.jvxl.readers
- IsoShapeReader() - Constructor for class org.jmol.jvxl.readers.IsoShapeReader
- IsoSolventReader - Class in org.jmol.jvxl.readers
- IsoSolventReader() - Constructor for class org.jmol.jvxl.readers.IsoSolventReader
- IsoSolventReader.Edge - Class in org.jmol.jvxl.readers
- IsoSolventReader.Face - Class in org.jmol.jvxl.readers
- isosurface - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- isosurface - Static variable in class org.jmol.script.T
- isosurface(int) - Method in class org.jmol.scriptext.IsoExt
- Isosurface - Class in org.jmol.shapesurface
- Isosurface() - Constructor for class org.jmol.shapesurface.Isosurface
- isosurfacekey - Static variable in class org.jmol.script.T
- isosurfaceKey - Variable in class org.jmol.viewer.GlobalSettings
- IsosurfaceMesh - Class in org.jmol.shapesurface
- IsosurfaceMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapesurface.IsosurfaceMesh
- isosurfacepropertysmoothing - Static variable in class org.jmol.script.T
- isosurfacePropertySmoothing - Variable in class org.jmol.viewer.GlobalSettings
- isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.T
- isosurfacePropertySmoothingPower - Variable in class org.jmol.viewer.GlobalSettings
- IsosurfaceRenderer - Class in org.jmol.rendersurface
- IsosurfaceRenderer() - Constructor for class org.jmol.rendersurface.IsosurfaceRenderer
- isotopeData - Variable in class org.jmol.quantum.NMRCalculation
-
isotopeData keyed by nnnSym, for example: 1H, 19F, etc.; and also by element name itself: H, F, etc., for default
- isotopeMass - Static variable in class org.jmol.util.Elements
- isotropy() - Method in class org.jmol.util.Tensor
-
isotropy = average of eigenvalues
- isOutput - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- isOutputFile - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- isP1 - Variable in class org.jmol.adapter.writers.CIFWriter
- isPaletteVariable(byte) - Static method in enum org.jmol.c.PAL
- isParallel - Variable in class org.jmol.viewer.Viewer
- isParallel() - Method in class org.jmol.viewer.Viewer
- isParallel(V3, V3) - Method in class org.jmol.symmetry.PointGroup
- isPartial() - Method in class org.jmol.modelset.Bond
- isPass2 - Variable in class org.jmol.render.SticksRenderer
- isPass2 - Variable in class org.jmol.util.GData
- isPathGuide - Variable in class org.jmol.navigate.Navigator
- isPaused - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- isPaused() - Method in interface org.jmol.api.JmolScriptEvaluator
- isPaused() - Method in class org.jmol.script.ScriptEval
- isPauseDelay - Variable in class org.jmol.script.ScriptDelayThread
- isPDB - Variable in class org.jmol.adapter.readers.more.Mol2Reader
- isPDB - Variable in class org.jmol.popup.JmolPopup
- isPdbWithMultipleBonds - Variable in class org.jmol.modelset.Model
- isPending - Variable in class org.jmol.modelset.Measurement
- isPeriodic - Variable in class org.jmol.jvxl.data.VolumeData
- isPeriodic - Variable in class org.jmol.jvxl.readers.Parameters
- isPeriodic - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isPermutation(int[], int[]) - Static method in class org.jmol.inchi.InChIJNI
- isPerpendicular - Variable in class org.jmol.shapespecial.Draw
- isPerpendicular(V3, V3) - Method in class org.jmol.symmetry.PointGroup
- isPhaseColored - Variable in class org.jmol.shapesurface.Isosurface
- isPhonon - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- isPhosphorusOnly - Variable in class org.jmol.renderbio.BioShapeRenderer
- isPickable(IsosurfaceMesh, BS) - Method in class org.jmol.shapesurface.Isosurface
- isPickAtomAssignCharge - Variable in class org.jmol.modelkit.ModelKit
- isPickAtomAssignCharge() - Method in class org.jmol.modelkit.ModelKit
- isPickingMode() - Method in class org.jmol.shape.Labels
- isPlanar(P3, P3, P3, P3) - Method in class org.jmol.shapespecial.Polyhedra
- isPlanarMapping - Variable in class org.jmol.jvxl.readers.IsoFxyReader
- isPlane - Variable in class org.jmol.shapespecial.Draw
- isPlugin - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- isPlugin() - Method in class org.openscience.jmol.app.janocchio.Nmr
- isPocket - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- isPoint3f(int) - Method in class org.jmol.script.ScriptParam
- isPolygonDisplayable(int) - Method in class org.jmol.render.MeshRenderer
- isPolygonDisplayable(int) - Method in class org.jmol.renderspecial.DrawRenderer
- isPolygonDisplayable(Mesh, int) - Static method in class org.jmol.shapespecial.Draw
- isPolyhedral - Variable in class org.jmol.smiles.SmilesGenerator
- isPolymer - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- isPolymer - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- isPolymer - Variable in class org.jmol.adapter.readers.xtal.OptimadeReader
- isPolymer - Variable in class org.jmol.render.CageRenderer
- isPolymer() - Method in interface org.jmol.api.SymmetryInterface
- isPolymer() - Method in class org.jmol.symmetry.Symmetry
- isPolymer() - Method in class org.jmol.util.SimpleUnitCell
- isPositiveOnly - Variable in class org.jmol.jvxl.readers.Parameters
- isPositiveTorsion(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPData
-
Checks the torsion angle and returns true if it is positive
- isPositiveTorsion(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPDataSmiles
-
Checks the torsion angle and returns true if it is positive
- isPossibleHBond(HB, HB) - Static method in enum org.jmol.c.HB
- isPQR - Variable in class org.jmol.adapter.writers.PDBWriter
- isPreliminary - Variable in class org.jmol.minimize.forcefield.Calculations
- isPreviewOnly - Variable in class org.jmol.viewer.Viewer
- isPrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- isPrimitive - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isPrintOnly - Variable in class org.jmol.viewer.Viewer
- isPrintOnly - Variable in class org.openscience.jmol.app.JmolApp
- isPrivate - Variable in class org.jmol.script.ScriptFunction
- isPrivateFunc - Variable in class org.jmol.script.ScriptCompiler
- isPrivateScript - Variable in class org.jmol.script.ScriptCompiler
- isProgressive - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isPromolecular - Variable in class org.jmol.quantum.NciCalculation
- isProperties - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- isProtein() - Method in enum org.jmol.c.STR
- isProtein() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isProtein() - Method in class org.jmol.modelsetbio.AlphaMonomer
- isPS - Variable in class org.jmol.rendercgo.CGORenderer
- isPurine - Variable in class org.jmol.modelsetbio.NucleicMonomer
- isPurine() - Method in class org.jmol.modelset.Atom
- isPurine() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isPurine() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isPurine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isPurine() - Method in class org.jmol.smiles.SmilesAtom
- isPurine() - Method in interface org.jmol.util.Node
- isPurineByID() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isPyMOLsession - Variable in class org.jmol.modelset.ModelLoader
- isPyrimidine - Variable in class org.jmol.modelsetbio.NucleicMonomer
- isPyrimidine() - Method in class org.jmol.modelset.Atom
- isPyrimidine() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isPyrimidine() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isPyrimidine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isPyrimidine() - Method in class org.jmol.smiles.SmilesAtom
- isPyrimidine() - Method in interface org.jmol.util.Node
- isPyrimidineByID() - Method in class org.jmol.modelset.Group
- isQ - Variable in class org.jmol.util.ModulationSet
- isQuantumBasisSupported(char) - Static method in class org.jmol.quantum.QS
- isQueueProcessing() - Method in interface org.jmol.api.JmolScriptManager
- isQueueProcessing() - Method in class org.jmol.script.ScriptManager
- isQuick - Variable in class org.jmol.minimize.Minimizer
- isQuiet - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isQuote(char) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
Includes all possible operator tokens
- isRadical - Variable in class org.jmol.shapesurface.LcaoCartoon
- isRadio - Variable in class org.jmol.awtjs.swing.JRadioButtonMenuItem
- isRawType(int) - Static method in class org.jmol.script.SV
- isReadableAsString(String) - Static method in class org.jmol.viewer.PropertyManager
- isReducedDensity - Variable in class org.jmol.quantum.NciCalculation
- isRenderScalable() - Method in class org.jmol.shapespecial.DrawMesh
- isRepaintPending() - Method in interface org.jmol.api.JmolRepaintManager
- isRepaintPending() - Method in class org.jmol.render.RepaintManager
- isRepaintPending() - Method in class org.jmol.viewer.Viewer
- isReset - Variable in class org.jmol.thread.JmolThread
- isReversed - Variable in class org.jmol.shapespecial.Draw
- isReversed - Variable in class org.jmol.util.ColorEncoder
- isrhombohedral - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
- isRingBond(Lst<BS>, BS, int, int) - Static method in class org.jmol.smiles.SmilesSearch
- isRingCheck - Variable in class org.jmol.smiles.SmilesSearch
- isRLE - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- isRna() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isRna() - Method in class org.jmol.modelsetbio.NucleicMonomer
- isRna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
- isRnaByID() - Method in class org.jmol.modelset.Group
-
group ID-based definition
- isRockets - Variable in class org.jmol.renderbio.RocketRenderer
- isRockets - Variable in class org.jmol.renderbio.RocketsRenderer
- isRotateBond - Variable in class org.jmol.modelkit.ModelKit
- isRotated45 - Variable in class org.jmol.shapespecial.Draw
- isRotateMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- isRubberBandSelect(int) - Method in class org.jmol.viewer.ActionManager
- isRule5Pseudo - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
odd/even toggle for comparisons of Rule5 results that would make for R/S, not r/s, if this flag is false.
- isSameAromaticRing(int, int) - Method in class org.jmol.smiles.SmilesGenerator
- isSameAs(UnitCell) - Method in class org.jmol.symmetry.UnitCell
- isSameAtoms(Dipole, String) - Method in class org.jmol.shapespecial.Dipoles
- isScalar(SV) - Static method in class org.jmol.script.SV
- isScaled - Variable in class org.jmol.shape.Labels
- isScaledAlready - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- isScaleSet - Variable in class org.jmol.shapespecial.DrawMesh
- isScaleSet - Variable in class org.jmol.util.BoxInfo
- isScriptExecuting() - Method in class org.jmol.api.JmolViewer
- isScriptExecuting() - Method in class org.jmol.viewer.Viewer
- isScriptQueued - Variable in class org.jmol.script.ScriptManager
- isScriptQueued() - Method in interface org.jmol.api.JmolScriptManager
- isScriptQueued() - Method in class org.jmol.script.ScriptManager
- isScriptQueued() - Method in class org.jmol.viewer.Viewer
- isScriptType(String) - Static method in class org.jmol.viewer.FileManager
- isSelectAction(int) - Method in class org.jmol.viewer.ActionManager
- isSelected() - Method in interface org.jmol.api.JmolAbstractButton
- isSelected() - Method in interface org.jmol.api.SC
- isSelected() - Method in class org.jmol.awt.AwtSwingComponent
- isSelected() - Method in class org.jmol.awtjs.swing.AbstractButton
- isSelected() - Method in class org.jmol.console.JmolLabel
- isSelected(int) - Method in class org.jmol.viewer.SelectionManager
- isSelected(BS) - Method in class org.jmol.modelset.Group
- isSelected(BS, int) - Method in class org.jmol.util.Tensor
- isSequential - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- isServer - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- isServer() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
- isServer() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- isServer() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- isSet - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- isSet - Variable in class org.jmol.shape.AtomShape
- isSet - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
a flag to prevent finalization of an atom node more than once
- isSetBrace - Variable in class org.jmol.script.ScriptTokenParser
- isSetOrDefine - Variable in class org.jmol.script.ScriptTokenParser
- isSheet() - Method in class org.jmol.modelsetbio.AlphaMonomer
- isSheet() - Method in class org.jmol.modelsetbio.Monomer
- isSheet(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
- isShell - Variable in class org.jmol.render.MeshRenderer
- isShell - Variable in class org.jmol.shape.Mesh
- isShell - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- isShifted - Variable in class org.jmol.awtjs2d.JsG2D
- isShowCommand - Variable in class org.jmol.script.ScriptCompiler
- isShowScriptOutput - Variable in class org.jmol.script.ScriptCompiler
- isSigned - Variable in class org.jmol.popup.GenericPopup
- isSigned - Variable in class org.jmol.util.GenericApplet
- isSignedApplet - Variable in class org.jmol.viewer.Viewer
- isSignedAppletLocal - Variable in class org.jmol.viewer.Viewer
- isSilent - Variable in class org.jmol.jvxl.readers.Parameters
- isSilent - Variable in class org.jmol.minimize.Minimizer
- isSilent - Variable in class org.jmol.script.ScriptCompiler
- isSilent - Variable in class org.jmol.smiles.SmilesSearch
- isSilent - Variable in class org.jmol.viewer.Viewer
- isSilent - Variable in class org.openscience.jmol.app.InputScannerThread
- isSilent - Variable in class org.openscience.jmol.app.JmolApp
- isSimple() - Method in interface org.jmol.api.SymmetryInterface
- isSimple() - Method in class org.jmol.symmetry.Symmetry
- isSingleThreaded - Variable in class org.jmol.viewer.Viewer
- isSingleThreaded() - Method in interface org.jmol.api.GenericPlatform
- isSingleThreaded() - Method in class org.jmol.awt.Platform
- isSingleThreaded() - Method in class org.jmol.awtjs2d.Platform
- isSlab - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- isSlab - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- isSlab - Variable in class org.jmol.adapter.readers.xtal.OptimadeReader
- isSlab - Variable in class org.jmol.adapter.writers.PWMATWriter
- isSlab - Variable in class org.jmol.render.CageRenderer
- isSlab() - Method in interface org.jmol.api.SymmetryInterface
- isSlab() - Method in class org.jmol.symmetry.Symmetry
- isSlab() - Method in class org.jmol.util.SimpleUnitCell
- isSlabbable - Variable in class org.jmol.jvxl.data.JvxlData
- isSlabEnabled - Variable in class org.jmol.export.__RayTracerExporter
- isSmarts - Variable in class org.jmol.smiles.SmilesParser
- isSmarts - Variable in class org.jmol.smiles.SmilesSearch
- isSmiles() - Method in class org.jmol.symmetry.CIPData
-
Subclass identifier
- isSmiles() - Method in class org.jmol.symmetry.CIPDataSmiles
- isSmilesCanonical(String) - Static method in class org.jmol.viewer.JC
- isSMOL - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- isSorting() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- isSp2Ring(int, Node[], BS, BS, float, boolean, boolean) - Static method in class org.jmol.smiles.SmilesAromatic
-
3D-SEARCH aromaticity test.
- isSP3 - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
a flag set false in evaluation of Rule 5 to indicate that there was more than one R/S decision made, so this center cannot be r/s; initially just indicates that the atom has 4 covalent bonds or is trigonal pyriamidal
- isSpaceOrColon(int) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
used by readTable
- isSpaceOrTab(char) - Static method in class org.jmol.script.ScriptCompiler
- isSpartanArchive(String) - Method in class org.jmol.adapter.readers.spartan.SpartanReader
- isSpartanZip(String[]) - Method in class org.jmol.io.JmolUtil
-
check for a Spartan directory.
- isSpecialAssignment - Variable in class org.jmol.script.ScriptMathProcessor
- isSpecialBondType(AtomType, AtomType) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
-
From forcefieldmmff94.cpp (flag BTij) a) single bond between atoms i and j, both i and j are not aromatic and both types have sbmb set in mmffprop.par, or b) between two aromatic atoms, but the bond is not aromatic (e.g.
- isSpherical - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- isSpinFixed - Variable in class org.jmol.viewer.TransformManager
- isSpinInternal - Variable in class org.jmol.viewer.TransformManager
- isSpinSelected - Variable in class org.jmol.viewer.TransformManager
- isSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isSquared - Variable in class org.jmol.jvxl.data.VolumeData
- isSquared - Variable in class org.jmol.jvxl.readers.Parameters
- isSquaredLinear - Variable in class org.jmol.jvxl.readers.Parameters
- isSquaredLinear - Variable in class org.jmol.quantum.MOCalculation
- isSSG - Variable in class org.jmol.symmetry.SpaceGroup
- isStarted() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- isStarted() - Method in interface org.openscience.jmol.app.JmolPlugin
- isStateScript - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- isStateScript - Variable in class org.jmol.script.ScriptContext
- isStateScript - Variable in class org.jmol.script.ScriptEval
- isStateScript - Variable in class org.jmol.script.ScriptTokenParser
- isStateScript() - Method in interface org.jmol.api.JmolScriptEvaluator
- isStateScript() - Method in class org.jmol.script.ScriptEval
- isStaticFunction(String) - Static method in class org.jmol.viewer.Viewer
- isStep - Variable in class org.jmol.navigate.Navigator
- isStepping() - Method in interface org.jmol.api.JmolScriptEvaluator
- isStepping() - Method in class org.jmol.script.ScriptEval
- isStereo() - Method in class org.jmol.modelset.Bond
- isStereoOpposite(int, int, int) - Method in class org.jmol.smiles.SmilesAtom
- isStereoSlave - Variable in class org.jmol.util.GenericApplet
- isStereoSlave - Variable in class org.jmol.viewer.Viewer
-
A flag to indicate that THIS is the right-side panel of a pair of synced applets running a left-right stereo display (that would be piped into a dual-image polarized projector system such as GeoWall).
- isStopped() - Method in interface org.jmol.api.JmolScriptEvaluator
- isStopped() - Method in class org.jmol.script.ScriptEval
- isStringArray(String) - Static method in class org.jmol.util.Escape
- isSubsystem - Variable in class org.jmol.util.ModulationSet
-
subsystems can deliver their own unique unit cell; they are commensurate
- isSupercell - Variable in class org.jmol.modelset.ModelLoader
- isSupercell() - Method in interface org.jmol.api.SymmetryInterface
- isSupercell() - Method in class org.jmol.symmetry.Symmetry
- isSupercell() - Method in class org.jmol.util.SimpleUnitCell
- isSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
- isSurface - Variable in class org.jmol.shapespecial.Dots
- isSurfacePoint - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- isSwingJS - Static variable in class org.jmol.viewer.Viewer
- isSwingJS - Static variable in class org.openscience.jmol.app.Jmol
- isSynced - Variable in class org.jmol.viewer.StatusManager
- isSyntaxAndFileCheck - Variable in class org.jmol.viewer.Viewer
- isSyntaxCheck - Variable in class org.jmol.viewer.Viewer
- isTainted - Variable in class org.jmol.popup.GenericPopup
- isTainted - Variable in class org.jmol.viewer.Viewer
- isTainted() - Method in class org.jmol.modelset.Measurement
- isTainted(BS[], int, int) - Static method in class org.jmol.viewer.StateCreator
- isTarget - Variable in class org.jmol.smiles.SmilesParser
- iStep - Variable in class org.jmol.navigate.Navigator
- iStep - Variable in class org.jmol.thread.MoveToThread
- isTerminal - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
a flag to indicate an atom that has no substituents; a branch end point; typically H or a halogen (F, Cl, Br, I); also set TRUE if there is a problem setting an atom; does not include duplicates
- isTerminator(int) - Method in class org.jmol.script.ScriptTokenParser
-
we allow : and % to have null values
- isTopoAtom - Variable in class org.jmol.smiles.SmilesAtom
- isTopology - Variable in class org.jmol.smiles.SmilesSearch
- isTraceAlpha - Variable in class org.jmol.renderbio.BioShapeRenderer
- isTracker() - Method in class org.jmol.symmetry.CIPData
-
Subclass identifier
- isTracker() - Method in class org.jmol.symmetry.CIPDataTracker
- isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- isTrajectory - Variable in class org.jmol.modelset.Measurement
- isTrajectory - Variable in class org.jmol.modelset.Model
- isTrajectory - Variable in class org.jmol.modelset.ModelLoader
- isTrajectory(int) - Method in class org.jmol.modelset.ModelSet
-
could be the base model or one of the subframes
- isTrajectoryMeasurement(int[]) - Method in class org.jmol.modelset.ModelSet
- isTrajectorySubFrame(int) - Method in class org.jmol.modelset.ModelSet
- isTranslucent - Variable in class org.jmol.render.MeshRenderer
- isTranslucent - Variable in class org.jmol.util.ColorEncoder
- isTranslucentInherit - Variable in class org.jmol.render.MeshRenderer
- istructure - Variable in class org.jmol.adapter.smarter.StructureIterator
- isTrue(Object) - Static method in class org.jmol.modelkit.ModelKit
- isTruncated - Variable in class org.jmol.jvxl.data.JvxlData
- isTryCatch - Variable in class org.jmol.script.ScriptContext
- isTS - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- isTurn(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
- isTwoSided - Variable in class org.jmol.shape.Mesh
- isType(String) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
- isTypeSet - Variable in class org.jmol.adapter.readers.quantum.GamessReader
- isUnitCell - Variable in class org.jmol.popup.JmolPopup
- isUnits(String) - Static method in class org.jmol.modelset.Measurement
- isUnmodulated - Variable in class org.jmol.util.Tensor
- isUserAction(int) - Method in class org.jmol.viewer.binding.Binding
- isUserFunction(String) - Method in class org.jmol.script.ScriptTokenParser
- isUserToken - Variable in class org.jmol.script.ScriptCompiler
- isUserValue - Variable in class org.jmol.shapespecial.Dipole
- isUserValue - Variable in class org.jmol.shapespecial.Dipoles
- isValid - Variable in class org.jmol.bspt.Bspf
- isValid - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
- isValid - Variable in class org.jmol.jvxl.data.JvxlData
- isValid - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- isValid - Variable in class org.jmol.modelset.Measurement
- isValid - Variable in class org.jmol.shape.Mesh
- isValid - Variable in class org.jmol.shapespecial.Dipole
- isValid - Variable in class org.jmol.shapespecial.Draw
- isValid - Variable in class org.jmol.shapespecial.Ellipsoid
- isValid - Variable in class org.jmol.shapespecial.Polyhedron
- isValid() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- isValid() - Method in class org.jmol.modelset.Measurement
- isValid() - Method in class org.jmol.modelset.StateScript
- isValid(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- isValidElementSymbolNoCaseSecondChar(String) - Static method in class org.jmol.adapter.readers.xtal.ShelxReader
- isValidSym1(char) - Static method in class org.jmol.adapter.smarter.Atom
- isValidSym2(char, char) - Static method in class org.jmol.adapter.smarter.Atom
- isValidSymChar1(char) - Static method in class org.jmol.adapter.smarter.Atom
- isValidSymNoCase(char, char) - Static method in class org.jmol.adapter.smarter.Atom
- isVariable(String) - Method in class org.jmol.script.ScriptFunction
- isVariableType(Object) - Static method in class org.jmol.script.SV
-
Must be updated if getVariable is updated!
- isVdw - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- isVector - Variable in class org.jmol.shapespecial.Draw
- isVector - Variable in class org.jmol.shapespecial.DrawMesh
- isVersion3 - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- isVertices - Variable in class org.jmol.shapespecial.Draw
- isVibration - Variable in class org.jmol.popup.JmolPopup
- isVibration(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- isVibrationOn() - Method in class org.jmol.viewer.TransformManager
- isVisible - Variable in class org.jmol.modelset.Measurement
- isVisible - Variable in class org.jmol.shape.Bbcage
- isVisible() - Method in interface org.jmol.api.JmolScriptEditorInterface
- isVisible() - Method in class org.jmol.awtjs.swing.Component
- isVisible(int) - Method in class org.jmol.modelset.Atom
- isVisibleForMe(Atom) - Method in class org.jmol.render.ShapeRenderer
- isVisibleNormix(short) - Method in class org.jmol.render.MeshRenderer
- isWebGL - Variable in class org.jmol.export.___Exporter
- isWebGL - Variable in class org.jmol.popup.GenericPopup
- isWebGL - Variable in class org.jmol.viewer.Viewer
- isWebGL() - Method in interface org.jmol.api.JmolRendererInterface
- isWebGL() - Method in class org.jmol.export.Export3D
- isWebGL() - Method in class org.jmol.g3d.Graphics3D
- isWignerSeitz - Variable in class org.jmol.util.BZone
- isWindowCentered() - Method in class org.jmol.viewer.TransformManager
- isWithin(int) - Method in class org.jmol.modelsetbio.ProteinStructure
- isWithin(P3) - Method in class org.jmol.util.BoxInfo
- isWithinCell(int, P3, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- isWithinFourBonds(Atom, Atom) - Method in class org.jmol.shapesurface.Contact
- isWithinNot - Variable in class org.jmol.shapesurface.Isosurface
- isWithinRadius(T3) - Method in class org.jmol.bspt.CubeIterator
-
checks one Point3f for box-based distance
- isWithinStructure(STR) - Method in class org.jmol.modelset.Group
- isWithinStructure(STR) - Method in class org.jmol.modelsetbio.AlphaMonomer
- isXLowToHigh - Variable in class org.jmol.jvxl.calc.MarchingCubes
- isXLowToHigh - Variable in class org.jmol.jvxl.data.JvxlData
- isXLowToHigh - Variable in class org.jmol.jvxl.readers.Parameters
- isXLowToHigh - Variable in class org.jmol.jvxl.readers.SurfaceReader
- isXmlFile - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- isXtalState() - Method in class org.jmol.modelkit.ModelKit
- isXYZ - Variable in class org.jmol.modelset.ModelSet
- isZapped - Variable in class org.jmol.popup.JmolPopup
- isZeroBased - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- isZipStream(Object) - Method in class org.jmol.viewer.FileManager
- isZoomArea(int) - Method in class org.jmol.viewer.ActionManager
- itemKeys - Variable in class org.jmol.console.KeyJMenu
- itemListener - Variable in class org.jmol.awtjs.swing.AbstractButton
- itemMax - Static variable in class org.jmol.popup.JmolPopup
- itemStateChanged(ItemEvent) - Method in class org.jmol.awt.AwtPopupHelper
- itemStateChanged(ItemEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- itemStateChanged(ItemEvent) - Method in class org.jmol.dialog.Dialog.ExportChoiceListener
- itemStateChanged(ItemEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
- iter - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
- iter - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- iter - Variable in class org.jmol.symmetry.PointGroup
- iterateOverAllNewAtoms(JmolAdapter, Object, boolean) - Method in class org.jmol.modelset.ModelLoader
- iterateOverAllNewBonds(JmolAdapterBondIterator) - Method in class org.jmol.modelset.ModelLoader
- iterateOverAllNewModels(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
- iterateOverAllNewStructures(JmolAdapter, Object) - Method in class org.jmol.modelsetbio.BioResolver
-
Pull in all spans of helix, etc.
- iToken - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
- iToken - Variable in class org.jmol.jvxl.readers.PmeshReader
- iToken - Variable in class org.jmol.script.ScriptContext
- iToken - Variable in class org.jmol.script.ScriptParam
- itokenInfix - Variable in class org.jmol.script.ScriptTokenParser
- iType - Variable in class org.jmol.util.Tensor
- ival(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- iVal - Variable in class org.jmol.minimize.forcefield.FFParam
- iValue(T) - Static method in class org.jmol.script.SV
J
- j - Variable in class org.jmol.quantum.NMRNoeMatrix
- J(double, double) - Static method in class org.jmol.quantum.NMRNoeMatrix
- J_FACTOR - Static variable in class org.jmol.quantum.NMRCalculation
- jaguarLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- JaguarReader - Class in org.jmol.adapter.readers.quantum
-
Jaguar reader tested for the two samples files in CVS.
- JaguarReader - Class in org.jmol.jvxl.readers
- JaguarReader() - Constructor for class org.jmol.adapter.readers.quantum.JaguarReader
- JaguarReader() - Constructor for class org.jmol.jvxl.readers.JaguarReader
- JANA_FWV_Q1_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- JANA_FWV_Q2_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- JANA_FWV_Q3_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- JANA_OCC_ABS_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- JANA_OCC_ABS_O_0 - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- JanaReader - Class in org.jmol.adapter.readers.xtal
-
A reader for Jana M50+M40 file pairs.
- JanaReader() - Constructor for class org.jmol.adapter.readers.xtal.JanaReader
- janaStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- javaname - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- javascript - Static variable in class org.jmol.script.T
- jbr - Variable in class org.jmol.modelset.ModelLoader
- jbr - Variable in class org.jmol.viewer.Viewer
- JButton - Class in org.jmol.awtjs.swing
- JButton() - Constructor for class org.jmol.awtjs.swing.JButton
- jc - Variable in class org.jmol.awt.AwtSwingComponent
- JC - Class in org.jmol.viewer
- JC() - Constructor for class org.jmol.viewer.JC
- JcampdxReader - Class in org.jmol.adapter.readers.more
-
A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS=
acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ... - JcampdxReader() - Constructor for class org.jmol.adapter.readers.more.JcampdxReader
- jcampdxStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- jcd - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- JCH3_AYDIN_GUETHER - Static variable in class org.jmol.quantum.NMRCalculation
- JCH3_NONE - Static variable in class org.jmol.quantum.NMRCalculation
- JCH3_TVAROSKA_TARAVEL - Static variable in class org.jmol.quantum.NMRCalculation
- JCH3_WASYLISHEN_SCHAEFER - Static variable in class org.jmol.quantum.NMRCalculation
- JCheckBox - Class in org.jmol.awtjs.swing
- JCheckBox() - Constructor for class org.jmol.awtjs.swing.JCheckBox
- JCheckBoxMenuItem - Class in org.jmol.awtjs.swing
- JCheckBoxMenuItem() - Constructor for class org.jmol.awtjs.swing.JCheckBoxMenuItem
- jcm - Variable in class org.jmol.viewer.Viewer
- JComboBox<T> - Class in org.jmol.awtjs.swing
- JComboBox(String[]) - Constructor for class org.jmol.awtjs.swing.JComboBox
- JComponent - Class in org.jmol.awtjs.swing
- JComponent(String) - Constructor for class org.jmol.awtjs.swing.JComponent
- JComponentImp - Class in org.jmol.awtjs.swing
-
implementation of a JComponent
- JComponentImp(String) - Constructor for class org.jmol.awtjs.swing.JComponentImp
- JContentPane - Class in org.jmol.awtjs.swing
- JContentPane() - Constructor for class org.jmol.awtjs.swing.JContentPane
- JDialog - Class in org.jmol.awtjs.swing
-
There is really no need here for awt.Dialog.
- JDialog() - Constructor for class org.jmol.awtjs.swing.JDialog
- JDXMOLParser - Class in org.jmol.jsv
-
Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.
- JDXMOLParser() - Constructor for class org.jmol.jsv.JDXMOLParser
- JEditorPane - Class in org.jmol.awtjs.swing
-
A simple implementation of a Swing JTextPane.
- JEditorPane() - Constructor for class org.jmol.awtjs.swing.JEditorPane
- JLabel - Class in org.jmol.awtjs.swing
- JLabel(String) - Constructor for class org.jmol.awtjs.swing.JLabel
- jLabel1 - Variable in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- jLabel1 - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- jLabel1 - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- jLabel2 - Variable in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- jLabel2 - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- jLabel2 - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- jLabel3 - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- jLabel3 - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- jLabel4 - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- jLabel4 - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- jLabel5 - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- jm - Variable in class org.jmol.awt.AwtSwingComponent
- JMenu - Class in org.jmol.awtjs.swing
- JMenu() - Constructor for class org.jmol.awtjs.swing.JMenu
- JMenuItem - Class in org.jmol.awtjs.swing
- JMenuItem(String) - Constructor for class org.jmol.awtjs.swing.JMenuItem
- JMenuItem(String, int) - Constructor for class org.jmol.awtjs.swing.JMenuItem
- JmeReader - Class in org.jmol.adapter.readers.simple
- JmeReader() - Constructor for class org.jmol.adapter.readers.simple.JmeReader
- jmi - Variable in class org.jmol.awt.AwtSwingComponent
- jmol - Static variable in class org.jmol.script.T
- jmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- Jmol - Class in org.jmol.appletjs
-
Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
- Jmol - Class in org.openscience.jmol.app
- Jmol(Map<String, Object>) - Constructor for class org.jmol.appletjs.Jmol
- Jmol(JmolApp, Splash, JFrame, Jmol, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.Jmol
- Jmol() - Static method in class org.jmol.awtjs2d.Platform
- JMOL - Enum constant in enum org.jmol.c.PAL
- JMOL - Enum constant in enum org.jmol.c.VDW
- JMOL - Static variable in class org.jmol.util.ColorEncoder
- JMOL_DIAMETER - Static variable in class org.jmol.shapecgo.CGOMesh
- JMOL_PS - Static variable in class org.jmol.shapecgo.CGOMesh
- JMOL_SCREEN - Static variable in class org.jmol.shapecgo.CGOMesh
- JMOL_UVMAP - Static variable in class org.jmol.shapecgo.CGOMesh
- JmolAbstractButton - Interface in org.jmol.api
- JmolAdapter - Class in org.jmol.api
-
The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.
- JmolAdapter() - Constructor for class org.jmol.api.JmolAdapter
- JmolAdapterAtomIterator - Interface in org.jmol.api
- JmolAdapterBondIterator - Class in org.jmol.api
- JmolAdapterBondIterator() - Constructor for class org.jmol.api.JmolAdapterBondIterator
- JmolAdapterStructureIterator - Class in org.jmol.api
- JmolAdapterStructureIterator() - Constructor for class org.jmol.api.JmolAdapterStructureIterator
- JmolAnnotationParser - Interface in org.jmol.api
- jmolApp - Variable in class org.openscience.jmol.app.JmolData
- jmolApp - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- JmolApp - Class in org.openscience.jmol.app
- JmolApp() - Constructor for class org.openscience.jmol.app.JmolApp
- JmolApp(String[]) - Constructor for class org.openscience.jmol.app.JmolApp
-
standard Jmol application entry point
- JmolApp.OptSort - Class in org.openscience.jmol.app
- JmolAppAPI - Interface in org.jmol.api
- JmolAppConsoleInterface - Interface in org.jmol.api
- JmolAppletInterface - Interface in org.jmol.api
-
This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.
- jmolAppViewer - Variable in class org.openscience.jmol.app.janocchio.NmrPlugin
- JmolAsyncException - Exception in org.jmol.viewer
- JmolAsyncException(String) - Constructor for exception org.jmol.viewer.JmolAsyncException
- jmolAtoms - Variable in class org.jmol.smiles.SmilesStereo
- JmolAudio - Class in org.jmol.util
- JmolAudio() - Constructor for class org.jmol.util.JmolAudio
- JmolAudioPlayer - Interface in org.jmol.api
- jmolBinding - Variable in class org.jmol.viewer.ActionManager
- JmolBinding - Class in org.jmol.viewer.binding
- JmolBinding() - Constructor for class org.jmol.viewer.binding.JmolBinding
- JmolButton - Class in org.jmol.console
- JmolButton(String) - Constructor for class org.jmol.console.JmolButton
- JmolButton(ImageIcon) - Constructor for class org.jmol.console.JmolButton
- JmolCallbackListener - Interface in org.jmol.api
- JmolChimeMessenger - Interface in org.jmol.viewer
- jmolConsole - Variable in class org.jmol.console.ScriptEditor
- JmolConsole - Class in org.jmol.console
- JmolConsole() - Constructor for class org.jmol.console.JmolConsole
- JmolConsole.FileChecker - Class in org.jmol.console
- jmolData - Variable in class org.jmol.modelset.Model
- jmolData - Variable in class org.jmol.modelset.ModelLoader
- JmolData - Class in org.openscience.jmol.app
- JmolData(JmolApp) - Constructor for class org.openscience.jmol.app.JmolData
- JmolDataManager - Interface in org.jmol.api
- JmolDataReader - Class in org.jmol.adapter.readers.pdb
-
JmolData file reader, for a modified PDB format
- JmolDataReader() - Constructor for class org.jmol.adapter.readers.pdb.JmolDataReader
- jmoldataStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- jmolDefaultProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- jmolDefaults - Static variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- jmolDefaultsButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- JmolDialogInterface - Interface in org.jmol.api
- JmolDropEditor - Interface in org.jmol.api
- JmolEnvCalc - Interface in org.jmol.api
- JmolFilesReaderInterface - Interface in org.jmol.api
- JmolFrame - Interface in org.jmol.awt
- jmolFrameType - Variable in class org.jmol.modelset.Model
- JmolGenericPopup - Class in org.jmol.popup
-
An abstract popup class that is instantiated for a given platform and context as one of:
- JmolGenericPopup() - Constructor for class org.jmol.popup.JmolGenericPopup
- JmolGestureServerInterface - Interface in org.jmol.api
- JmolGraphicsInterface - Interface in org.jmol.api
- JmolInChI - Interface in org.jmol.api
- jmolIndex - Variable in class org.jmol.smiles.SmilesAtom
- jmolinjspecview - Static variable in class org.jmol.script.T
- jmolInJSpecView - Variable in class org.jmol.viewer.GlobalSettings
- JmolInstance - Class in org.openscience.jmol.app.webexport
- JmolInstance(JmolViewer, String, int, int, int) - Constructor for class org.openscience.jmol.app.webexport.JmolInstance
- jmolJarPath() - Method in class org.openscience.jmol.app.webexport.WebPanel
-
Returns a string version of the path to Jmol.jar (including the trailing Jmol.jar) decoded using the system default text encoding (usually UTF-8).
- jmolJarURL() - Method in class org.openscience.jmol.app.webexport.WebPanel
- JmolJDXMOLParser - Interface in org.jmol.api
- JmolJDXMOLReader - Interface in org.jmol.api
- JmolJniClientAdapter - Class in org.jmol.multitouch.jni
- JmolJniClientAdapter() - Constructor for class org.jmol.multitouch.jni.JmolJniClientAdapter
- JmolJSpecView - Interface in org.jmol.api
- JmolLabel - Class in org.jmol.console
- JmolLabel(String, int) - Constructor for class org.jmol.console.JmolLabel
- JmolMeasurementClient - Interface in org.jmol.api
- JmolModulationSet - Interface in org.jmol.api
- JmolMolecule - Class in org.jmol.util
-
an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings
- JmolMolecule() - Constructor for class org.jmol.util.JmolMolecule
- JmolMovieCreatorInterface - Interface in org.jmol.api
- JmolMultiTouchAdapter - Interface in org.jmol.multitouch
- JmolMultiTouchClient - Interface in org.jmol.multitouch
- JmolMultiTouchClientAdapter - Class in org.jmol.multitouch
- JmolMultiTouchClientAdapter() - Constructor for class org.jmol.multitouch.JmolMultiTouchClientAdapter
- jmolName - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- JmolNavigatorInterface - Interface in org.jmol.api
- JmolNMRInterface - Interface in org.jmol.api
- jmolObject - Static variable in class org.jmol.viewer.Viewer
- JmolObject - Class in org.jmol.adapter.readers.pymol
-
a class to store rendering information prior to finishing file loading, specifically designed for reading PyMOL PSE files.
- JmolObject(int, String, BS, Object) - Constructor for class org.jmol.adapter.readers.pymol.JmolObject
- jmolObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- jmolPanel - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- jmolPanel - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- JmolPanel - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel(JmolApp, Splash, JFrame, JmolPanel, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel
- JmolPanel.AboutAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ActionChangedListener - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.AnimButton - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.AppCloser - Class in org.openscience.jmol.app.jmolpanel
-
To shutdown when run as an application.
- JmolPanel.AtomSetChooserAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.CloseAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ConsoleAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.CopyImageAction - Class in org.openscience.jmol.app.jmolpanel
-
An Action to copy the current image into the clipboard.
- JmolPanel.CopyScriptAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.CreditsAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ExecuteScriptAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ExitAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ExportAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.GaussianAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.NewAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.NewwinAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.OpenAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.OpenMolAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.OpenPdbAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.OpenUrlAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.PasteClipboardAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.PovrayAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.PrintAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.RecentFilesAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ResizeAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ScriptEditorAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ScriptWindowAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.SurfaceToolAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ToWebAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.UguideAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.ViewMeasurementTableAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.WhatsNewAction - Class in org.openscience.jmol.app.jmolpanel
- JmolPanel.WriteAction - Class in org.openscience.jmol.app.jmolpanel
- JmolParallelProcessor - Interface in org.jmol.api
- JmolPatternMatcher - Interface in org.jmol.api
- JmolPdfCreatorInterface - Interface in org.jmol.api
- JmolPlugin - Interface in org.openscience.jmol.app
- jmolpopup - Variable in class org.jmol.viewer.Viewer
- JmolPopup - Class in org.jmol.popup
-
An abstract popup class that is instantiated for a given platform and context as one of:
- JmolPopup() - Constructor for class org.jmol.popup.JmolPopup
- jmolPosition - Variable in class org.openscience.jmol.app.JmolApp
- JmolPropertyManager - Interface in org.jmol.api
- JmolRendererInterface - Interface in org.jmol.api
- JmolRepaintManager - Interface in org.jmol.api
- JmolResourceHandler - Class in org.openscience.jmol.app.jmolpanel
-
Provides access to resources (for example, strings and images).
- JmolResourceHandler() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- JmolSceneGenerator - Interface in org.jmol.api
- jmolScriptCallbacks - Variable in class org.jmol.viewer.StatusManager
- JmolScriptEditorInterface - Interface in org.jmol.api
- JmolScriptEvaluator - Interface in org.jmol.api
- JmolScriptFunction - Interface in org.jmol.api
- JmolScriptManager - Interface in org.jmol.api
- JmolSelectionListener - Interface in org.jmol.api
-
listen to atom selections in a Jmol Viewer
- JmolSparshClientAdapter - Class in org.jmol.multitouch.sparshui
- JmolSparshClientAdapter() - Constructor for class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- JmolStateCreator - Class in org.jmol.viewer
- JmolStateCreator() - Constructor for class org.jmol.viewer.JmolStateCreator
- JmolStatusListener - Interface in org.jmol.api
- JmolSyncInterface - Interface in org.jmol.api
- jmolTest() - Method in class org.jmol.viewer.Viewer
- JmolThread - Class in org.jmol.thread
- JmolThread() - Constructor for class org.jmol.thread.JmolThread
- JmolToggleButton - Class in org.jmol.console
- JmolToggleButton(ImageIcon) - Constructor for class org.jmol.console.JmolToggleButton
- JmolToJSmolInterface - Interface in org.jmol.api.js
-
methods in JSmol JavaScript accessed in Jmol
- JmolTouchSimulatorInterface - Interface in org.jmol.api
- jmolUnits - Variable in class org.openscience.jmol.app.janocchio.NmrPlugin
- JmolUtil - Class in org.jmol.io
- JmolUtil() - Constructor for class org.jmol.io.JmolUtil
- JmolViewer - Class in org.jmol.api
-
JmolViewer is the main API for the Viewer class.
- JmolViewer() - Constructor for class org.jmol.api.JmolViewer
- JmolWriter - Interface in org.jmol.api
- JmolZipUtilities - Interface in org.jmol.api
- job - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- jobCount - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- join - Static variable in class org.jmol.script.T
- join(Lst<P3[]>) - Method in class org.jmol.util.BZone
- joinList - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- JPanel - Class in org.jmol.awtjs.swing
- JPanel(LayoutManager) - Constructor for class org.jmol.awtjs.swing.JPanel
- JPEG_CONTINUE_STRING - Static variable in class org.jmol.viewer.FileManager
- JPEG_EXTENSIONS - Static variable in class org.jmol.viewer.JC
- jpiDispose() - Method in interface org.jmol.api.GenericMenuInterface
- jpiDispose() - Method in class org.jmol.popup.GenericPopup
- jpiDispose() - Method in class org.jmol.popup.JmolGenericPopup
- jpiDispose() - Method in class org.jmol.popup.JmolPopup
- jpiGetMenuAsObject() - Method in interface org.jmol.api.GenericMenuInterface
- jpiGetMenuAsObject() - Method in class org.jmol.popup.JmolGenericPopup
- jpiGetMenuAsString(String) - Method in interface org.jmol.api.GenericMenuInterface
- jpiGetMenuAsString(String) - Method in class org.jmol.popup.GenericPopup
- jpiInitialize(PlatformViewer, String) - Method in interface org.jmol.api.GenericMenuInterface
- jpiInitialize(PlatformViewer, String) - Method in class org.jmol.popup.JmolGenericPopup
- jpiShow(int, int) - Method in interface org.jmol.api.GenericMenuInterface
- jpiShow(int, int) - Method in class org.jmol.modelkit.ModelKitPopup
- jpiShow(int, int) - Method in class org.jmol.popup.JmolGenericPopup
- jpiUpdateComputedMenus() - Method in interface org.jmol.api.GenericMenuInterface
- jpiUpdateComputedMenus() - Method in class org.jmol.modelkit.ModelKitPopup
- jpiUpdateComputedMenus() - Method in class org.jmol.popup.JmolPopup
- JPopupMenu - Class in org.jmol.awtjs.swing
- JPopupMenu(String) - Constructor for class org.jmol.awtjs.swing.JPopupMenu
- JRadioButtonMenuItem - Class in org.jmol.awtjs.swing
- JRadioButtonMenuItem() - Constructor for class org.jmol.awtjs.swing.JRadioButtonMenuItem
- jsc - Variable in class org.jmol.viewer.Viewer
- jsConsole - Variable in class org.jmol.consolejs.AppletConsole
- JSConsole - Interface in org.jmol.api.js
- JSConsole - Interface in org.jmol.consolejs
- JScrollPane - Class in org.jmol.awtjs.swing
- JScrollPane(JComponent) - Constructor for class org.jmol.awtjs.swing.JScrollPane
- jsCylinder(Object, String, boolean, P3, P3, Object[]) - Method in class org.jmol.export.JSExporter
- jsDocumentBase - Static variable in class org.jmol.viewer.Viewer
- jsEndExport(Object) - Method in class org.jmol.export.JSExporter
- jsEval(String) - Method in class org.jmol.viewer.StatusManager
- jsEval(String) - Method in class org.jmol.viewer.Viewer
- jsEvalSV(String) - Method in class org.jmol.viewer.Viewer
- JSExporter - Class in org.jmol.export
-
A class to output WebGL graphics.
- JSExporter() - Constructor for class org.jmol.export.JSExporter
- jsExporter3D - Variable in class org.jmol.viewer.Viewer
- JSFile - Class in org.jmol.awtjs2d
-
A class that mimics java.io.File
- JSFile(String) - Constructor for class org.jmol.awtjs2d.JSFile
- JSFont - Class in org.jmol.awtjs2d
-
methods required by Jmol that access java.awt.Font private to org.jmol.awtjs2d
- JSFont() - Constructor for class org.jmol.awtjs2d.JSFont
- JsG2D - Class in org.jmol.awtjs2d
-
generic 2D drawing methods -- JavaScript version
- JsG2D() - Constructor for class org.jmol.awtjs2d.JsG2D
- jsInitExport(Object) - Method in class org.jmol.export.JSExporter
- JSJmolPopup - Class in org.jmol.awtjs2d
- JSJmolPopup() - Constructor for class org.jmol.awtjs2d.JSJmolPopup
-
The main popup window for the applet -- as JavaScript
- jsl - Variable in class org.jmol.viewer.StatusManager
- JSModelKitPopup - Class in org.jmol.awtjs2d
- JSModelKitPopup() - Constructor for class org.jmol.awtjs2d.JSModelKitPopup
- JSmolAppletObject - Interface in org.jmol.api.js
- jsObjectGetMember(Object[], String) - Method in class org.jmol.adapter.readers.xml.XmlReader
- json - Static variable in class org.jmol.script.T
- jsonArrayContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- jsonContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- JsonNioClient - Interface in org.openscience.jmol.app.jsonkiosk
-
a client of a JsonNioService -- just needs notices of the service shutting down or indicating that a banner needs to be changed.
- JsonNioClient.TouchHandler - Class in org.openscience.jmol.app.jsonkiosk
- JsonNioClientThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioClientThread
- JsonNioServer - Interface in org.openscience.jmol.app.jsonkiosk
- JsonNioServerThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
- JsonNioService - Class in org.openscience.jmol.app.jsonkiosk
-
A class for interacting with Jmol over local sockets.
- JsonNioService() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService
- JsonNioService.JsonNioClientThread - Class in org.openscience.jmol.app.jsonkiosk
- JsonNioService.JsonNioServerThread - Class in org.openscience.jmol.app.jsonkiosk
- jsonParser - Variable in class org.jmol.viewer.Viewer
- JSONReader - Class in org.jmol.adapter.readers.simple
- JSONReader() - Constructor for class org.jmol.adapter.readers.simple.JSONReader
- jsonStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- JSONWriter - Class in org.jmol.util
- JSONWriter() - Constructor for class org.jmol.util.JSONWriter
- jsParams - Variable in class org.jmol.viewer.Viewer
- JSpecView - Class in org.jmol.jsv
- JSpecView() - Constructor for class org.jmol.jsv.JSpecView
- jSpecViewForceNew - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- jSpecViewFrame - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- JSplitPane - Class in org.jmol.awtjs.swing
- JSplitPane(int) - Constructor for class org.jmol.awtjs.swing.JSplitPane
- JSPopupHelper - Class in org.jmol.awtjs2d
-
For menus, popup-related awt/swing class references are in this file.
- JSPopupHelper(GenericPopup) - Constructor for class org.jmol.awtjs2d.JSPopupHelper
- jsSphere(Object, String, boolean, T3, Object[]) - Method in class org.jmol.export.JSExporter
- jsSurface(Object, T3[], T3[], int[][], int, int, int, BS, int, int, int[], int[]) - Method in class org.jmol.export.JSExporter
- jsTriangle(Object, int, T3, T3, T3) - Method in class org.jmol.export.JSExporter
- jsv - Variable in class org.jmol.viewer.Viewer
- JSV_CLOSE - Static variable in class org.jmol.viewer.JC
- JSV_NOT - Static variable in class org.jmol.viewer.JC
- JSV_SELECT - Static variable in class org.jmol.viewer.JC
- JSV_SEND_C13SIMULATE - Static variable in class org.jmol.viewer.JC
- JSV_SEND_H1SIMULATE - Static variable in class org.jmol.viewer.JC
- JSV_SEND_JDXMOL - Static variable in class org.jmol.viewer.JC
- JSV_SETPEAKS - Static variable in class org.jmol.viewer.JC
- JSV_STRUCTURE - Static variable in class org.jmol.viewer.JC
- JSVInterface - Interface in org.jmol.api
-
and interface for JSpecView for the Jmol application
- JTable - Class in org.jmol.awtjs.swing
- JTable(AbstractTableModel) - Constructor for class org.jmol.awtjs.swing.JTable
- JTextField - Class in org.jmol.awtjs.swing
- JTextField(String) - Constructor for class org.jmol.awtjs.swing.JTextField
- JTextPane - Class in org.jmol.awtjs.swing
-
A simple implementation of a Swing JTextPane.
- JTextPane() - Constructor for class org.jmol.awtjs.swing.JTextPane
- jumpBestFrame() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- jumpBestFrameAction - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- JumpBestFrameAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.JumpBestFrameAction
- junk - Variable in class org.jmol.thread.JmolThread
- justifymeasurements - Static variable in class org.jmol.script.T
- justifyMeasurements - Variable in class org.jmol.viewer.GlobalSettings
- justOneModel - Variable in class org.jmol.modelset.MeasurementData
- Jvxl - Class in org.openscience.jvxl
- Jvxl() - Constructor for class org.openscience.jvxl.Jvxl
- JVXL_VERSION - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- JVXL_VERSION_XML - Static variable in class org.jmol.jvxl.data.JvxlCoder
- JVXL_VERSION1 - Static variable in class org.jmol.jvxl.data.JvxlCoder
- jvxlAppendCharacter2(float, float, float, int, int, SB, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlAppendCommandState(SB, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlAppendEncodedNumber(SB, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- JvxlCoder - Class in org.jmol.jvxl.data
- JvxlCoder() - Constructor for class org.jmol.jvxl.data.JvxlCoder
- jvxlColorData - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlColorDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlColorEncodingRead - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlCompressString(String, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlCreateColorData(JvxlData, float[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlCreateHeader(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
Creates a two-line header for the XJVXL file.
- jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlCutoffRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlData - Variable in class org.jmol.shape.MeshCollection
- jvxlData - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- JvxlData - Class in org.jmol.jvxl.data
- JvxlData() - Constructor for class org.jmol.jvxl.data.JvxlData
- jvxlDataIs2dContour - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlDataIs2dContour - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlDataIsPrecisionColor - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlDecodeBitSet(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlDecodeBitSetRange(String, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlDecodeContourData(JvxlData, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlDecodeTriangleData(String, String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
decode triangle data found within
element as created with jvxlEncodeTriangleData (see above) - jvxlDecodeVertexData(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
decode vertex data found within
element as created by jvxlEncodeVertexData (see above) - jvxlDecompressString(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlEdgeData - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlEdgeDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlEncodeBitSet(BS) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlEncodeBitSet0(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlEncodeBitSetBuffer(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlEncodeContourData(Lst<Object>[], SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
contour data are appended to a string buffer in the form of a
triangle bitset data triangle bitset data triangle bitset data ... - jvxlExcluded - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlFileHeaderBuffer - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlFileMessage - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlFileSource - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlFileTitle - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlFractionAsCharacter(float) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlFractionAsCharacterRange(float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlFractionFromCharacter(int, int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlFractionFromCharacter2(int, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlGetData(VoxelDataCreator, Parameters, VolumeData, String[], Lst<P3>, float[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
- jvxlGetFile(JvxlData, MeshData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlGetFile(VolumeData, JvxlData, String[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlGetInfo(JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlGetInfoData(JvxlData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlGetNextFraction(int, int, float) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlNSurfaceInts - Variable in class org.jmol.jvxl.readers.SurfaceReader
- jvxlParseEncodedInt(String, int, int, int[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlPlane - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlReadDefinitionLine(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- JvxlReader - Class in org.jmol.jvxl.readers
- JvxlReader() - Constructor for class org.jmol.jvxl.readers.JvxlReader
- jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlReader
- jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
-
"edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge.
- jvxlReadSurfaceInfo() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlSetColorRanges(float, float, float, float, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlSetCompressionRatio(SB, JvxlData, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- jvxlSkipDataBlock(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- jvxlSurfaceData - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlUpdateInfo() - Method in class org.jmol.jvxl.readers.SurfaceReader
- jvxlUpdateInfo(String[], long) - Method in class org.jmol.jvxl.data.JvxlData
- jvxlValueAsCharacter(float, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlValueFromCharacter2(int, int, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
- jvxlVolumeDataXml - Variable in class org.jmol.jvxl.data.JvxlData
- jvxlVoxelBitSet - Variable in class org.jmol.jvxl.readers.SurfaceReader
- JvxlWrite - Class in org.openscience.jvxl.simplewriter
- JvxlWrite() - Constructor for class org.openscience.jvxl.simplewriter.JvxlWrite
- JvxlXmlReader - Class in org.jmol.jvxl.readers
- JvxlXmlReader() - Constructor for class org.jmol.jvxl.readers.JvxlXmlReader
- jzt - Variable in class org.jmol.viewer.Viewer
- jzu - Variable in class org.jmol.viewer.FileManager
K
- k - Variable in class org.jmol.quantum.NMRNoeMatrix
- ka - Variable in class org.jmol.minimize.MinAngle
- kb - Variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
- kb - Variable in class org.jmol.minimize.forcefield.UFFDistanceCalc
- KCAL_TO_KJ - Static variable in class org.jmol.minimize.forcefield.Calculations
- KCAL22 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- KCAL332 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- KCAL44 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- KCAL6 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- KCAL644 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- keep_alive - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- keepChars - Variable in class org.jmol.adapter.readers.xml.XmlReader
- keepCharsList - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- keepRunning - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
- key - Variable in class org.jmol.adapter.readers.cif.CifReader
- key - Variable in class org.jmol.console.KeyJCheckBox
- key - Variable in class org.jmol.console.KeyJCheckBoxMenuItem
- key - Variable in class org.jmol.console.KeyJMenu
- key - Variable in class org.jmol.console.KeyJMenuItem
- key - Variable in class org.jmol.console.KeyJRadioButtonMenuItem
- key - Variable in class org.jmol.minimize.forcefield.Calculation
- key - Variable in class org.jmol.minimize.MinObject
- key - Variable in class org.jmol.modelset.LabelToken
- key - Variable in class org.jmol.script.FileLoadThread
- key - Variable in class org.jmol.util.Int2IntHashEntry
- KEY_BNDK - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- KEY_LIST - Static variable in class org.jmol.shapecgo.CGOMesh
- KEY_OOP - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- KEY_PBCI - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- KEY_SBDEF - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- KEY_VDW - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- key0 - Variable in class org.jmol.adapter.readers.cif.CifReader
- key2col - Variable in class org.jmol.adapter.readers.cif.CifReader
- keyBuffer - Variable in class org.jmol.awt.Mouse
- keyBuffer - Variable in class org.jmol.awtjs2d.Mouse
- KeyJCheckBox - Class in org.jmol.console
- KeyJCheckBox(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBox
- KeyJCheckBoxMenuItem - Class in org.jmol.console
- KeyJCheckBoxMenuItem(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBoxMenuItem
- KeyJMenu - Class in org.jmol.console
- KeyJMenu(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenu
- KeyJMenuItem - Class in org.jmol.console
- KeyJMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenuItem
- KeyJRadioButtonMenuItem - Class in org.jmol.console
- KeyJRadioButtonMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJRadioButtonMenuItem
- keyMap - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- keyMap - Static variable in class org.jmol.shapecgo.CGOMesh
- keyPressed(int, int) - Method in interface org.jmol.api.EventManager
- keyPressed(int, int) - Method in class org.jmol.viewer.ActionManager
-
called by MouseManager.keyPressed
- keyPressed(KeyEvent) - Method in class org.jmol.awt.Mouse
- keyPressed(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
- keyPressed(KeyEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- keyProcessing - Variable in class org.jmol.viewer.ActionManager
- keyReleased(int) - Method in interface org.jmol.api.EventManager
- keyReleased(int) - Method in class org.jmol.viewer.ActionManager
- keyReleased(KeyEvent) - Method in class org.jmol.awt.Mouse
- keyReleased(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
- keyReleased(KeyEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- keys - Static variable in class org.jmol.script.T
- keys - Static variable in class org.jmol.symmetry.SymmetryDesc
- keyTyped(int, int) - Method in interface org.jmol.api.EventManager
- keyTyped(int, int) - Method in class org.jmol.viewer.ActionManager
- keyTyped(KeyEvent) - Method in class org.jmol.awt.Mouse
- keyTyped(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
- keyTyped(KeyEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
-
Custom key event processing for command 0 implementation.
- keyword - Variable in class org.jmol.export.UseTable
- keyword - Static variable in class org.jmol.script.T
- keyXy - Variable in class org.jmol.shapesurface.Isosurface
- kind - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- KinemageReader - Class in org.jmol.jvxl.readers
- KinemageReader() - Constructor for class org.jmol.jvxl.readers.KinemageReader
- kinEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- kioskFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- KioskFrame - Class in org.openscience.jmol.app.jsonkiosk
-
A borderless rectangle, like the applet, that contains the application for use in kiosk-style displays, as for example projected on the wall as in http://molecularPlayground.org
- KioskFrame(int, int, int, int, JPanel) - Constructor for class org.openscience.jmol.app.jsonkiosk.KioskFrame
- KNOWN_TYPES - Static variable in class org.jmol.util.Tensor
- knownGroupID(String) - Static method in class org.jmol.modelsetbio.BioResolver
- kvec - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
L
- label - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- label - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- label - Static variable in class org.jmol.script.T
- label - Variable in class org.jmol.shapespecial.Ellipsoid
- label - Variable in class org.openscience.jmol.app.janocchio.FrameCounter
- label - Variable in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- label - Variable in class org.openscience.jmol.app.janocchio.LabelSetter
- label - Variable in class org.openscience.jmol.app.janocchio.MyFileFilter
- label - Variable in class org.openscience.jmol.app.janocchio.PopulationDisplay
- LABEL - Static variable in class org.jmol.adapter.readers.cif.CifReader
- LABEL - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- label_anchor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- label_angle_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- LABEL_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- LABEL_ATOM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- LABEL_CENTERED - Static variable in class org.jmol.viewer.JC
- label_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- LABEL_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- LABEL_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
- LABEL_DEFAULT_OFFSET - Static variable in class org.jmol.viewer.JC
- LABEL_DEFAULT_X_OFFSET - Static variable in class org.jmol.viewer.JC
- LABEL_DEFAULT_Y_OFFSET - Static variable in class org.jmol.viewer.JC
- label_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- label_dihedral_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- label_distance_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- LABEL_EXPLICIT - Static variable in class org.jmol.viewer.JC
- LABEL_FLAGS - Static variable in class org.jmol.viewer.JC
- LABEL_FLAGX_OFFSET_SHIFT - Static variable in class org.jmol.viewer.JC
- LABEL_FLAGY_OFFSET_SHIFT - Static variable in class org.jmol.viewer.JC
- label_font_id - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- LABEL_MAXIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
- LABEL_MINIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
- LABEL_OFFSET_MASK - Static variable in class org.jmol.viewer.JC
- LABEL_OFFSET_MAX - Static variable in class org.jmol.viewer.JC
- label_outline_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- LABEL_POINTER_BACKGROUND - Static variable in class org.jmol.viewer.JC
- LABEL_POINTER_FLAGS - Static variable in class org.jmol.viewer.JC
- LABEL_POINTER_NONE - Static variable in class org.jmol.viewer.JC
- LABEL_POINTER_ON - Static variable in class org.jmol.viewer.JC
- label_position - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- LABEL_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- label_shadow_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- label_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- LABEL_ZPOS_FLAGS - Static variable in class org.jmol.viewer.JC
- LABEL_ZPOS_FRONT - Static variable in class org.jmol.viewer.JC
- LABEL_ZPOS_GROUP - Static variable in class org.jmol.viewer.JC
- label1 - Variable in class org.jmol.console.GenericConsole
- labelArray - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- labelArray - Variable in class org.openscience.jmol.app.janocchio.LabelSetter
- labelArray - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- labelArray - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- labelAsymList - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- labelBoxes - Variable in class org.jmol.shape.Labels
- labelColix - Variable in class org.jmol.modelset.Measurement
- labelColix - Variable in class org.jmol.render.LabelsRenderer
- labelColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- labeler - Variable in class org.jmol.modelset.AtomCollection
- labelFontId - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- labelFormat - Variable in class org.jmol.shape.Hover
- labelMode - Variable in class org.jmol.viewer.ActionManager
- labelNmrAction - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- LabelNmrAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.LabelNmrAction
- labelpointerwidth - Static variable in class org.jmol.script.T
- labelPointerWidth - Variable in class org.jmol.viewer.GlobalSettings
- labelPosition - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- labelPosition0 - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- labels - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- labels - Static variable in class org.jmol.console.GenericConsole
- labels - Variable in class org.jmol.dssx.DSSP
- labels - Variable in class org.jmol.jvxl.readers.MrcBinaryReader
- labels - Variable in class org.jmol.shape.Axes
- labels - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
- Labels - Class in org.jmol.shape
- Labels() - Constructor for class org.jmol.shape.Labels
- labelSetter - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- LabelSetter - Class in org.openscience.jmol.app.janocchio
- LabelSetter(NMR_Viewer, NoeTable, CoupleTable) - Constructor for class org.openscience.jmol.app.janocchio.LabelSetter
- labelSize - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- LabelsRenderer - Class in org.jmol.render
- LabelsRenderer() - Constructor for class org.jmol.render.LabelsRenderer
- labelsXn - Static variable in class org.jmol.symmetry.SymmetryOperation
- labelsXnSub - Static variable in class org.jmol.symmetry.SymmetryOperation
- labelsXYZ - Static variable in class org.jmol.symmetry.SymmetryOperation
- LabelToken - Class in org.jmol.modelset
- LabelToken() - Constructor for class org.jmol.modelset.LabelToken
- labelTokenIds - Static variable in class org.jmol.modelset.LabelToken
- labelTokenParams - Static variable in class org.jmol.modelset.LabelToken
- ladder - Variable in class org.jmol.dssx.Bridge
- language - Variable in class org.jmol.i18n.GT
- language - Variable in class org.jmol.i18n.Language
- language - Static variable in class org.jmol.script.T
- language - Variable in class org.jmol.util.GenericApplet
- language - Static variable in class org.openscience.jmol.app.jmolpanel.GuiMap
- Language - Class in org.jmol.i18n
- Language(String, String, String, boolean) - Constructor for class org.jmol.i18n.Language
- languageList - Static variable in class org.jmol.i18n.GT
- languagetranslation - Static variable in class org.jmol.script.T
- last - Variable in class org.jmol.awtjs.swing.JPanel
- last - Static variable in class org.jmol.script.T
- LAST - Static variable in class org.jmol.util.MeshCapper
- LAST_AVAILABLE_COLIX - Static variable in class org.jmol.util.C
- lastAltLoc - Variable in class org.jmol.adapter.readers.cif.CifReader
- lastAltLoc - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- lastAssignedString - Variable in class org.jmol.script.ScriptMathProcessor
- lastAtom - Variable in class org.jmol.jvxl.readers.KinemageReader
- lastAtomIndex - Variable in class org.jmol.modelset.Group
- lastBasisID - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- lastCenter - Variable in class org.jmol.modelkit.ModelKit
- lastChainAtom - Variable in class org.jmol.smiles.SmilesSearch
- lastColix - Variable in class org.jmol.util.MeshSurface
- lastColor - Variable in class org.jmol.util.MeshSurface
- lastConnections - Variable in class org.jmol.viewer.StateManager
- lastContext - Variable in class org.jmol.viewer.StateManager
- lastCoordinates - Variable in class org.jmol.viewer.StateManager
- lastData - Variable in class org.jmol.viewer.Viewer
- lastDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
- lastDisorderAssembly - Variable in class org.jmol.adapter.readers.cif.CifReader
- lastElement - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- lastElement() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- lastElementType - Variable in class org.jmol.modelkit.ModelKit
- lastError - Static variable in exception org.jmol.smiles.InvalidSmilesException
- lastFileType - Variable in class org.jmol.viewer.FileManager
- lastFlowCommand - Variable in class org.jmol.script.ScriptTokenParser
- lastFrameDelay - Variable in class org.jmol.viewer.AnimationManager
- lastFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
- lastFrameIndex - Variable in class org.jmol.viewer.AnimationManager
- lastFramePainted - Variable in class org.jmol.viewer.AnimationManager
- lastFullPathName - Variable in class org.jmol.viewer.FileManager
- lastGaussianPtr - Variable in class org.jmol.quantum.MOCalculation
- lastGroup - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- lastIndex - Variable in class org.jmol.modelset.MeasurementPending
- lastIndex - Variable in class org.jmol.symmetry.CIPDataTracker
- lastIndices - Variable in class org.jmol.console.ScriptEditor
- lastInfo - Variable in class org.jmol.symmetry.CIPDataTracker
- lastInfo - Static variable in class org.jmol.symmetry.SpaceGroup
- lastInsertion - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- lastLogTime - Variable in class org.jmol.multitouch.ActionManagerMT
- lastMark - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- lastMoData - Variable in class org.jmol.adapter.readers.quantum.MOReader
- lastModel - Variable in class org.jmol.jsv.JDXMOLParser
- lastModel - Variable in class org.jmol.modelset.ModelLoader
- lastModelIndex - Variable in class org.jmol.atomdata.AtomData
- lastModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- lastModelPainted - Variable in class org.jmol.viewer.AnimationManager
- lastModelSet - Variable in class org.jmol.modelkit.ModelKit
- lastMotionEventNumber - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- lastName - Variable in class org.jmol.adapter.readers.xtal.CgdReader
- lastNameAsGiven - Variable in class org.jmol.viewer.FileManager
- lastOffset - Variable in class org.jmol.modelkit.ModelKit
- lastOpened - Static variable in class org.jmol.console.ScriptEditor
- lastOrientation - Variable in class org.jmol.viewer.StateManager
- lastPicked - Variable in class org.jmol.shape.Labels
- lastPressTime - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- lastQPt - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- lastRawColor - Variable in class org.jmol.g3d.Graphics3D
- lastRepaintTime - Variable in class org.jmol.thread.JmolThread
- lastScene - Variable in class org.jmol.viewer.StateManager
- lastSelected - Variable in class org.jmol.viewer.StateManager
- lastSequenceNumber - Variable in class org.jmol.adapter.readers.more.Mol2Reader
- lastSetH - Variable in class org.jmol.modelsetbio.BioResolver
- lastShape - Variable in class org.jmol.viewer.StateManager
- lastSimulate - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- lastSourceSerial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- lastSpaceGroupName - Variable in class org.jmol.adapter.readers.cif.CifReader
- lastState - Variable in class org.jmol.viewer.StateManager
- lastTargetSerial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- lastToken - Variable in class org.jmol.script.ScriptTokenParser
- latestMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- LATT - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- lattice - Static variable in class org.jmol.script.T
- lattice - Variable in class org.jmol.shape.Mesh
- LATTICE_VECTOR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- latticeCells - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- latticeCode - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
- latticeCode - Variable in class org.jmol.symmetry.HallInfo
- latticeConstant - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- latticeExtension - Variable in class org.jmol.symmetry.HallInfo
- latticeOffset - Variable in class org.jmol.render.MeshRenderer
- latticeOnly - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- latticeOp - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- latticeOp - Variable in class org.jmol.symmetry.SpaceGroup
- latticeParameter - Variable in class org.jmol.symmetry.SpaceGroup
- latticePts - Variable in class org.jmol.util.BZone
- latticeScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- latticeShift(P3, P3) - Method in class org.jmol.symmetry.SpaceGroupFinder
-
Look for true {1 0 0}, {0 1 0}, {0 0 1} difference.
- latticeTranslationData - Static variable in class org.jmol.symmetry.HallTranslation
- latticeType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- latticeType - Variable in class org.jmol.symmetry.SpaceGroup
- latticeType - Variable in class org.jmol.symmetry.SymmetryInfo
- latticeUnits - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- latticeVectorPtr - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- lattvecs - Variable in class org.jmol.adapter.readers.cif.CifReader
- lattvecs - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- launchMainFrame() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- launchMainFrame() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- LayoutManager - Class in org.jmol.awtjs.swing
- LayoutManager() - Constructor for class org.jmol.awtjs.swing.LayoutManager
- layoutWindow(Container) - Method in class org.jmol.console.ScriptEditor
- layoutWindow(Container) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- layoutWindow(String) - Method in class org.jmol.console.AppletConsole
- layoutWindow(String) - Method in class org.jmol.console.GenericConsole
- layoutWindow(String) - Method in class org.jmol.consolejs.AppletConsole
- layoutWindow(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- lcaocartoon - Static variable in class org.jmol.script.T
- lcaoCartoon() - Method in class org.jmol.scriptext.IsoExt
- LcaoCartoon - Class in org.jmol.shapesurface
- LcaoCartoon() - Constructor for class org.jmol.shapesurface.LcaoCartoon
- LcaoCartoonRenderer - Class in org.jmol.rendersurface
- LcaoCartoonRenderer() - Constructor for class org.jmol.rendersurface.LcaoCartoonRenderer
- lcaoColorNeg - Variable in class org.jmol.shapesurface.LcaoCartoon
- lcaoColorPos - Variable in class org.jmol.shapesurface.LcaoCartoon
- lcaoDir - Variable in class org.jmol.shapesurface.Isosurface
- lcaoID - Variable in class org.jmol.shapesurface.LcaoCartoon
- lcaoScale - Variable in class org.jmol.shapesurface.LcaoCartoon
- lcaoTranslucent - Variable in class org.jmol.shapesurface.LcaoCartoon
- lcaoTranslucentLevel - Variable in class org.jmol.shapesurface.LcaoCartoon
- lcaoType - Variable in class org.jmol.jvxl.readers.Parameters
- leadatom - Static variable in class org.jmol.script.T
- leadAtomIndex - Variable in class org.jmol.modelset.Group
- leadAtomIndices - Variable in class org.jmol.modelsetbio.BioPolymer
- leadAtomIndices - Variable in class org.jmol.renderbio.BioShapeRenderer
- leadAtomIndices - Variable in class org.jmol.shapebio.BioShape
- LEADER_CHAR_MAX - Static variable in class org.jmol.adapter.smarter.Resolver
- leadMidpoints - Variable in class org.jmol.modelsetbio.BioPolymer
- leadPoints - Variable in class org.jmol.modelsetbio.BioPolymer
- leaf - Variable in class org.jmol.bspt.CubeIterator
- Leaf - Class in org.jmol.bspt
-
A leaf of Point3f objects in the bsp tree
- Leaf(Bspt, Leaf, int) - Constructor for class org.jmol.bspt.Leaf
- leafCountMax - Static variable in class org.jmol.bspt.Bspt
- leafIndex - Variable in class org.jmol.bspt.CubeIterator
- left - Variable in class org.jmol.awtjs.swing.Insets
- left - Variable in class org.jmol.awtjs.swing.JSplitPane
- left - Static variable in class org.jmol.script.T
- left - Variable in class org.jmol.util.Modulation
- LEFT - Static variable in class org.jmol.awtjs.swing.SwingConstants
- LEFT - Static variable in class org.jmol.viewer.binding.Binding
- LEFT_DRAGGED - Variable in class org.jmol.viewer.ActionManager
- LEFT_HELIX - Enum constant in enum org.jmol.modelsetbio.AlphaPolymer.Code
- LEFT_TURN - Enum constant in enum org.jmol.modelsetbio.AlphaPolymer.Code
- leftAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- leftbrace - Static variable in class org.jmol.script.T
- leftdivide - Static variable in class org.jmol.script.T
- leftOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- leftparen - Static variable in class org.jmol.script.T
- leftPlane - Variable in class org.openscience.jmol.app.surfacetool.Slice
- leftsquare - Static variable in class org.jmol.script.T
- LEG_DISP_AXIS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_DISP_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_DISP_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_DISP_ORDER - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_OCC_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_OCC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_OCC_ORDER - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_U_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_U_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_U_ORDER - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- LEG_U_TENS - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- legacy_mouse_zoom - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- legacy_vdw_radii - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- legacyautobonding - Static variable in class org.jmol.script.T
- legacyAutoBonding - Variable in class org.jmol.viewer.GlobalSettings
- legacyhaddition - Static variable in class org.jmol.script.T
- legacyHAddition - Variable in class org.jmol.viewer.GlobalSettings
- legacyjavafloat - Static variable in class org.jmol.script.T
- legacyJavaFloat - Variable in class org.jmol.viewer.GlobalSettings
- legacyResolver - Static variable in class org.jmol.viewer.JC
- legendre - Static variable in class org.jmol.util.Modulation
- legendres - Variable in class org.jmol.adapter.readers.cif.MSRdr
- len - Variable in class org.jmol.adapter.writers.XSFWriter
- LEN - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- length - Static variable in class org.jmol.script.T
- length - Variable in class org.jmol.shapespecial.Draw
- length - Variable in class org.openscience.jvxl.MonitorInputStream
- length() - Method in interface org.jmol.api.GenericFileInterface
- length() - Method in class org.jmol.awtjs2d.JSFile
- lengths - Variable in class org.jmol.shapespecial.Ellipsoid
- lengthsFreeEnum - Variable in class org.jmol.util.TempArray
- lengthsFreePoints - Variable in class org.jmol.util.TempArray
- lengthsFreeScreens - Variable in class org.jmol.util.TempArray
- lengthUnitFactors - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
- lengthUnitIds - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
- lenLine - Variable in class org.jmol.adapter.readers.more.MdCrdReader
- LEVEL_DEBUG - Static variable in class org.jmol.util.Logger
- LEVEL_DEBUGHIGH - Static variable in class org.jmol.util.Logger
- LEVEL_ERROR - Static variable in class org.jmol.util.Logger
- LEVEL_FATAL - Static variable in class org.jmol.util.Logger
- LEVEL_INFO - Static variable in class org.jmol.util.Logger
- LEVEL_MAX - Static variable in class org.jmol.util.Logger
- LEVEL_WARN - Static variable in class org.jmol.util.Logger
- LEXICAL_COMPARATOR - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- lexpNoes - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- ligandModels - Variable in class org.jmol.viewer.Viewer
- ligandModelSet - Variable in class org.jmol.viewer.Viewer
- light - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- light_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- light2 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- light3 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- light4 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- light5 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- light6 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- light7 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- light8 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- light9 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- lighting - Variable in class org.jmol.export._TachyonExporter
- lighting - Static variable in class org.jmol.script.T
- lighting - Variable in class org.jmol.shape.Mesh
- lighting - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- lightSource - Variable in class org.jmol.export.___Exporter
- lightSource - Variable in class org.jmol.util.Shader
- LIME - Static variable in class org.jmol.util.C
- line - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- line - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- line - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- line - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- line - Variable in class org.jmol.adapter.readers.molxyz.V3000Rdr
- line - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- line - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- line - Variable in class org.jmol.jsv.JDXMOLParser
- line - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
- line - Variable in class org.jmol.jvxl.readers.XmlReader
- line - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- line - Static variable in class org.jmol.script.T
- LINE - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- line_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- line_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- line_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- LINE_SEGMENT - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- line_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- line_stick_helper - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- line_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- line_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- line0 - Variable in class org.jmol.script.ScriptFlowContext
- line3d - Variable in class org.jmol.g3d.CylinderRenderer
- line3d - Variable in class org.jmol.g3d.Graphics3D
- linearCombination - Variable in class org.jmol.jvxl.readers.IsoMOReader
- linearCombination - Variable in class org.jmol.quantum.MOCalculation
- linearOffsets - Variable in class org.jmol.jvxl.calc.MarchingCubes
- linearRotTrans - Variable in class org.jmol.symmetry.SymmetryOperation
-
A linear array for the matrix.
- linearSearch() - Method in class org.jmol.minimize.forcefield.ForceField
- linearTolerance - Variable in class org.jmol.symmetry.PointGroup
- lineBits - Variable in class org.jmol.g3d.LineRenderer
- lineBuffer - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- lineBuffer - Variable in class org.jmol.adapter.readers.simple.InputReader
- lineCache - Variable in class org.jmol.g3d.LineRenderer
- lineCurrent - Variable in class org.jmol.script.ScriptTokenParser
- linedata - Static variable in class org.jmol.script.T
- lineData - Variable in class org.jmol.shape.Mesh
- lineData - Variable in class org.jmol.shapespecial.Draw
- lineEnd - Variable in class org.jmol.script.ScriptContext
- lineEnd - Variable in class org.jmol.script.ScriptEval
- lineheight - Variable in class org.jmol.render.UccageRenderer
- lineHeight - Variable in class org.jmol.modelset.Text
- lineIndices - Variable in class org.jmol.script.ScriptCompiler
- lineIndices - Variable in class org.jmol.script.ScriptContext
- lineIndices - Variable in class org.jmol.script.ScriptEval
- lineIndices - Variable in class org.jmol.script.ScriptFunction
- lineLength - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- lineNumbers - Variable in class org.jmol.script.ScriptCompiler
- lineNumbers - Variable in class org.jmol.script.ScriptContext
- lineNumbers - Variable in class org.jmol.script.ScriptEval
- lineNumbers - Variable in class org.jmol.script.ScriptFunction
- lineOptions - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
- linePt - Variable in class org.jmol.jvxl.readers.XplorReader
- LineRenderer - Class in org.jmol.g3d
- LineRenderer(Graphics3D) - Constructor for class org.jmol.g3d.LineRenderer
- lines - Variable in class org.jmol.modelset.Text
- lines - Static variable in class org.jmol.script.T
- lineStart - Variable in class org.jmol.script.ScriptFlowContext
- lineStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- lineTo(Object, int, int) - Method in interface org.jmol.api.GenericGraphics
- lineTo(Object, int, int) - Method in class org.jmol.awt.AwtG2D
- lineTo(Object, int, int) - Method in class org.jmol.awtjs2d.JsG2D
- lineTypeX - Variable in class org.jmol.g3d.LineRenderer
- LINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
- lineWidthMad - Variable in class org.jmol.export.___Exporter
- link - Static variable in class org.jmol.script.T
- link(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.CapVertex
-
Link this vertex with v or remove it from the chain.
- LINK_TYPE_AROM - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_BITS - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_DELO - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_DOUBLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_GENERIC_LINK - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
types set by filter TOPOSE_TYPES in the format of one or more of {v, vw, hb} separated by "+"; default is v+hb
- LINK_TYPE_HBOND - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_OCTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_OTHER - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_PI - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_POLY - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_QUADRUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_QUINTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_SEPTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_SEXTUPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_SINGLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_TRIPLE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- LINK_TYPE_VDW - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
-
Opens a web page in an external browser
- linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
-
Follows the reference in an link.
- linkCount - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- linkedMesh - Variable in class org.jmol.shape.Mesh
- linkedMesh - Variable in class org.jmol.shape.MeshCollection
- linkID - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- linkNodes - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- links - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
list of TOPOL_LINK loop data
- linkSymop - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- linkTrans - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- linkTypes - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- list - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- list - Variable in class org.jmol.awtjs.swing.Container
- list - Variable in class org.jmol.minimize.forcefield.MMFFOOPCalc
- list - Static variable in class org.jmol.script.T
- listAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- listBS(BS) - Method in class org.jmol.script.ScriptExpr
- listCommands - Variable in class org.jmol.script.ScriptEval
- listCommands - Variable in class org.jmol.viewer.Viewer
- listCompositions() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- listeners - Variable in class org.jmol.viewer.SelectionManager
- listf - Static variable in class org.jmol.script.T
- listIsosurface(int) - Method in class org.jmol.scriptext.IsoExt
- listKey - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- listKeyCase - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- listLabel - Variable in class org.openscience.jmol.app.webexport.WebPanel
- listParameter(int, int, int) - Method in class org.jmol.script.ScriptParam
- listParameter4(int, int, int, boolean) - Method in class org.jmol.script.ScriptParam
- listPt - Variable in class org.jmol.symmetry.UnitCellIterator
- listRS - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
bitsets for tracking R and S for Rule 4b
- listSavedStates() - Method in class org.jmol.viewer.StateManager
- ListSelectionModel - Interface in org.jmol.awtjs.swing
- listToMap(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
return a map of lists of the type: [ [name1,...], [name2,...], ...]
- listToSettings(Lst<Object>, Map<Integer, Lst<Object>>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- lltoken - Variable in class org.jmol.script.ScriptCompiler
- lnLength - Variable in class org.jmol.script.ScriptCompiler
- lo - Variable in class org.jmol.util.ColorEncoder
- load - Static variable in class org.jmol.script.T
- load() - Method in class org.openscience.jmol.app.HistoryFile
-
Loads properties from the history file.
- LOAD_ATOM_DATA_TYPES - Static variable in class org.jmol.viewer.JC
- loadAndRun(String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- loadAtomDataAndReturnError(Object, int) - Method in class org.jmol.viewer.Viewer
-
or just apply the data to the current model set
- loadatomdatatolerance - Static variable in class org.jmol.script.T
- loadAtomDataTolerance - Variable in class org.jmol.viewer.GlobalSettings
- loadButton - Variable in class org.jmol.console.GenericConsole
- loadButton - Variable in class org.jmol.console.ScriptEditor
- loadContent(String) - Method in interface org.jmol.api.JmolDropEditor
- loadContent(String) - Method in class org.jmol.console.ScriptEditor
- loadContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- loadCoordinates(String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
- loadData(Viewer, Object) - Static method in class org.jmol.symmetry.SpaceGroupFinder
- loadDefaultModelKitModel(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- loadDefaultShapes(ModelSet) - Method in class org.jmol.viewer.ShapeManager
- loadDOMNode(Object) - Method in interface org.jmol.api.JmolAppletInterface
- loadDOMNode(Object) - Method in class org.jmol.util.GenericApplet
- loadDssr(int, String) - Method in class org.jmol.script.ScriptEval
- loader - Variable in class org.jmol.jsv.JDXMOLParser
- loadFile(String) - Method in interface org.jmol.api.JmolDropEditor
- loadFile(String) - Method in class org.jmol.console.ScriptEditor
- loadFile(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- loadFile(String, int, int) - Method in class org.jmol.awt.FileDropper
- loadFileAsync(String, String, int, boolean) - Method in class org.jmol.script.ScriptEval
-
Allows asynchronous file loading from the LOAD or SCRIPT command.
- loadFileResourceAsync(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- loadFileResourceAsync(String) - Method in class org.jmol.script.ScriptEval
-
load a static file asynchronously
- loadFiles(List<File>) - Method in class org.jmol.awt.FileDropper
- loadformat - Static variable in class org.jmol.script.T
- loadFormat - Variable in class org.jmol.viewer.GlobalSettings
- loadGeometries - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- loadImage(Object, String, boolean) - Method in class org.jmol.viewer.FileManager
-
Load an image
- loadImage(GenericPlatform, String, String, byte[], Object) - Method in interface org.jmol.api.js.JmolToJSmolInterface
- loadImageData(Object, String, String, Object) - Method in class org.jmol.viewer.Viewer
-
NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java as well as from FileManager.loadImage
- loading - Variable in class org.jmol.util.GenericApplet
- loadInline(String) - Method in interface org.jmol.api.JmolAppletInterface
-
Deprecated.
- loadInline(String) - Method in class org.jmol.api.JmolViewer
- loadInline(String) - Method in class org.jmol.util.GenericApplet
-
Deprecated.
- loadInline(String) - Method in class org.jmol.viewer.Viewer
-
from Applet and external applications only
- loadInline(String[]) - Method in interface org.jmol.api.JmolAppletInterface
-
Deprecated.
- loadInline(String[]) - Method in class org.jmol.api.JmolViewer
- loadInline(String[]) - Method in class org.jmol.util.GenericApplet
-
Deprecated.
- loadInline(String[]) - Method in class org.jmol.viewer.Viewer
-
external apps only
- loadInline(String[], boolean) - Method in class org.jmol.api.JmolViewer
- loadInline(String[], boolean) - Method in class org.jmol.viewer.Viewer
-
external apps and applet only
- loadInline(String[], String) - Method in interface org.jmol.api.JmolAppletInterface
-
Deprecated.
- loadInline(String[], String) - Method in class org.jmol.util.GenericApplet
-
Deprecated.
- loadInline(String, char) - Method in class org.jmol.api.JmolViewer
- loadInline(String, char) - Method in class org.jmol.viewer.Viewer
-
external apps only
- loadInline(String, String) - Method in interface org.jmol.api.JmolAppletInterface
-
Deprecated.
- loadInline(String, String) - Method in class org.jmol.util.GenericApplet
-
Deprecated.
- loadInline(List<Object>, boolean) - Method in class org.jmol.api.JmolViewer
-
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
- loadInline(List<Object>, boolean) - Method in class org.jmol.viewer.Viewer
-
External applications only; does not preserve state -- intentionally!
- loadInlineAppend(String, boolean) - Method in class org.jmol.api.JmolViewer
- loadInlineAppend(String, boolean) - Method in class org.jmol.viewer.Viewer
-
used by applet and console
- loadInlineArray(String[], String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
- loadInlineArray(String[], String, boolean) - Method in class org.jmol.util.GenericApplet
- loadInlineScript(String, char, boolean, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
-
used by loadInline and openFileFull
- loadInlineScriptRepaint(String, char, boolean) - Method in class org.jmol.viewer.Viewer
- loadInlineString(String, String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
- loadInlineString(String, String, boolean) - Method in class org.jmol.util.GenericApplet
- loadligandformat - Static variable in class org.jmol.script.T
- LoadMeasureThread - Class in org.openscience.jmol.app.janocchio
- LoadMeasureThread() - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThread
- LoadMeasureThread(NMR_JmolPanel, String) - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThread
- LoadMeasureThreadJSON - Class in org.openscience.jmol.app.janocchio
- LoadMeasureThreadJSON(NMR_JmolPanel, Map<String, Object>) - Constructor for class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- loadModelFromFile(String, String, String[], Object, boolean, Map<String, Object>, SB, SB, int, String) - Method in class org.jmol.viewer.Viewer
-
Used by the ScriptEvaluator LOAD command to open one or more files.
- loadModelFromFileRepaint(String, String, String[], Object) - Method in class org.jmol.viewer.Viewer
-
for JmolSimpleViewer -- external applications only (and no-script JavaScript)
- loadNote - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- loadPNGJVar(String, Object, Map<String, Object>) - Method in class org.jmol.script.ScriptEval
- loadScript - Variable in class org.jmol.modelset.Model
- loadShape(int) - Method in class org.jmol.viewer.ShapeManager
- loadState - Variable in class org.jmol.modelset.Model
- LOADSTRUCT - Enum constant in enum org.jmol.c.CBK
- loadVibrations - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- lobe - Static variable in class org.jmol.script.T
- loc - Variable in class org.jmol.awtjs.swing.JDialog
- localAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
- localAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
- localArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- localArrayListType - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- localEnvOnly - Variable in class org.jmol.symmetry.PointGroup
- localFunctions - Variable in class org.jmol.viewer.Viewer
- localize(boolean, Properties) - Method in class org.jmol.popup.PopupResource
- localSpaceGroupName - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- lock - Variable in class org.jmol.script.ScriptParallelProcessor
- locked - Static variable in class org.jmol.modelkit.ModelKit
- log - Static variable in class org.jmol.script.T
- log(PrintStream, int, String, Throwable) - Method in class org.jmol.util.DefaultLogger
-
Method to output a log.
- log(String) - Method in class org.jmol.adapter.readers.pymol.PickleReader
- log(String) - Method in interface org.jmol.atomdata.AtomDataServer
- log(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- log(String) - Method in class org.jmol.minimize.forcefield.ForceField
- log(String) - Method in class org.jmol.viewer.Viewer
- log(String) - Static method in class org.openscience.jmol.app.webexport.LogPanel
- log_box_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- log_conformations - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- logArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
- logcommands - Static variable in class org.jmol.script.T
- logCommands - Variable in class org.jmol.viewer.GlobalSettings
- logCompression - Variable in class org.jmol.jvxl.readers.Parameters
- logCube - Variable in class org.jmol.jvxl.readers.Parameters
- logData - Variable in class org.jmol.minimize.forcefield.Calculations
- logDebugScript(T[], int) - Method in class org.jmol.script.ScriptEval
- logEvent(String, P3) - Method in class org.jmol.multitouch.ActionManagerMT
- logfile - Static variable in class org.jmol.script.T
- logFileName - Variable in class org.jmol.viewer.Viewer
- logFilePath - Variable in class org.jmol.viewer.Viewer
- Logger - Class in org.jmol.util
-
Logger mechanism.
- Logger() - Constructor for class org.jmol.util.Logger
- LoggerInterface - Interface in org.jmol.util
-
Interface used for the logging mechanism.
- loggestures - Static variable in class org.jmol.script.T
- logGestures - Variable in class org.jmol.viewer.GlobalSettings
- logging - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- logging - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- logging - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- logging - Variable in class org.jmol.minimize.forcefield.Calculations
- loggingEnabled - Variable in class org.jmol.minimize.forcefield.Calculations
- loglevel - Static variable in class org.jmol.script.T
- logLevel() - Static method in class org.jmol.util.Logger
-
Indicates if the level is logged.
- logLoadInfo(String, boolean) - Method in class org.jmol.script.ScriptEval
- logMessages - Variable in class org.jmol.jvxl.readers.Parameters
- logMessages - Variable in class org.jmol.script.ScriptTokenParser
- LogPanel - Class in org.openscience.jmol.app.webexport
- LogPanel() - Constructor for class org.openscience.jmol.app.webexport.LogPanel
- logToFile(String) - Method in class org.jmol.viewer.OutputManager
- lonepair - Static variable in class org.jmol.script.T
- LONG - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- LONG_BINGET - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- LONG_BINPUT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- lookForSyncID() - Method in class org.jmol.script.ScriptCompiler
-
Check for a set of characters that does not start with double quote or at-sign and terminates with #, }, or an end of line.
- lookingAtBitset() - Method in class org.jmol.script.ScriptCompiler
- lookingAtComment() - Method in class org.jmol.script.ScriptCompiler
- lookingAtDecimal() - Method in class org.jmol.script.ScriptCompiler
- lookingAtEndOfLine() - Method in class org.jmol.script.ScriptCompiler
-
Look for end of script or a new line.
- lookingAtExponential() - Method in class org.jmol.script.ScriptCompiler
- lookingAtImpliedString(boolean, boolean, boolean) - Method in class org.jmol.script.ScriptCompiler
-
An "implied string" is a parameter that is not quoted but because of its position in a command is implied to be a string.
- lookingAtInteger() - Method in class org.jmol.script.ScriptCompiler
- lookingAtLeadingWhitespace() - Method in class org.jmol.script.ScriptCompiler
- lookingAtLoadFormat(boolean) - Method in class org.jmol.script.ScriptCompiler
- lookingAtLookupToken(int) - Method in class org.jmol.script.ScriptCompiler
- lookingAtMathContinuation(int) - Method in class org.jmol.script.ScriptCompiler
- lookingAtMatrix() - Method in class org.jmol.script.ScriptCompiler
- lookingAtObjectID() - Method in class org.jmol.script.ScriptCompiler
-
Look for a valid $...
- lookingAtSeqcode() - Method in class org.jmol.script.ScriptCompiler
- lookingAtSetBraceSyntax() - Method in class org.jmol.script.ScriptCompiler
-
look for '{' at the start of a command, allowing for syntaxes {xxx}.yyy = ...
- lookingAtString(boolean) - Method in class org.jmol.script.ScriptCompiler
-
look for a quoted string, possibly allowing single quotes.
- lookingAtTerminator() - Method in class org.jmol.script.ScriptCompiler
-
Look for valid terminating semicolon -- one not within for(), for example.
- lookup(String) - Static method in class org.jmol.symmetry.HallRotation
- lookupCode - Variable in class org.jmol.symmetry.HallRotationTerm
- lookupIdentifierValue(String) - Method in class org.jmol.script.ScriptEval
- lookupInterpolatedVoxelValue(T3, boolean) - Method in class org.jmol.jvxl.data.VolumeData
- lookupSpecialAtomID(String) - Method in class org.jmol.modelsetbio.BioResolver
- lookupValue(String, boolean) - Method in class org.jmol.script.ScriptEval
- loop - Static variable in class org.jmol.script.T
- LoopedStreams - Class in org.openscience.jmol.app.jmolpanel
- LoopedStreams() - Constructor for class org.openscience.jmol.app.jmolpanel.LoopedStreams
- LOW - Static variable in class org.jmol.util.ColorEncoder
- lowdenCharges - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
- lp - Static variable in class org.jmol.script.T
- lrefSingle - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- lstCoords - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- lstDipoles - Variable in class org.jmol.shapespecial.Dipole
- lstGaussians - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- lstMatrix - Variable in class org.jmol.export._StlExporter
- lstNCS - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- lstRegions - Variable in class org.jmol.util.MeshCapper
-
dynamic region processing.
- lstSmallRings - Variable in class org.jmol.symmetry.CIPData
-
all 3- to 7-membered rings; used to exclude E/Z and N-SP3 descriptors
- lstStates - Variable in class org.jmol.util.CommandHistory
- lstTriangles - Variable in class org.jmol.util.MeshCapper
- ltoken - Variable in class org.jmol.script.ScriptCompiler
- ltokenPostfix - Variable in class org.jmol.script.ScriptTokenParser
- lumo - Static variable in class org.jmol.script.T
- lumoEnergy - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
M
- m - Variable in class org.jmol.export._IdtfExporter
- m - Variable in class org.jmol.quantum.NMRNoeMatrix
- m - Variable in class org.jmol.render.MeasuresRenderer
- m - Variable in class org.jmol.util.MeshSlicer
- m2_rotate - Variable in class org.jmol.viewer.TransformManager4D
- m3 - Variable in class org.jmol.util.MeshCapper
- m3_toScreen - Variable in class org.jmol.viewer.TransformManager4D
- m3dStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- m3inv - Variable in class org.jmol.util.MeshCapper
- m4 - Variable in class org.jmol.export._StlExporter
- m4 - Variable in class org.jmol.thread.SpinThread
- m4 - Variable in class org.jmol.viewer.TransformManager4D
- m4a - Variable in class org.jmol.export._StlExporter
- MAC_COMMAND - Static variable in class org.jmol.awtjs.Event
- MAC_COMMAND - Static variable in class org.jmol.viewer.binding.Binding
- macro - Static variable in class org.jmol.script.T
- macro() - Method in class org.jmol.scriptext.CmdExt
- macrodirectory - Static variable in class org.jmol.script.T
- macroDirectory - Variable in class org.jmol.viewer.GlobalSettings
- macros - Static variable in class org.jmol.viewer.JC
- macros - Variable in class org.jmol.viewer.Viewer
- mad - Variable in class org.jmol.modelset.Bond
- mad - Variable in class org.jmol.modelset.Measurement
- mad - Variable in class org.jmol.modelset.MeasurementData
- mad - Variable in class org.jmol.render.ShapeRenderer
- mad - Variable in class org.jmol.renderbio.RocketRenderer
- mad - Variable in class org.jmol.shape.AtomShape
- mad - Variable in class org.jmol.shapespecial.Dipole
- mad - Variable in class org.jmol.shapespecial.Dipoles
- mad - Variable in class org.jmol.viewer.Connection
- MAD_GLOBAL - Static variable in class org.jmol.modelset.Atom
- mad0 - Variable in class org.jmol.render.MeasuresRenderer
- madAtom - Variable in class org.jmol.modelset.Atom
- madBeg - Variable in class org.jmol.renderbio.BioShapeRenderer
- madDnaRna - Variable in class org.jmol.shapebio.BioShapeCollection
- madEnd - Variable in class org.jmol.renderbio.BioShapeRenderer
- madHelixSheet - Variable in class org.jmol.shapebio.BioShapeCollection
- madMid - Variable in class org.jmol.renderbio.BioShapeRenderer
- madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JC
- madOn - Variable in class org.jmol.shapebio.BioShapeCollection
- mads - Variable in class org.jmol.geodesic.EnvelopeCalculation
- mads - Variable in class org.jmol.renderbio.BioShapeRenderer
- mads - Variable in class org.jmol.shape.AtomShape
- madTurnRandom - Variable in class org.jmol.shapebio.BioShapeCollection
- mag2d - Variable in class org.jmol.render.SticksRenderer
- magCenterings - Variable in class org.jmol.adapter.readers.cif.CifReader
- magCifContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- MAGENTA - Static variable in class org.jmol.util.C
- MAGNETIC_SUSCEPTIBILITY_FACTOR - Static variable in class org.jmol.util.Tensor
- magneticshielding - Static variable in class org.jmol.script.T
- MAGNETOGYRIC_RATIO - Static variable in class org.jmol.quantum.NMRCalculation
- magOp - Variable in class org.jmol.symmetry.SymmetryOperation
- magresFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- MagresReader - Class in org.jmol.adapter.readers.xtal
- MagresReader() - Constructor for class org.jmol.adapter.readers.xtal.MagresReader
- magresUnits - Variable in class org.jmol.adapter.readers.xtal.MagresReader
- main(String[]) - Static method in class org.jmol.quantum.NMRNoeMatrix
- main(String[]) - Static method in class org.jmol.symmetry.SpaceGroupFinder
- main(String[]) - Static method in class org.openscience.jmol.app.janocchio.Nmr
- main(String[]) - Static method in class org.openscience.jmol.app.Jmol
- main(String[]) - Static method in class org.openscience.jmol.app.JmolData
- main(String[]) - Static method in class org.openscience.jvxl.Jvxl
- main(String[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
- MAIN - Static variable in class org.jmol.thread.JmolThread
- mainFrame - Variable in class org.openscience.jmol.app.janocchio.Nmr
- mainLoop() - Method in class org.openscience.jmol.app.InputScannerThread
- MainPopupResourceBundle - Class in org.jmol.popup
- MainPopupResourceBundle(String, Properties) - Constructor for class org.jmol.popup.MainPopupResourceBundle
- mainSplitPane - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- majorVersion - Static variable in class org.jmol.viewer.JC
- makeBonds(String[][], boolean) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
- makeColorScheme(String, int[], boolean) - Method in class org.jmol.util.ColorEncoder
- makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.modelset.ModelSet
- makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.viewer.Viewer
- makeConnections2(float, float, int, int, BS, BS, BS, boolean, boolean, float, SB) - Method in class org.jmol.modelset.ModelSet
- makeNewAtomSet() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- makePlane(float, float, float, P4) - Static method in class org.openscience.jmol.app.surfacetool.Slice
- makePoints - Variable in class org.jmol.shapespecial.Draw
- manager - Variable in class org.jmol.awt.Mouse
- manager - Variable in class org.jmol.awtjs2d.Mouse
- manager - Variable in class org.jmol.util.Font
- manifest - Static variable in class org.jmol.script.T
- mantissa(float) - Method in class org.jmol.jvxl.data.VolumeData
- map - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- map - Variable in class org.jmol.console.ScriptEditor
- map - Variable in class org.jmol.quantum.MOCalculation
- map - Variable in class org.jmol.viewer.PropertyManager
- map - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
- map(Object, String, String, Map<String, Object>) - Static method in class org.jmol.console.GenericConsole
- map_auto_expand_sym - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- map0 - Variable in class org.jmol.rendercgo.CGORenderer
-
UV mapping Cartesian origin, X, and Y
- mapAddKey(String) - Method in class org.jmol.util.JSONWriter
- mapAddKeyValue(String, Object, String) - Method in class org.jmol.util.JSONWriter
- mapAddKeyValueRaw(String, Object, String) - Method in class org.jmol.util.JSONWriter
-
Add a key:value pair where value is already quoted
- mapAddMapAllExcept(String, Map<String, Object>, String) - Method in class org.jmol.util.JSONWriter
- mapAtomResIDs(Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
-
Map all atom and residue unit ids to atom indexes
- mapc - Variable in class org.jmol.jvxl.readers.MapFileReader
- mapClose() - Method in class org.jmol.util.JSONWriter
- MapFileReader - Class in org.jmol.jvxl.readers
- MapFileReader() - Constructor for class org.jmol.jvxl.readers.MapFileReader
- mapGet(String) - Method in class org.jmol.script.SV
- mapIndex - Variable in class org.jmol.smiles.SmilesAtom
- mapLattice - Variable in class org.jmol.jvxl.data.JvxlData
- mapLattice - Variable in class org.jmol.jvxl.readers.Parameters
- mapObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- mapOpen() - Method in class org.jmol.util.JSONWriter
- mapPartialCharge(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- mappedDataMax - Variable in class org.jmol.jvxl.data.JvxlData
- mappedDataMax - Variable in class org.jmol.jvxl.readers.Parameters
- mappedDataMin - Variable in class org.jmol.jvxl.data.JvxlData
- mappedDataMin - Variable in class org.jmol.jvxl.readers.Parameters
- mappingPlane - Variable in class org.jmol.jvxl.calc.MarchingCubes
- mappingPlane - Variable in class org.jmol.jvxl.data.VolumeData
- mappingPlaneNormalMag - Variable in class org.jmol.jvxl.data.VolumeData
- mapPlanar - Variable in class org.jmol.inchi.InChIJNI
- mapPolyhedra(int, int, boolean, M4) - Method in class org.jmol.scriptext.SmilesExt
- mapproperty - Static variable in class org.jmol.script.T
- mapProperty() - Method in class org.jmol.scriptext.CmdExt
- mapPut(String, SV) - Method in class org.jmol.script.SV
- mapr - Variable in class org.jmol.jvxl.readers.MapFileReader
- mapRtoA - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- maps - Variable in class org.jmol.jvxl.readers.MapFileReader
- mapSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- mapT - Variable in class org.jmol.geodesic.EnvelopeCalculation
- mapTet - Variable in class org.jmol.inchi.InChIJNI
- mapUnique - Variable in class org.jmol.smiles.SmilesSearch
- mapValue(String) - Method in class org.jmol.script.SV
- mapWidth - Variable in class org.jmol.g3d.TextRenderer
- mar - Variable in class org.jmol.render.StarsRenderer
- marBond - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- marchingCubes - Variable in class org.jmol.jvxl.readers.SurfaceReader
- MarchingCubes - Class in org.jmol.jvxl.calc
- MarchingCubes() - Constructor for class org.jmol.jvxl.calc.MarchingCubes
- MarchingCubes(VertexDataServer, VolumeData, Parameters, BS) - Constructor for class org.jmol.jvxl.calc.MarchingCubes
- marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceReader
- MarchingSquares - Class in org.jmol.jvxl.calc
- MarchingSquares(VertexDataServer, VolumeData, P4, float[], int, int, boolean) - Constructor for class org.jmol.jvxl.calc.MarchingSquares
- MarchingSquares.ContourVertex - Class in org.jmol.jvxl.calc
- MarchingSquares.Triangle - Class in org.jmol.jvxl.calc
- margin - Variable in class org.jmol.jvxl.readers.AtomDataReader
- margin - Variable in class org.jmol.util.BoxInfo
- mark(int) - Method in class org.openscience.jvxl.MonitorInputStream
- MARK - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- markCount - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- markFaceVoxels(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- markLines(String, char) - Static method in class org.jmol.util.Parser
- markPlaneVoxels(P3, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
- markPosition - Variable in class org.openscience.jvxl.MonitorInputStream
- marks - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- markSphereVoxels(float, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
- markToroidVoxels() - Method in class org.jmol.jvxl.readers.IsoSolventReader
- MAROON - Static variable in class org.jmol.util.C
- MASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MASMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mass - Static variable in class org.jmol.script.T
- mass - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Rule 2 isotope mass number if identified or average atomic mass if not C (12.011) > 12C, O (15.999) < 16O, and F (18.998) < 19F Source:
- mat - Variable in class org.jmol.g3d.SphereRenderer
- mat - Variable in class org.jmol.renderbio.BioMeshRenderer
- mat - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- mat - Variable in class org.jmol.symmetry.PointGroup.Operation
- mat4 - Variable in class org.jmol.modelset.Model
-
mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected
- mat4 - Variable in class org.jmol.modelset.ModelSet
- mat4 - Variable in class org.jmol.util.MeshSurface
- mat4t - Variable in class org.jmol.modelset.ModelSet
- match(String) - Method in class org.jmol.symmetry.CIPData
-
Return a bit set corresponding to a SMARTS
- match(String) - Method in class org.jmol.symmetry.CIPDataSmiles
- matchingBond - Variable in class org.jmol.smiles.SmilesBond
- matchingComponent - Variable in class org.jmol.smiles.SmilesAtom
- matchingIndex - Variable in class org.jmol.smiles.SmilesAtom
- matchingNode - Variable in class org.jmol.smiles.SmilesAtom
- matchPriv(String, Node[], int, BS, BS, boolean, int, int, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
- matEllipsoidToScreen - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- mathExpressionCommand - Static variable in class org.jmol.script.T
- mathExt - Variable in class org.jmol.script.ScriptExpr
- MathExt - Class in org.jmol.scriptext
- MathExt() - Constructor for class org.jmol.scriptext.MathExt
- mathfunc - Static variable in class org.jmol.script.T
- mathop - Static variable in class org.jmol.script.T
- mathproperty - Static variable in class org.jmol.script.T
- matInv - Variable in class org.jmol.modelset.ModelSet
- matR - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- matrix_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- matrix3f - Static variable in class org.jmol.script.T
- matrix4f - Static variable in class org.jmol.script.T
- matrixCartesianToFractional - Variable in class org.jmol.util.SimpleUnitCell
- matrixCtoFNoOffset - Variable in class org.jmol.util.SimpleUnitCell
- matrixEnd - Variable in class org.jmol.thread.MoveToThread
- matrixFractionalToCartesian - Variable in class org.jmol.util.SimpleUnitCell
- matrixFtoCNoOffset - Variable in class org.jmol.util.SimpleUnitCell
- matrixRotate - Variable in class org.jmol.viewer.TransformManager
- matrixStart - Variable in class org.jmol.thread.MoveToThread
- matrixStartInv - Variable in class org.jmol.thread.MoveToThread
- matrixStep - Variable in class org.jmol.thread.MoveToThread
- matrixStereo - Variable in class org.jmol.viewer.TransformManager
- matrixT - Variable in class org.jmol.render.MeasuresRenderer
- matrixTemp - Variable in class org.jmol.viewer.TransformManager
- matrixTemp3 - Variable in class org.jmol.viewer.TransformManager
- matrixTemp4 - Variable in class org.jmol.viewer.TransformManager
- matrixTest - Variable in class org.jmol.viewer.TransformManager
- matrixToScript(Object) - Static method in class org.jmol.util.Escape
- matrixTransform - Variable in class org.jmol.viewer.TransformManager
- matrixTransformInv - Variable in class org.jmol.viewer.TransformManager
- matRot - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- matScreenToCartesian - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- matScreenToEllipsoid - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- matSupercell - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- matTemp - Variable in class org.jmol.modelset.ModelSet
- matUnitCellOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- max - Static variable in class org.jmol.script.T
- MAX_ACTION_UNDO - Static variable in class org.jmol.viewer.StateCreator
- MAX_ADJACENT_PHOSPHORUS_DISTANCE - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
- MAX_BOND_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shape.Sticks
- MAX_BONDS_LENGTH_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
- MAX_COUNT - Static variable in class org.jmol.symmetry.SpaceGroupFinder
-
maximum allowable supercell
- MAX_DISTANCE_TO_PLANE - Static variable in class org.jmol.shapespecial.Polyhedra
- MAX_DOUBLE_CLICK_MILLIS - Static variable in class org.jmol.viewer.ActionManager
- MAX_FILES - Static variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- MAX_INTERCHAIN_BOND_2 - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
- MAX_LABEL - Static variable in class org.jmol.modelkit.ModelKitPopup
- MAX_LEVEL - Static variable in class org.jmol.shapespecial.Dots
- MAX_LOOP - Static variable in class org.jmol.util.JmolAudio
- MAX_NUM_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
- MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapespecial.Draw
- MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapespecial.Ellipsoids
- MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapesurface.Isosurface
- MAX_OTHER - Static variable in class org.jmol.shapespecial.Polyhedra
- MAX_PATH - Static variable in class org.jmol.symmetry.CIPChirality
-
maximum path to display for debugging only using SET DEBUG in Jmol
- max_squarable_double - Static variable in class org.jmol.minimize.Util
- max_threads - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MAX_TREE_DEPTH - Static variable in class org.jmol.bspt.Bspt
- max_triangles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MAX_TYPE_SUPPORTED - Static variable in class org.jmol.quantum.QS
- MAX_UNDO_DEFAULT - Static variable in class org.jmol.viewer.StateManager
- max_ups - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MAX_VERTICES - Static variable in class org.jmol.shapespecial.Polyhedra
- maxAtoms - Variable in class org.jmol.symmetry.PointGroup
- maxAxis - Static variable in class org.jmol.symmetry.PointGroup
- maxBondingRadius - Variable in class org.jmol.modelset.AtomCollection
- maxBondWarned - Variable in class org.jmol.modelset.ModelSet
- maxColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
- maxContraction - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- maxData - Variable in class org.jmol.shapesurface.Contact
- maxDistance - Variable in class org.jmol.jvxl.readers.AtomDataReader
- maxDistance2 - Variable in class org.jmol.symmetry.UnitCellIterator
- maxElement - Variable in class org.jmol.symmetry.PointGroup
- maxGrid - Variable in class org.jmol.jvxl.data.VolumeData
- maxGrid - Variable in class org.jmol.jvxl.readers.VolumeDataReader
- maxHbondAlphaDistance - Static variable in class org.jmol.modelsetbio.AminoPolymer
- maxHbondAlphaDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
- MAXID - Static variable in class org.jmol.quantum.QS
- MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JC
- MAXIMUM_CLICK_TIME - Static variable in class org.jmol.multitouch.sparshui.SinglePointGesture
- MAXIMUM_QUEUE_LENGTH - Static variable in class org.jmol.viewer.StatusManager
- MAXIMUM_ZOOM_PERCENTAGE - Static variable in class org.jmol.viewer.TransformManager
- MAXIMUM_ZOOM_PERSPECTIVE_DEPTH - Static variable in class org.jmol.viewer.TransformManager
- maximumSize - Variable in class org.jmol.viewer.Viewer
- maxL - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- maxLeft - Variable in class org.jmol.bspt.Node
- maxLength - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- maxLevel - Static variable in class org.jmol.util.Geodesic
- maxOddSizeSphere - Static variable in class org.jmol.g3d.SphereRenderer
- maxOffDiag() - Method in class org.jmol.quantum.NMRNoeMatrix
- maxp - Variable in class org.openscience.jmol.app.janocchio.PopulationDisplay
- maxr - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- maxRadius - Variable in class org.jmol.geodesic.EnvelopeCalculation
- maxRight - Variable in class org.jmol.bspt.Node
- maxRS - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
maximun (atom radius + solvent radius)
- maxSerial - Variable in class org.jmol.adapter.readers.cif.CifReader
- maxSerial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- maxSerial - Variable in class org.jmol.modelsetbio.BioResolver
- maxset - Static variable in class org.jmol.script.T
- maxSet - Variable in class org.jmol.jvxl.readers.Parameters
- maxSize - Variable in class org.jmol.util.CommandHistory
- maxSphereCache - Static variable in class org.jmol.util.Shader
- maxSphereDiameter - Static variable in class org.jmol.g3d.SphereRenderer
- maxSphereDiameter2 - Static variable in class org.jmol.g3d.SphereRenderer
- maxUndo - Variable in class org.jmol.viewer.StateManager
- MAXUNDO - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- maxVanderwaalsRadius - Variable in class org.jmol.modelset.AtomCollection
- maxVectorLength - Variable in class org.jmol.jvxl.data.VolumeData
- maxX - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- maxXYZ - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- maxXYZ - Variable in class org.jmol.symmetry.UnitCellIterator
- maxXYZ0 - Variable in class org.jmol.adapter.readers.cif.MSRdr
- maxXYZ0 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- maxY - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- maxZ - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- maybeGetBaseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- mayScript - Variable in class org.jmol.util.GenericApplet
- mc - Variable in class org.jmol.modelset.ModelSet
-
model count
- MdCrdReader - Class in org.jmol.adapter.readers.more
-
Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command
- MdCrdReader() - Constructor for class org.jmol.adapter.readers.more.MdCrdReader
- mDeriv - Variable in class org.jmol.g3d.SphereRenderer
- mDeriv - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- mdlLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- mDsimulation - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- mdTopLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- MdTopReader - Class in org.jmol.adapter.readers.more
-
A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file
- MdTopReader() - Constructor for class org.jmol.adapter.readers.more.MdTopReader
- MEAS_DIGITS - Static variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- measure - Static variable in class org.jmol.script.T
- measure() - Method in class org.jmol.scriptext.CmdExt
- Measure - Class in org.openscience.jmol.app.janocchio
- Measure(String, double, int) - Constructor for class org.openscience.jmol.app.janocchio.Measure
- MEASURE - Enum constant in enum org.jmol.c.CBK
- MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
- measureallmodels - Static variable in class org.jmol.script.T
- measureAllModels - Variable in class org.jmol.shape.Measures
- measureAllModels - Variable in class org.jmol.viewer.GlobalSettings
- measureAngstroms - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- MeasureCouple - Class in org.openscience.jmol.app.janocchio
- MeasureCouple(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureCouple
- MeasureDist - Class in org.openscience.jmol.app.janocchio
-
Calculates the difference between calculated and experimental values for coloring table
- MeasureDist(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureDist
- measureDistanceUnits - Variable in class org.jmol.viewer.GlobalSettings
- Measurement - Class in org.jmol.modelset
- Measurement() - Constructor for class org.jmol.modelset.Measurement
- measurementCount - Variable in class org.jmol.shape.Measures
- MeasurementData - Class in org.jmol.modelset
- MeasurementData() - Constructor for class org.jmol.modelset.MeasurementData
- measurementHeaders - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
- measurementlabels - Static variable in class org.jmol.script.T
- measurementLabels - Variable in class org.jmol.viewer.GlobalSettings
- MeasurementListWindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementListWindowListener
- measurementnumbers - Static variable in class org.jmol.script.T
- MeasurementPending - Class in org.jmol.modelset
- MeasurementPending() - Constructor for class org.jmol.modelset.MeasurementPending
- measurementQueued - Variable in class org.jmol.viewer.ActionManager
- measurements - Variable in class org.jmol.modelset.MeasurementData
- measurements - Static variable in class org.jmol.script.T
- measurements - Variable in class org.jmol.shape.Measures
- measurementsAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- measurementStrings - Variable in class org.jmol.modelset.MeasurementData
- measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- MeasurementTable - Class in org.openscience.jmol.app.jmolpanel
- MeasurementTable(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable
-
Constructor
- MeasurementTable.MeasurementListWindowListener - Class in org.openscience.jmol.app.jmolpanel
- MeasurementTable.MeasurementTableModel - Class in org.openscience.jmol.app.jmolpanel
- measurementTableModel - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- MeasurementTableModel() - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
- measurementunits - Static variable in class org.jmol.script.T
- MeasureNoe - Class in org.openscience.jmol.app.janocchio
- MeasureNoe(String, double) - Constructor for class org.openscience.jmol.app.janocchio.MeasureNoe
- measures - Variable in class org.jmol.smiles.SmilesSearch
- Measures - Class in org.jmol.shape
- Measures() - Constructor for class org.jmol.shape.Measures
- measuresEnabled - Variable in class org.jmol.viewer.ActionManager
- MeasuresRenderer - Class in org.jmol.render
- MeasuresRenderer() - Constructor for class org.jmol.render.MeasuresRenderer
- mem - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- memBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- memo - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- MEMORY_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- menu - Variable in class org.jmol.modelkit.ModelKit
- menu - Static variable in class org.jmol.script.T
- MENU_NAME - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
- MENU_NAME - Static variable in class org.jmol.popup.MainPopupResourceBundle
- menuAddButtonGroup(SC) - Method in class org.jmol.awt.AwtPopupHelper
- menuAddButtonGroup(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
- menuAddButtonGroup(SC) - Method in interface org.jmol.popup.PopupHelper
- menuAddItem(SC, SC) - Method in class org.jmol.popup.GenericPopup
- menuAddSeparator(SC) - Method in class org.jmol.popup.GenericPopup
- menuAddSubMenu(SC, SC) - Method in class org.jmol.popup.GenericPopup
- menubar - Variable in class org.jmol.console.ImageDialog
- menubar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- menuCheckBoxCallback(SC) - Method in class org.jmol.awtjs2d.JSModelKitPopup
- menuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericPopup
- menuClearListeners(SC) - Method in class org.jmol.awt.AwtPopupHelper
- menuClearListeners(SC) - Method in class org.jmol.awtjs2d.JSPopupHelper
- menuClearListeners(SC) - Method in interface org.jmol.popup.PopupHelper
- menuClickCallback(SC, String) - Method in class org.jmol.modelkit.ModelKitPopup
- menuClickCallback(SC, String) - Method in class org.jmol.popup.GenericPopup
- menuContents - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
- menuContents - Static variable in class org.jmol.popup.MainPopupResourceBundle
- menuCreateCheckboxItem(SC, String, String, String, boolean, boolean) - Method in class org.jmol.popup.GenericPopup
- menuCreateItem(SC, String, String, String) - Method in class org.jmol.popup.GenericPopup
- menuCreatePopup(String, Object) - Method in class org.jmol.awt.AwtPopupHelper
- menuCreatePopup(String, Object) - Method in class org.jmol.awtjs2d.JSPopupHelper
- menuCreatePopup(String, Object) - Method in interface org.jmol.popup.PopupHelper
- menuEnable(SC, boolean) - Method in class org.jmol.popup.GenericPopup
- menuEnabled() - Method in class org.jmol.viewer.Viewer
- menuFile - Variable in class org.openscience.jmol.app.JmolApp
- menuFocusCallback(String, String, boolean) - Method in class org.jmol.awt.AwtJmolPopup
- menuFocusCallback(String, String, boolean) - Method in class org.jmol.awtjs2d.JSJmolPopup
- menuFocusCallback(String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
- menuFocusCallback(String, String, boolean) - Method in class org.jmol.popup.GenericPopup
- menuGetAsText(SB, int, SC, String) - Method in class org.jmol.popup.GenericPopup
- menuGetId(SC) - Method in class org.jmol.popup.GenericPopup
- menuGetListPosition(SC) - Method in class org.jmol.popup.GenericPopup
- menuHidePopup(SC) - Method in class org.jmol.awt.AwtModelKitPopup
- menuHidePopup(SC) - Method in class org.jmol.awtjs2d.JSModelKitPopup
- menuHidePopup(SC) - Method in class org.jmol.modelkit.ModelKitPopup
- menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awt.AwtPopupHelper
- menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.awtjs2d.JSPopupHelper
- menuInsertSubMenu(SC, SC, int) - Method in interface org.jmol.popup.PopupHelper
- MENUITEM_HEIGHT - Static variable in class org.jmol.popup.JmolPopup
- menuItems - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- menuMap - Variable in class org.jmol.console.GenericConsole
- menuName - Variable in class org.jmol.popup.GenericPopup
- menuNewSubMenu(String, String) - Method in class org.jmol.popup.GenericPopup
- menuRemoveAll(SC, int) - Method in class org.jmol.popup.GenericPopup
- menuSetAutoscrolls(SC) - Method in class org.jmol.popup.GenericPopup
- menuSetLabel(SC, String) - Method in class org.jmol.popup.GenericPopup
- menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtJmolPopup
- menuShowPopup(SC, int, int) - Method in class org.jmol.awt.AwtModelKitPopup
- menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSJmolPopup
- menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSModelKitPopup
- menuShowPopup(SC, int, int) - Method in class org.jmol.popup.GenericPopup
- menuStructure - Variable in class org.jmol.api.JmolViewer
- menuText - Variable in class org.jmol.popup.JmolGenericPopup
- mep - Static variable in class org.jmol.script.T
- mep_calcType - Variable in class org.jmol.jvxl.readers.Parameters
- mep_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
- mep_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
- MEP_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
- mep_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
- mepCalc - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
- MepCalculation - Class in org.jmol.quantum
- MepCalculation() - Constructor for class org.jmol.quantum.MepCalculation
- mepList - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- mepType - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
- merge(MeshData) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- merge(MeshCollection) - Method in class org.jmol.shape.MeshCollection
-
called by ParallelProcessor at completion
- merge(MeshCollection) - Method in class org.jmol.shapesurface.LcaoCartoon
- merge(MeshCollection) - Method in class org.jmol.shapesurface.MolecularOrbital
- mergeAssociatedNormalCount - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- mergeAtomArrays(AtomCollection) - Method in class org.jmol.modelset.AtomCollection
- mergeBufferPixel(int, int, int) - Static method in class org.jmol.g3d.Graphics3D
- mergeGroups - Variable in class org.jmol.modelset.ModelLoader
- mergeGroups() - Method in class org.jmol.modelset.ModelLoader
- mergeMesh(MeshData) - Method in class org.jmol.shapesurface.Contact
- mergeModelArrays(ModelSet) - Method in class org.jmol.modelset.ModelSet
-
initial transfer of model data from old to new model set.
- mergePolygonCount0 - Variable in class org.jmol.util.MeshSurface
- mergePolygons(MeshSurface, int, int, int[][]) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
- mergeResults(Lst<ShapeManager>) - Method in class org.jmol.script.ScriptParallelProcessor
- mergeSets(int, int) - Method in class org.jmol.jvxl.data.MeshData
- mergeShapes(ShapeManager) - Method in class org.jmol.script.ScriptParallelProcessor
- mergeTrajAndVib(ModelSet, ModelSet) - Method in class org.jmol.modelset.ModelLoader
- mergeTrajectories(AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- mergeVertexCount0 - Variable in class org.jmol.util.MeshSurface
- merging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- merging - Variable in class org.jmol.modelset.ModelLoader
- mesh - Variable in class org.jmol.render.MeshRenderer
- mesh - Static variable in class org.jmol.script.T
- Mesh - Class in org.jmol.shape
- Mesh() - Constructor for class org.jmol.shape.Mesh
-
always use Mesh().mesh1(thisID, colix, index)
- mesh_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_carve_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_carve_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_carve_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_clear_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_clear_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_clear_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_grid_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_negative_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_negative_visible - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_normals - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_skip - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_type - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mesh1(Viewer, String, short, int) - Method in class org.jmol.shape.Mesh
- MeshCapper - Class in org.jmol.util
-
A class to properly cap a convoluted, closed slice of an isosurface inspired by: Computational Geometry: Algorithms and Applications Mark de Berg, Marc van Kreveld, Mark Overmars, and Otfried Schwarzkopf Springer-Verlag, Berlin Heidelberg 1997 Chapter 3.
- MeshCapper() - Constructor for class org.jmol.util.MeshCapper
- MeshCapper.CapVertex - Class in org.jmol.util
-
A class to provide linked vertices for MeshCapper
- MeshCapper.MeshCapperSorter - Class in org.jmol.util
- MeshCapperSorter() - Constructor for class org.jmol.util.MeshCapper.MeshCapperSorter
- meshColix - Variable in class org.jmol.shape.Mesh
- meshColix - Variable in class org.jmol.shapesurface.Isosurface
- MeshCollection - Class in org.jmol.shape
- MeshCollection() - Constructor for class org.jmol.shape.MeshCollection
- meshColor - Variable in class org.jmol.jvxl.data.JvxlData
- meshColor - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- meshCount - Variable in class org.jmol.shape.MeshCollection
- meshData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- meshData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- MeshData - Class in org.jmol.export
-
Class to generate mesh data (faces, vertices, and normals) for several kinds of generic meshes.
- MeshData - Class in org.jmol.jvxl.data
- MeshData() - Constructor for class org.jmol.export.MeshData
- MeshData() - Constructor for class org.jmol.jvxl.data.MeshData
- MeshData.SortSet - Class in org.jmol.jvxl.data
- MeshData.SSet - Class in org.jmol.jvxl.data
- meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceReader
- MeshDataServer - Interface in org.jmol.jvxl.api
- meshes - Variable in class org.jmol.renderbio.BioMeshRenderer
- meshes - Variable in class org.jmol.shape.MeshCollection
- meshes - Variable in class org.jmol.shapebio.BioShape
- meshOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- meshReady - Variable in class org.jmol.renderbio.BioMeshRenderer
- meshReady - Variable in class org.jmol.shapebio.BioShape
- meshRenderer - Variable in class org.jmol.renderbio.BioShapeRenderer
- MeshRenderer - Class in org.jmol.render
-
an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
- MeshRenderer() - Constructor for class org.jmol.render.MeshRenderer
- meshRibbon - Static variable in class org.jmol.script.T
- MeshRibbon - Class in org.jmol.shapebio
- MeshRibbon() - Constructor for class org.jmol.shapebio.MeshRibbon
- MeshRibbonRenderer - Class in org.jmol.renderbio
- MeshRibbonRenderer() - Constructor for class org.jmol.renderbio.MeshRibbonRenderer
- meshscale - Static variable in class org.jmol.script.T
- meshScale - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- meshScale - Variable in class org.jmol.viewer.GlobalSettings
- meshSlabValue - Variable in class org.jmol.render.MeshRenderer
- MeshSlicer - Class in org.jmol.util
- MeshSlicer() - Constructor for class org.jmol.util.MeshSlicer
- meshSurface - Variable in class org.jmol.renderbio.RocketRenderer
- meshSurface - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- MeshSurface - Class in org.jmol.util
- MeshSurface() - Constructor for class org.jmol.util.MeshSurface
- meshTranslucency - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- meshType - Variable in class org.jmol.util.MeshSurface
- meshWidth - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- message - Variable in exception org.jmol.script.ScriptException
- message - Static variable in class org.jmol.script.T
- MESSAGE - Enum constant in enum org.jmol.c.CBK
- messageQueue - Variable in class org.jmol.viewer.StatusManager
- messagestylechime - Static variable in class org.jmol.script.T
- messageStyleChime - Variable in class org.jmol.viewer.GlobalSettings
- META_MASK - Static variable in class org.jmol.awtjs.Event
- meth - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- methBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- METHOD_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- methyl - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- mf - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- mf - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- mf - Variable in class org.jmol.util.JmolMolecule
- mi - Variable in class org.jmol.util.Point3fi
-
model index -- may be to a trajectory
- middle - Static variable in class org.jmol.script.T
- middle - Variable in class org.openscience.jmol.app.surfacetool.Slice
- MIDDLE - Static variable in class org.jmol.viewer.binding.Binding
- mident - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- mident - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
- millis - Variable in class org.jmol.script.ScriptDelayThread
- min - Static variable in class org.jmol.script.T
- MIN_ADDH - Static variable in class org.jmol.viewer.Viewer
- MIN_ALIGNED - Static variable in class org.jmol.smiles.PolyhedronStereoSorter
- MIN_AXIS_LEN - Static variable in class org.jmol.shape.Axes
- MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- MIN_DELAY_MS - Static variable in class org.jmol.viewer.MouseState
- MIN_HAVE_FIXED - Static variable in class org.jmol.viewer.Viewer
- MIN_MESH_RENDER_SIZE - Static variable in class org.jmol.renderbio.BioMeshRenderer
- min_mesh_spacing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MIN_NO_RANGE - Static variable in class org.jmol.viewer.Viewer
- MIN_QUICK - Static variable in class org.jmol.viewer.Viewer
- MIN_RESNO - Static variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- MIN_SILENT - Static variable in class org.jmol.viewer.Viewer
- MIN_SIZE - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- min_squarable_double - Static variable in class org.jmol.minimize.Util
- MIN_XX - Static variable in class org.jmol.viewer.Viewer
- MinAngle - Class in org.jmol.minimize
- MinAngle(int[]) - Constructor for class org.jmol.minimize.MinAngle
- minAngles - Variable in class org.jmol.minimize.forcefield.Calculations
- minAngles - Variable in class org.jmol.minimize.forcefield.ForceField
- minAngles - Variable in class org.jmol.minimize.Minimizer
- minArray - Variable in class org.jmol.modelset.MeasurementData
- MinAtom - Class in org.jmol.minimize
- MinAtom(int, Atom, double[], int) - Constructor for class org.jmol.minimize.MinAtom
- minAtomCount - Variable in class org.jmol.minimize.forcefield.ForceField
- minAtoms - Variable in class org.jmol.minimize.forcefield.Calculations
- minAtoms - Variable in class org.jmol.minimize.forcefield.ForceField
- minAtoms - Variable in class org.jmol.minimize.Minimizer
- MinBond - Class in org.jmol.minimize
- MinBond(int, int, int, int, int, int, Integer) - Constructor for class org.jmol.minimize.MinBond
- minBondCount - Variable in class org.jmol.minimize.forcefield.ForceField
- minbonddistance - Static variable in class org.jmol.script.T
- minBondDistance - Variable in class org.jmol.viewer.GlobalSettings
- minBondDistance - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- minBonds - Variable in class org.jmol.minimize.forcefield.Calculations
- minBonds - Variable in class org.jmol.minimize.forcefield.ForceField
- minBonds - Variable in class org.jmol.minimize.Minimizer
- minColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
- minData - Variable in class org.jmol.shapesurface.Contact
- minGrid - Variable in class org.jmol.jvxl.data.VolumeData
- minHeight - Variable in class org.jmol.awtjs.swing.Component
- miniLogArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
- MINIMIZATION - Enum constant in enum org.jmol.c.CBK
- minimizationcriterion - Static variable in class org.jmol.script.T
- minimizationCriterion - Variable in class org.jmol.viewer.GlobalSettings
- minimizationmaxatoms - Static variable in class org.jmol.script.T
- minimizationMaxAtoms - Variable in class org.jmol.viewer.GlobalSettings
- minimizationOn - Variable in class org.jmol.minimize.Minimizer
- minimizationOn() - Method in class org.jmol.minimize.Minimizer
- minimizationrefresh - Static variable in class org.jmol.script.T
- minimizationRefresh - Variable in class org.jmol.viewer.GlobalSettings
- minimizationsilent - Static variable in class org.jmol.script.T
- minimizationSilent - Variable in class org.jmol.viewer.GlobalSettings
- minimizationsteps - Static variable in class org.jmol.script.T
- minimizationSteps - Variable in class org.jmol.viewer.GlobalSettings
- minimizationThread - Variable in class org.jmol.minimize.Minimizer
- MinimizationThread - Class in org.jmol.minimize
- MinimizationThread() - Constructor for class org.jmol.minimize.MinimizationThread
- minimize - Static variable in class org.jmol.script.T
- minimize() - Method in class org.jmol.scriptext.CmdExt
- minimize(boolean) - Method in class org.jmol.viewer.ActionManager
- minimize(int, double, BS, BS, BS, int, String) - Method in class org.jmol.minimize.Minimizer
- minimize(JmolScriptEvaluator, int, float, BS, BS, float, int) - Method in class org.jmol.viewer.Viewer
- MINIMIZE_FIXED_RANGE - Static variable in class org.jmol.viewer.JC
- minimizer - Variable in class org.jmol.minimize.forcefield.ForceField
- minimizer - Variable in class org.jmol.minimize.MinimizationThread
- minimizer - Variable in class org.jmol.viewer.Viewer
- Minimizer - Class in org.jmol.minimize
- Minimizer() - Constructor for class org.jmol.minimize.Minimizer
- minimizeWithoutThread() - Method in class org.jmol.minimize.Minimizer
- minimumHbondDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
- minindex - Variable in class org.openscience.jmol.app.janocchio.LabelSetter
- MININUM_GESTURE_DELAY_MILLISECONDS - Static variable in class org.jmol.viewer.ActionManager
- minL - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- minLeft - Variable in class org.jmol.bspt.Node
- minList - Variable in class org.jmol.minimize.MMConstraint
- minmax - Variable in class org.jmol.smiles.SmilesMeasure
- minMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
- minmaxmask - Static variable in class org.jmol.script.T
- MinObject - Class in org.jmol.minimize
- MinObject() - Constructor for class org.jmol.minimize.MinObject
- minpixelselradius - Static variable in class org.jmol.script.T
- minPixelSelRadius - Variable in class org.jmol.viewer.GlobalSettings
- MinPosition - Class in org.jmol.minimize
-
not implemented -- would be a force toward a given position in space
- MinPosition(int[], double[]) - Constructor for class org.jmol.minimize.MinPosition
- minPositions - Variable in class org.jmol.minimize.forcefield.Calculations
- minPositions - Variable in class org.jmol.minimize.forcefield.ForceField
- minPositions - Variable in class org.jmol.minimize.Minimizer
- minPtsPerAng - Variable in class org.jmol.jvxl.readers.AtomDataReader
- minRight - Variable in class org.jmol.bspt.Node
- minScreenDimension - Variable in class org.jmol.export.__RayTracerExporter
- minset - Static variable in class org.jmol.script.T
- minSet - Variable in class org.jmol.jvxl.readers.Parameters
- minSyncRepeatMs - Variable in class org.jmol.viewer.StatusManager
- minToPlaneDistance - Variable in class org.jmol.jvxl.data.VolumeData
- MinTorsion - Class in org.jmol.minimize
- MinTorsion(int[]) - Constructor for class org.jmol.minimize.MinTorsion
- minTorsions - Variable in class org.jmol.minimize.forcefield.Calculations
- minTorsions - Variable in class org.jmol.minimize.forcefield.ForceField
- minTorsions - Variable in class org.jmol.minimize.Minimizer
- minus - Static variable in class org.jmol.script.T
- minusMinus - Static variable in class org.jmol.script.T
- mInv - Static variable in class org.jmol.symmetry.PointGroup
- minWidth - Variable in class org.jmol.awtjs.swing.Component
- minX - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- minXYZ - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- minXYZ - Variable in class org.jmol.symmetry.UnitCellIterator
- minXYZ0 - Variable in class org.jmol.adapter.readers.cif.MSRdr
- minXYZ0 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- minY - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- minZ - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- minZ - Variable in class org.jmol.render.LabelsRenderer
- misc - Static variable in class org.jmol.script.T
- missingHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
- mixingChanged - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- mkBondPressed - Variable in class org.jmol.viewer.ActionManager
-
set to true in checkPressedAction if the screen coordinates of the press are relatively close to the coordinates of the hover that highlighted the bond, indicating that we can alias a left-click to a shift-left-click
- ml - Variable in class org.jmol.modelsetbio.BioResolver
- mlp - Static variable in class org.jmol.script.T
- MlpCalculation - Class in org.jmol.quantum
- MlpCalculation() - Constructor for class org.jmol.quantum.MlpCalculation
- mltb - Variable in class org.jmol.minimize.forcefield.AtomType
-
MMFF multiple bond type "specifies cases in which double (2) or triple (3) bonds are expected to be made to an atom having the listed atom type" [https://hpc.nih.gov/apps/charmm/c39b2html/mmff_params.html]
- mm - Variable in class org.jmol.viewer.Viewer
- mmcifLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- MMCifReader - Class in org.jmol.adapter.readers.cif
-
mmCIF files are recognized prior to class creation.
- MMCifReader() - Constructor for class org.jmol.adapter.readers.cif.MMCifReader
- MMCifValidationParser - Class in org.jmol.adapter.readers.cif
- MMCifValidationParser() - Constructor for class org.jmol.adapter.readers.cif.MMCifValidationParser
- MMConstraint - Class in org.jmol.minimize
- MMConstraint(int[], double) - Constructor for class org.jmol.minimize.MMConstraint
- mmff - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- mmff2DParams - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- MMFFAngleCalc - Class in org.jmol.minimize.forcefield
- MMFFAngleCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFAngleCalc
- MMFFDistanceCalc - Class in org.jmol.minimize.forcefield
- MMFFDistanceCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFDistanceCalc
- MMFFESCalc - Class in org.jmol.minimize.forcefield
- MMFFESCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFESCalc
- MMFFOOPCalc - Class in org.jmol.minimize.forcefield
- MMFFOOPCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFOOPCalc
- mmffParams - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- MMFFSBCalc - Class in org.jmol.minimize.forcefield
- MMFFSBCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFSBCalc
- MMFFTorsionCalc - Class in org.jmol.minimize.forcefield
- MMFFTorsionCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFTorsionCalc
- MMFFVDWCalc - Class in org.jmol.minimize.forcefield
- MMFFVDWCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFVDWCalc
- MMSTEREO - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MMTFReader - Class in org.jmol.adapter.readers.cif
-
JmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md full specification Version: v0.2+dev (as of 2016.08.08) is implemented,including: reading atoms, bonds, and DSSP 1.0 secondary structure load =1f88.mmtf filter "DSSP1" [Note that the filter "DSSP1" is required, since mmtf included DSSP 1.0 calculations, while the standard for Jmol itself is DSSP 2.0.
- MMTFReader() - Constructor for class org.jmol.adapter.readers.cif.MMTFReader
- mmType - Variable in class org.jmol.minimize.forcefield.AtomType
- mo - Variable in class org.jmol.jvxl.readers.IsoMOReader
- mo - Static variable in class org.jmol.script.T
- mo(boolean, int) - Method in class org.jmol.scriptext.IsoExt
- MO_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
- MO_OCC - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- moBases - Variable in class org.jmol.adapter.writers.QCJSONWriter
- MOCalculation - Class in org.jmol.quantum
- MOCalculation() - Constructor for class org.jmol.quantum.MOCalculation
- moCoeff - Variable in class org.jmol.quantum.MOCalculation
- moCoefficients - Variable in class org.jmol.quantum.MOCalculation
- moColorNeg - Variable in class org.jmol.shapesurface.MolecularOrbital
- moColorPos - Variable in class org.jmol.shapesurface.MolecularOrbital
- moCombo(Lst<Object[]>) - Method in class org.jmol.scriptext.IsoExt
- moCount - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
- moCount - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
- moCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- moCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- moCutoff - Variable in class org.jmol.shapesurface.MolecularOrbital
- moData - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- moData - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
- moData - Variable in class org.jmol.jvxl.readers.Parameters
- modAverage - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modAxes - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modAxes - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- modCalc - Variable in class org.jmol.util.ModulationSet
-
modCalc is used for calculations independent of what the current setting is
- modCell - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modCoord - Variable in class org.jmol.adapter.readers.cif.MSRdr
-
not used
- modCount - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modDebug - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modDim - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modDim - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- modDim - Variable in class org.jmol.symmetry.SpaceGroup
- modDim - Variable in class org.jmol.symmetry.SymmetryOperation
- modDim - Variable in class org.jmol.util.Vibration
-
modDim will be > 0 for modulation
- mode - Variable in class org.jmol.jvxl.calc.MarchingCubes
- mode - Variable in class org.jmol.jvxl.readers.MapFileReader
- mode - Variable in class org.jmol.render.LabelsRenderer
- mode - Static variable in class org.jmol.script.T
- mode - Variable in class org.jmol.viewer.TransformManager
- MODE_3D - Static variable in class org.jmol.viewer.TransformManager4D
- MODE_4D_WX - Static variable in class org.jmol.viewer.TransformManager4D
- MODE_4D_WY - Static variable in class org.jmol.viewer.TransformManager4D
- MODE_4D_WZ - Static variable in class org.jmol.viewer.TransformManager4D
- MODE_ARRAY - Static variable in class org.jmol.smiles.SmilesMatcher
- MODE_ATROP - Static variable in class org.jmol.smiles.SmilesMatcher
- MODE_BITSET - Static variable in class org.jmol.shapespecial.Polyhedra
- MODE_BITSET - Static variable in class org.jmol.smiles.SmilesMatcher
- MODE_BONDING - Static variable in class org.jmol.shapespecial.Polyhedra
- MODE_CALC_2JHH - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_3JCH - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_3JHH - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_ALL - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_INVALID - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_J - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_JHH - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CALC_NOE - Static variable in class org.jmol.quantum.NMRCalculation
- MODE_CUBE - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- MODE_ELLIPTICAL - Static variable in class org.jmol.renderbio.BioMeshRenderer
- MODE_FILL_COORDS - Static variable in class org.jmol.atomdata.AtomData
- MODE_FILL_MODEL - Static variable in class org.jmol.atomdata.AtomData
- MODE_FILL_MOLECULES - Static variable in class org.jmol.atomdata.AtomData
- MODE_FILL_MULTIMODEL - Static variable in class org.jmol.atomdata.AtomData
- MODE_FILL_RADII - Static variable in class org.jmol.atomdata.AtomData
- MODE_FLAT - Static variable in class org.jmol.renderbio.BioMeshRenderer
- MODE_GET_ATTACHED_HYDROGENS - Static variable in class org.jmol.atomdata.AtomData
- MODE_GET_COLOR_INDEXES - Static variable in class org.jmol.jvxl.data.MeshData
- MODE_GET_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
- MODE_HEX - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
- MODE_HYBRID36 - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
- MODE_INFO - Static variable in class org.jmol.shapespecial.Polyhedra
- MODE_IS_ANTIALIASED - Static variable in class org.jmol.render.TextRenderer
- MODE_JVXL - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- MODE_MAP - Static variable in class org.jmol.smiles.SmilesMatcher
- MODE_MASK - Static variable in class org.jmol.viewer.binding.Binding
- MODE_NAVIGATION - Static variable in class org.jmol.viewer.TransformManager
- MODE_NONELLIPTICAL - Static variable in class org.jmol.renderbio.BioMeshRenderer
- MODE_OPTIONS - Static variable in class org.jmol.modelkit.ModelKit
- MODE_P_ALLOW_FRACTIONAL - Static variable in class org.jmol.script.ScriptParam
- MODE_P_CONVERT_TO_CARTESIAN - Static variable in class org.jmol.script.ScriptParam
- MODE_P_IMPLICIT_FRACTIONAL - Static variable in class org.jmol.script.ScriptParam
- MODE_P_INT_ONLY - Static variable in class org.jmol.script.ScriptParam
- MODE_P_NULL_ON_ERROR - Static variable in class org.jmol.script.ScriptParam
- MODE_P3 - Static variable in class org.jmol.script.ScriptParam
- MODE_P34 - Static variable in class org.jmol.script.ScriptParam
- MODE_P4 - Static variable in class org.jmol.script.ScriptParam
- MODE_PDB - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
- MODE_PERSPECTIVE_PYMOL - Static variable in class org.jmol.viewer.TransformManager
- MODE_PLANES - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- MODE_POINTS - Static variable in class org.jmol.shapespecial.Polyhedra
- MODE_PUT_SETS - Static variable in class org.jmol.jvxl.data.MeshData
- MODE_PUT_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
- MODE_RADIUS - Static variable in class org.jmol.shapespecial.Polyhedra
- MODE_STANDARD - Static variable in class org.jmol.viewer.TransformManager
- MODE_TUBE - Static variable in class org.jmol.renderbio.BioMeshRenderer
- MODE_UNITCELL - Static variable in class org.jmol.shapespecial.Polyhedra
- moDebug - Variable in class org.jmol.shapesurface.MolecularOrbital
- model - Variable in class org.jmol.modelset.Chain
- model - Variable in class org.jmol.modelset.ModelLoader
- model - Variable in class org.jmol.modelsetbio.BioPolymer
- model - Static variable in class org.jmol.script.T
- model(int, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- Model - Class in org.jmol.modelset
- Model() - Constructor for class org.jmol.modelset.Model
- MODEL_CURRENT - Static variable in class org.jmol.viewer.AnimationManager
- MODEL_NO - Static variable in class org.jmol.adapter.readers.cif.CifReader
- modelAdapter - Variable in class org.jmol.viewer.Viewer
- modelAdapter - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- modelAtomCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- modelAtomCount - Variable in class org.jmol.adapter.readers.spartan.SpartanInputReader
- modelbased - Static variable in class org.jmol.script.T
- modelCenterOffset - Variable in class org.jmol.viewer.TransformManager
- modelCount - Variable in class org.jmol.adapter.readers.quantum.QCJSONReader
- modelCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- modelCount - Variable in class org.jmol.popup.JmolPopup
- modelFilename - Variable in class org.openscience.jmol.app.JmolApp
- modelFileNumberFromFloat(float) - Static method in class org.jmol.modelset.ModelSet
- modelFileNumbers - Variable in class org.jmol.modelset.ModelSet
- modelFlags - Variable in class org.jmol.shapespecial.DrawMesh
- modelHasVibrationVectors(int) - Method in class org.jmol.viewer.Viewer
- modelIdList - Variable in class org.jmol.jsv.JDXMOLParser
- modelindex - Static variable in class org.jmol.script.T
- modelIndex - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- modelIndex - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- modelIndex - Variable in class org.jmol.atomdata.AtomData
- modelIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
- modelIndex - Variable in class org.jmol.jvxl.readers.Parameters
- modelIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- modelIndex - Variable in class org.jmol.modelset.Model
- modelIndex - Variable in class org.jmol.modelset.StateScript
- modelIndex - Variable in class org.jmol.modelset.Text
- modelIndex - Variable in class org.jmol.popup.JmolPopup
- modelIndex - Variable in class org.jmol.shape.Mesh
- modelIndex - Variable in class org.jmol.shape.MeshCollection
- modelIndex - Variable in class org.jmol.shapebio.BioShape
- modelIndex - Variable in class org.jmol.shapespecial.Dipole
- modelIndex - Variable in class org.jmol.shapespecial.Ellipsoid
- modelIndex - Variable in class org.jmol.shapespecial.Polyhedra
- modelIndex - Variable in class org.jmol.shapespecial.Polyhedron
- modelIndex - Variable in class org.jmol.util.JmolMolecule
- modelIndex - Variable in class org.jmol.util.Tensor
- modelIndex - Variable in class org.openscience.jmol.app.janocchio.TableSorter.Row
- modelIndex(int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- modelIndexForFrame(int) - Method in class org.jmol.viewer.AnimationManager
- modelInfo - Variable in class org.jmol.popup.JmolPopup
- modelInfo - Variable in class org.jmol.shapespecial.Draw
- modelInvRotation - Variable in class org.jmol.jvxl.readers.Parameters
- modelIsRawPDB() - Method in class org.jmol.modelset.Atom
- modelIsRawPDB() - Method in class org.jmol.smiles.SmilesAtom
- modelIsRawPDB() - Method in interface org.jmol.util.Node
- modelkit - Variable in class org.jmol.modelkit.ModelKitPopup
-
set by MODELKIT [DISPLAY/HIDE]
- modelkit - Variable in class org.jmol.viewer.Viewer
- modelkit() - Method in class org.jmol.scriptext.CmdExt
-
Configure the ModelKitPopup for Crystallographic symmetry viewing and structure editing new 14.29.45 see modelkit.ModelKitPopup.java
- ModelKit - Class in org.jmol.modelkit
-
An abstract popup class that is instantiated for a given platform and context as one of:
- ModelKit() - Constructor for class org.jmol.modelkit.ModelKit
- MODELKIT - Enum constant in enum org.jmol.c.CBK
- MODELKIT_ZAP_STRING - Static variable in class org.jmol.viewer.JC
- MODELKIT_ZAP_TITLE - Static variable in class org.jmol.viewer.JC
- ModelKit.Constraint - Class in org.jmol.modelkit
- modelkitmode - Static variable in class org.jmol.script.T
- modelKitMode - Variable in class org.jmol.viewer.GlobalSettings
- ModelKitPopup - Class in org.jmol.modelkit
-
An abstract popup class that is instantiated for a given platform and context as one of:
- ModelKitPopup() - Constructor for class org.jmol.modelkit.ModelKitPopup
- ModelKitPopupResourceBundle - Class in org.jmol.modelkit
- ModelKitPopupResourceBundle(String, Properties) - Constructor for class org.jmol.modelkit.ModelKitPopupResourceBundle
- ModelLoader - Class in org.jmol.modelset
- ModelLoader(Viewer, String, SB, Object, ModelSet, BS) - Constructor for class org.jmol.modelset.ModelLoader
- ModelManager - Class in org.jmol.viewer
- ModelManager(Viewer) - Constructor for class org.jmol.viewer.ModelManager
- modelMap - Variable in class org.jmol.adapter.readers.cif.CifReader
- modelMolecule - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- modelName - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
- modelName - Variable in class org.jmol.atomdata.AtomData
- modelNames - Variable in class org.jmol.modelset.ModelSet
- modelNo - Variable in class org.jmol.adapter.readers.xtal.OptimadeReader
- modelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- modelNumberParameter(int) - Method in class org.jmol.script.ScriptParam
- modelNumbers - Variable in class org.jmol.modelset.ModelSet
- modelNumbersForAtomLabel - Variable in class org.jmol.modelset.ModelSet
- modelRadius - Variable in class org.jmol.viewer.TransformManager
- modelRadiusPixels - Variable in class org.jmol.viewer.TransformManager
- models - Variable in class org.jmol.export._IdtfExporter
- modelSet - Variable in class org.jmol.symmetry.SymmetryDesc
- modelSet - Variable in class org.jmol.viewer.ModelManager
- ModelSet - Class in org.jmol.modelset
- ModelSet(Viewer, String) - Constructor for class org.jmol.modelset.ModelSet
- modelSet0 - Variable in class org.jmol.modelset.ModelLoader
- modelSetFileName - Variable in class org.jmol.popup.JmolPopup
- modelSetHasVibrationVectors() - Method in class org.jmol.modelset.AtomCollection
- modelSetInfo - Variable in class org.jmol.popup.JmolPopup
- modelSetName - Variable in class org.jmol.modelset.ModelSet
- modelSetName - Variable in class org.jmol.popup.JmolPopup
- modelSetPathName - Variable in class org.jmol.viewer.ModelManager
- modelSetProperties - Variable in class org.jmol.modelset.ModelSet
- modelSetRoot - Variable in class org.jmol.popup.JmolPopup
- modelSetTypeName - Variable in class org.jmol.modelset.ModelSet
- modelsOf(BS, BS) - Method in class org.jmol.modelsetbio.BioModelSet
-
general purpose; return models associated with specific atoms
- modelStartEnd - Variable in class org.jmol.adapter.smarter.Structure
- modelStrings - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- modelToView - Variable in class org.openscience.jmol.app.janocchio.TableSorter
- modelVisibilityFlags - Variable in class org.jmol.shapebio.BioShape
- modelZeroBased - Variable in class org.jmol.geodesic.EnvelopeCalculation
- modeMultipleBond - Variable in class org.jmol.render.SticksRenderer
- modeMultipleBond - Variable in class org.jmol.viewer.GlobalSettings
- modificationMode - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- modifiedKeys - Variable in class org.jmol.util.JSONWriter
-
allows writing of one or more keys different from the original
- modifiers - Variable in class org.jmol.export._IdtfExporter
- modifiers - Variable in class org.jmol.viewer.MouseState
- modifiersDown - Variable in class org.jmol.awt.Mouse
- modifiersDown - Variable in class org.jmol.awtjs2d.Mouse
- modifiersWhenPressed10 - Variable in class org.jmol.awt.Mouse
- modifiersWhenPressed10 - Variable in class org.jmol.awtjs2d.Mouse
- modify - Static variable in class org.jmol.script.T
- MODIFY_DELETE_ATOM - Static variable in class org.jmol.viewer.Viewer
- MODIFY_DELETE_ATOMS - Static variable in class org.jmol.viewer.Viewer
- MODIFY_DELETE_BONDS - Static variable in class org.jmol.viewer.Viewer
- MODIFY_DELETE_MODEL - Static variable in class org.jmol.viewer.Viewer
- MODIFY_MAKE_BOND - Static variable in class org.jmol.viewer.Viewer
- MODIFY_SET_COORD - Static variable in class org.jmol.viewer.Viewer
- modifyorcreate - Static variable in class org.jmol.script.T
- modLast - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modMatrices - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modMatrices - Variable in class org.jmol.adapter.readers.cif.Subsystem
- modo - Static variable in class org.jmol.script.T
- moDots - Variable in class org.jmol.shapesurface.MolecularOrbital
- modPack - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modr - Variable in class org.jmol.adapter.readers.cif.CifReader
- mods - Variable in class org.jmol.util.ModulationSet
-
the list of all modulations associated with this atom
- modScale - Variable in class org.jmol.util.Vibration
- modSelected - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modt1 - Static variable in class org.jmol.script.T
- modt2 - Static variable in class org.jmol.script.T
- modt3 - Static variable in class org.jmol.script.T
- modTUV - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modType - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modulateAtom(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
The displacement will be set as the atom vibration vector; the string buffer will be appended with the t value for a given unit cell.
- modulated - Variable in class org.jmol.adapter.readers.cif.CifReader
- modulateoccupancy - Static variable in class org.jmol.script.T
- modulateOccupancy - Variable in class org.jmol.viewer.GlobalSettings
- modulating - Variable in class org.jmol.render.MeasuresRenderer
- modulation - Static variable in class org.jmol.script.T
- modulation() - Method in class org.jmol.scriptext.CmdExt
-
Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).
- Modulation - Class in org.jmol.util
-
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals, including Fourier series, Crenel functions, and sawtooth functions
- Modulation(char, char, double[], String, double[]) - Constructor for class org.jmol.util.Modulation
-
Each atomic modulation involves a fractional coordinate wave vector q, a Fourier power n, a modulation axis (x, y, or, z), and specified parameters that depend upon the type of function.
- modulationFields - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- modulationOn - Variable in class org.jmol.modelset.ModelLoader
- modulationscale - Static variable in class org.jmol.script.T
- modulationScale - Variable in class org.jmol.viewer.GlobalSettings
- ModulationSet - Class in org.jmol.util
-
A class to group a set of modulations for an atom as a "vibration" Extends V3 so that it will be a displacement, and its value will be an occupancy
- ModulationSet() - Constructor for class org.jmol.util.ModulationSet
- modulationTUV - Variable in class org.jmol.modelset.ModelLoader
- MODULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- moduleNestingLevel - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- modVib - Variable in class org.jmol.adapter.readers.cif.MSRdr
- modx - Static variable in class org.jmol.script.T
- modxyz - Static variable in class org.jmol.script.T
- mody - Static variable in class org.jmol.script.T
- modz - Static variable in class org.jmol.script.T
- moe_separate_chains - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MOEnergySorter() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
- moFactor - Variable in class org.jmol.quantum.MOCalculation
- moFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- moFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- moFill - Variable in class org.jmol.shapesurface.MolecularOrbital
- moFrontOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
- MOInfo() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
- moIsPositiveOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
- Mol2Reader - Class in org.jmol.adapter.readers.more
-
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
- Mol2Reader() - Constructor for class org.jmol.adapter.readers.more.Mol2Reader
- mol2Records - Static variable in class org.jmol.adapter.smarter.Resolver
- Mol3DReader - Class in org.jmol.adapter.readers.molxyz
-
3D only
- Mol3DReader() - Constructor for class org.jmol.adapter.readers.molxyz.Mol3DReader
- molAtoms - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- molCDKuptodate - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- molCDKuptodate - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- moldenFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- MoldenReader - Class in org.jmol.adapter.readers.quantum
-
A molecular structure and orbital reader for MolDen files.
- MoldenReader() - Constructor for class org.jmol.adapter.readers.quantum.MoldenReader
- molecular - Static variable in class org.jmol.script.T
- MolecularOrbital - Class in org.jmol.shapesurface
- MolecularOrbital() - Constructor for class org.jmol.shapesurface.MolecularOrbital
- MolecularOrbitalRenderer - Class in org.jmol.rendersurface
- MolecularOrbitalRenderer() - Constructor for class org.jmol.rendersurface.MolecularOrbitalRenderer
- molecularType - Variable in class org.jmol.adapter.readers.cif.CifReader
- molecule - Static variable in class org.jmol.script.T
- MOLECULE - Enum constant in enum org.jmol.c.PAL
- MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_ATOM_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_ATOM_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_ATOM_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_BOND - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_BOND_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_BOND_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_BOND_STEREO - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- MOLECULE_FORMULA - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- moleculeCount - Variable in class org.jmol.modelset.BondCollection
- moleculeCount - Variable in class org.jmol.modelset.Model
- MoleculeDependentAction(String) - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.MoleculeDependentAction
- moleculeID - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- moleculeIndex - Variable in class org.jmol.util.JmolMolecule
- moleculeNames - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- moleculeNesting - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- molecules - Variable in class org.jmol.modelset.BondCollection
- Molecules - Class in org.openscience.jmol.app.webexport
- Molecules() - Constructor for class org.openscience.jmol.app.webexport.Molecules
- moleculeXml - Variable in class org.jmol.jvxl.data.JvxlData
- molHasTLS - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- moLinearCombination - Variable in class org.jmol.shapesurface.Isosurface
- moLinearCombination - Variable in class org.jmol.shapesurface.MolecularOrbital
- molName - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- MolReader - Class in org.jmol.adapter.readers.molxyz
-
A reader for MDLI mol and sdf files.
- MolReader() - Constructor for class org.jmol.adapter.readers.molxyz.MolReader
- molTtypes - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- MOLWriter - Class in org.jmol.adapter.writers
- MOLWriter() - Constructor for class org.jmol.adapter.writers.MOLWriter
- MOMENT_LABEL - Static variable in class org.jmol.adapter.readers.cif.CifReader
- MOMENT_PRELIM_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
- MOMENT_PRELIM_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
- MOMENT_PRELIM_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
- MOMENT_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
- MOMENT_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
- MOMENT_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
- moMesh - Variable in class org.jmol.shapesurface.MolecularOrbital
- moModelSet - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
- moModelSet - Variable in class org.jmol.adapter.readers.quantum.OrcaReader
- moMonteCarloCount - Variable in class org.jmol.shapesurface.MolecularOrbital
- monitorenergy - Static variable in class org.jmol.script.T
- monitorEnergy - Variable in class org.jmol.viewer.GlobalSettings
- MonitorInputStream - Class in org.openscience.jvxl
- MonitorInputStream(InputStream, int) - Constructor for class org.openscience.jvxl.MonitorInputStream
- monomer - Static variable in class org.jmol.script.T
- Monomer - Class in org.jmol.modelsetbio
-
A class to maintain information about biomolecule groups that are (potentially) part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.
- Monomer() - Constructor for class org.jmol.modelsetbio.Monomer
- MONOMER - Enum constant in enum org.jmol.c.PAL
- monomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
- monomerCount - Variable in class org.jmol.renderbio.BioShapeRenderer
- monomerCount - Variable in class org.jmol.shape.AtomShape
- monomerIndex - Variable in class org.jmol.modelsetbio.Monomer
- monomerIndexFirst - Variable in class org.jmol.modelsetbio.ProteinStructure
- monomerIndexLast - Variable in class org.jmol.modelsetbio.ProteinStructure
- monomers - Variable in class org.jmol.modelsetbio.BioPolymer
- monomers - Variable in class org.jmol.renderbio.BioShapeRenderer
- monomers - Variable in class org.jmol.shapebio.BioShape
- monteCarloCount - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- moNumber - Variable in class org.jmol.shapesurface.Isosurface
- moNumber - Variable in class org.jmol.shapesurface.MolecularOrbital
- moOffset(int) - Method in class org.jmol.scriptext.IsoExt
- MOPAC_TYPES - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- mopacArchiveContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- MopacArchiveReader - Class in org.jmol.adapter.readers.simple
-
Mopac Archive reader -- presumes "zMatrix" is really Cartesians use FILTER "NOCENTER" to NOT center atoms in unit cell use CENTROID for complete molecules with centroids within unit cell use PACKED CENTROID for complete molecules with any atoms within unit cell
- MopacArchiveReader() - Constructor for class org.jmol.adapter.readers.simple.MopacArchiveReader
- mopacBasis - Variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
GAMESS may need AM1, PMn, or RM1 zeta/coef data
- mopacContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- MopacGraphfReader - Class in org.jmol.adapter.readers.quantum
-
Reads Mopac 2007 GRAPHF output files
- MopacGraphfReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacGraphfReader
- mopacParams - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- MopacReader - Class in org.jmol.adapter.readers.simple
-
Reads Mopac 93, 6, 7, 2002, or 2009 output files
- MopacReader() - Constructor for class org.jmol.adapter.readers.simple.MopacReader
- MopacSlaterReader - Class in org.jmol.adapter.readers.quantum
- MopacSlaterReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacSlaterReader
- mopacVersion - Variable in class org.jmol.adapter.readers.simple.MopacReader
- moPlane - Variable in class org.jmol.shapesurface.MolecularOrbital
- moRandomSeed - Variable in class org.jmol.shapesurface.MolecularOrbital
- moReader - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- MOReader - Class in org.jmol.adapter.readers.quantum
-
General methods for reading molecular orbital data, including embedded output from the NBO program.
- MOReader() - Constructor for class org.jmol.adapter.readers.quantum.MOReader
- moreColors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- moreInfo - Variable in class org.jmol.symmetry.UnitCell
- moreLabels(Map<String, String>) - Method in class org.openscience.jmol.app.janocchio.NmrGuiMap
-
See NMR_JmolPanel where "NMR." is processed, and ./Properties/Nmr.properties where they are defined
- moreLabels(Map<String, String>) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
-
Add more labels if desired
- moResolution - Variable in class org.jmol.shapesurface.MolecularOrbital
- moreTokens() - Method in class org.jmol.script.ScriptTokenParser
- moreUnitCellInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- morph - Static variable in class org.jmol.script.T
- morph(float) - Method in class org.jmol.viewer.AnimationManager
- morph(int, int, float) - Method in class org.jmol.modelset.Trajectory
- morphCount - Variable in class org.jmol.viewer.AnimationManager
- morphTrajectories(int, int, float) - Method in class org.jmol.modelset.ModelSet
- mos - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
- mos - Variable in class org.jmol.jvxl.readers.IsoMOReader
- mosaicPreviewChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Called when the MosaicPreview check box is modified
- mosaicPreviewCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- mosaicPreviewComboEnd - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- mosaicPreviewComboStart - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- mosaicPreviewEnd - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- mosaicPreviewStart - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- moScale - Variable in class org.jmol.shapesurface.MolecularOrbital
- moShell - Variable in class org.jmol.shapesurface.MolecularOrbital
- moSlab - Variable in class org.jmol.shapesurface.MolecularOrbital
- moSlabValue - Variable in class org.jmol.shapesurface.MolecularOrbital
- moSquareData - Variable in class org.jmol.shapesurface.MolecularOrbital
- moSquareLinear - Variable in class org.jmol.shapesurface.MolecularOrbital
- moSymmetry - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
- motion_bias - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- motion_hand - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- motion_linear - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- motion_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- motion_simple - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- motionEventNumber - Variable in class org.jmol.viewer.Viewer
- MotionPoint - Class in org.jmol.viewer
- MotionPoint() - Constructor for class org.jmol.viewer.MotionPoint
- moTitleFormat - Variable in class org.jmol.shapesurface.MolecularOrbital
- moTranslucency - Variable in class org.jmol.shapesurface.MolecularOrbital
- moTranslucentLevel - Variable in class org.jmol.shapesurface.MolecularOrbital
- moTypes - Variable in class org.jmol.adapter.readers.quantum.MOReader
- mouse - Static variable in class org.jmol.script.T
- mouse - Variable in class org.jmol.viewer.Viewer
-
either org.jmol.awt.Mouse or org.jmol.awtjs2d.Mouse
- Mouse - Class in org.jmol.awt
-
formerly org.jmol.viewer.MouseManager14 methods required by Jmol that access java.awt.event private to org.jmol.awt
- Mouse - Class in org.jmol.awtjs2d
-
JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now)
- Mouse(double, PlatformViewer, Object) - Constructor for class org.jmol.awt.Mouse
-
Mouse is the listener for all events.
- Mouse(double, Viewer, Object) - Constructor for class org.jmol.awtjs2d.Mouse
- MOUSE_DOWN - Static variable in class org.jmol.awtjs.Event
- MOUSE_DRAG - Static variable in class org.jmol.awtjs.Event
- MOUSE_ENTER - Static variable in class org.jmol.awtjs.Event
- MOUSE_EXIT - Static variable in class org.jmol.awtjs.Event
- mouse_grid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MOUSE_LEFT - Static variable in class org.jmol.awtjs.Event
- mouse_limit - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MOUSE_MIDDLE - Static variable in class org.jmol.awtjs.Event
- MOUSE_MOVE - Static variable in class org.jmol.awtjs.Event
- MOUSE_NONE - Static variable in class org.jmol.viewer.JC
- mouse_restart_movie_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MOUSE_RIGHT - Static variable in class org.jmol.awtjs.Event
- mouse_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mouse_selection_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- MOUSE_UP - Static variable in class org.jmol.awtjs.Event
- MOUSE_WHEEL - Static variable in class org.jmol.awtjs.Event
- mouse_wheel_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mouse_z_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- mouseAction(int, long, int, int, int, int) - Method in interface org.jmol.api.EventManager
- mouseAction(int, long, int, int, int, int) - Method in class org.jmol.multitouch.ActionManagerMT
- mouseAction(int, long, int, int, int, int) - Method in class org.jmol.viewer.ActionManager
- mouseClicked(long, int, int, int, int) - Method in class org.jmol.awt.Mouse
- mouseClicked(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mouseClicked(MouseEvent) - Method in class org.jmol.awt.Mouse
- mouseClicked(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.janocchio.TableSorter.MouseHandler
- mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- mouseDown - Variable in class org.jmol.multitouch.ActionManagerMT
- mousedragfactor - Static variable in class org.jmol.script.T
- mouseDragFactor - Variable in class org.jmol.viewer.ActionManager
- mouseDragged(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- mouseDragged(long, int, int) - Method in class org.jmol.awt.Mouse
- mouseDragged(MouseEvent) - Method in class org.jmol.awt.Mouse
- mouseDragged(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseEntered(long, int, int) - Method in class org.jmol.awt.Mouse
- mouseEntered(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mouseEntered(MouseEvent) - Method in class org.jmol.awt.Mouse
- mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- mouseEnterExit(long, int, int, boolean) - Method in interface org.jmol.api.EventManager
- mouseEnterExit(long, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
- mouseExited(long, int, int) - Method in class org.jmol.awt.Mouse
- mouseExited(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mouseExited(MouseEvent) - Method in class org.jmol.awt.Mouse
- mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.JSPopupHelper
- mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- MouseHandler() - Constructor for class org.openscience.jmol.app.janocchio.TableSorter.MouseHandler
- mouseListener - Variable in class org.jmol.awtjs.swing.Component
- mouseListener - Variable in class org.openscience.jmol.app.janocchio.TableSorter
- mouseMode - Variable in class org.jmol.viewer.TransformManager4D
- mouseMoved(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
- mouseMoved(int, int) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- mouseMoved(long, int, int, int) - Method in class org.jmol.awt.Mouse
- mouseMoved(MouseEvent) - Method in class org.jmol.awt.Mouse
- mouseMoved(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mousePressed(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- mousePressed(long, int, int, int, boolean) - Method in class org.jmol.awt.Mouse
- mousePressed(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mousePressed(MouseEvent) - Method in class org.jmol.awt.Mouse
- mousePressed(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- mouseReleased(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- mouseReleased(long, int, int, int) - Method in class org.jmol.awt.Mouse
- mouseReleased(MouseEvent) - Method in class org.jmol.awt.AwtPopupHelper
- mouseReleased(MouseEvent) - Method in class org.jmol.awt.Mouse
- mouseReleased(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
- mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- mouseScript(String) - Method in class org.jmol.viewer.StatusManager
- MouseState - Class in org.jmol.viewer
- MouseState(String) - Constructor for class org.jmol.viewer.MouseState
- mouseWheel(long, int, int) - Method in class org.jmol.awt.Mouse
- mousewheelfactor - Static variable in class org.jmol.script.T
- mouseWheelFactor - Variable in class org.jmol.viewer.ActionManager
- mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awt.Mouse
- mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awtjs2d.Mouse
- movableBitSet - Variable in class org.jmol.viewer.Viewer
- movableX - Variable in class org.jmol.modelset.Text
- movableXPercent - Variable in class org.jmol.modelset.Text
- movableY - Variable in class org.jmol.modelset.Text
- movableYPercent - Variable in class org.jmol.modelset.Text
- movableZ - Variable in class org.jmol.modelset.Text
- movableZPercent - Variable in class org.jmol.modelset.Text
- move - Static variable in class org.jmol.script.T
- move(M4, BS) - Method in class org.jmol.shapespecial.Polyhedron
- move(JmolScriptEvaluator, V3, float, V3, float, float, int) - Method in class org.jmol.viewer.TransformManager
- move(JmolScriptEvaluator, V3, float, V3, float, float, int) - Method in class org.jmol.viewer.Viewer
- MOVE - Static variable in class org.jmol.multitouch.ActionManagerMT
- move2D(int, int, int) - Method in class org.jmol.shape.Labels
- move2D(DrawMesh, int[], int, int, int, boolean) - Method in class org.jmol.shapespecial.Draw
- moveAtoms(M4, M3, M3, V3, BS, P3, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
- moveAtoms(M4, M3, M3, V3, P3, boolean, BS, boolean) - Method in class org.jmol.viewer.Viewer
- moveAtomWithHydrogens(int, int, int, int, BS) - Method in class org.jmol.viewer.Viewer
- moveConstrained(int, P3, boolean, boolean) - Method in class org.jmol.modelkit.ModelKit
-
This is the main method from viewer.moveSelected.
- moved - Variable in class org.jmol.thread.HoverWatcherThread
- moved - Variable in class org.jmol.viewer.ActionManager
- moved(long, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
- MOVED - Static variable in class org.jmol.awtjs.Event
- movepict(String) - Method in class org.openscience.jmol.app.webexport.JmolInstance
- moveRotationCenter(P3, boolean) - Method in class org.jmol.viewer.TransformManager
- moveSelected(int, int, int, int, int, BS, boolean, boolean, int) - Method in class org.jmol.viewer.Viewer
- moveto - Static variable in class org.jmol.script.T
- moveTo(String) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- moveTo(JmolScriptEvaluator, float, P3, T3, float, M3, float, float, float, float, P3, float, float, float, float, float, float) - Method in class org.jmol.viewer.TransformManager
- moveTo(JmolScriptEvaluator, float, P3, V3, float, M3, float, float, float, float, P3, float, float, float, float, float, float) - Method in class org.jmol.viewer.Viewer
- MoveToAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
- moveToPyMOL(JmolScriptEvaluator, float, float[]) - Method in class org.jmol.viewer.TransformManager
- moveToText - Variable in class org.jmol.modelset.Orientation
- movetoThread - Variable in class org.jmol.viewer.TransformManager
- MoveToThread - Class in org.jmol.thread
- MoveToThread() - Constructor for class org.jmol.thread.MoveToThread
- MoveToThread.Slider - Class in org.jmol.thread
- movetoTime - Variable in class org.openscience.jmol.app.webexport.Test
- moveUpdate(float) - Method in class org.jmol.viewer.Viewer
- movie - Static variable in class org.jmol.script.T
- movie_animate_by_frame - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movie_auto_interpolate - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movie_auto_store - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movie_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movie_fps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movie_loop - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movie_panel - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movie_panel_row_height - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movie_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movie_rock - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- movingSelected - Variable in class org.jmol.viewer.Viewer
- mp - Variable in class org.jmol.viewer.ActionManager
- mPending - Variable in class org.jmol.shape.Measures
- mpr - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- mpts - Variable in class org.jmol.render.MeasuresRenderer
-
modulation points, which must be refreshed based on phase of the vibration; keyed on atom index.
- mr - Variable in class org.jmol.adapter.readers.molxyz.V3000Rdr
- mrc - Static variable in class org.jmol.script.T
- MrcBinaryReader - Class in org.jmol.jvxl.readers
- MrcBinaryReader() - Constructor for class org.jmol.jvxl.readers.MrcBinaryReader
- ms - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ms - Variable in class org.jmol.modelset.Measurement
- ms - Variable in class org.jmol.modelset.MeasurementData
- ms - Variable in class org.jmol.modelset.Model
-
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
- ms - Variable in class org.jmol.modelset.ModelLoader
- ms - Variable in class org.jmol.modelset.Trajectory
- ms - Variable in class org.jmol.modelsetbio.BioExt
- ms - Variable in class org.jmol.modelsetbio.BioModelSet
- ms - Variable in class org.jmol.modelsetbio.BioResolver
- ms - Variable in class org.jmol.render.ShapeRenderer
- ms - Variable in class org.jmol.shape.Shape
- ms - Variable in class org.jmol.viewer.ShapeManager
- ms - Variable in class org.jmol.viewer.Viewer
- MSCifParser - Class in org.jmol.adapter.readers.cif
- MSCifParser() - Constructor for class org.jmol.adapter.readers.cif.MSCifParser
- msg - Variable in class org.jmol.jvxl.data.JvxlData
- msInfo - Variable in class org.jmol.modelset.ModelSet
- MSInterface - Interface in org.jmol.adapter.smarter
-
Modulated Structure Reader Interface
- msms - Static variable in class org.jmol.script.T
- MsmsReader - Class in org.jmol.jvxl.readers
- MsmsReader() - Constructor for class org.jmol.jvxl.readers.MsmsReader
- msRdr - Variable in class org.jmol.adapter.readers.cif.Subsystem
- MSRdr - Class in org.jmol.adapter.readers.cif
-
generalized modulated structure reader class for CIF and Jana -- includes Fourier, Crenel, Sawtooth; displacement, occupancy, and Uij -- handles up to 6 modulation wave vectors -- commensurate and incommensurate, including composites -- not handling _cell_commen_t_section_1
- MSRdr() - Constructor for class org.jmol.adapter.readers.cif.MSRdr
- mTemp - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- mTemp - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- mtlout - Variable in class org.jmol.export._ObjExporter
-
BufferedWriter for the .mtl file.
- mu - Variable in class org.jmol.modelsetbio.Monomer
- mul - Static variable in class org.jmol.script.T
- mul3 - Static variable in class org.jmol.script.T
- mult - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- MULTI_POINT_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JC
- MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JC
- MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JC
- MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JC
- multiModel - Variable in class org.jmol.geodesic.EnvelopeCalculation
- MULTIPLE - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- multiplebondbananas - Static variable in class org.jmol.script.T
- multipleBondBananas - Variable in class org.jmol.viewer.GlobalSettings
- multipleBondDuplicate - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
potentially useful information that this duplicate is from an double- or triple-bond, not a ring closure
- multiplebondradiusfactor - Static variable in class org.jmol.script.T
- multipleBondRadiusFactor - Variable in class org.jmol.render.SticksRenderer
- multipleBondRadiusFactor - Variable in class org.jmol.viewer.GlobalSettings
- multiplebondspacing - Static variable in class org.jmol.script.T
- multipleBondSpacing - Variable in class org.jmol.render.SticksRenderer
- multipleBondSpacing - Variable in class org.jmol.viewer.GlobalSettings
- multiplex - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- multiplicity - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- multiplier - Variable in class org.jmol.navigate.Navigator
- multiprocessor - Static variable in class org.jmol.script.T
- multiProcessor - Variable in class org.jmol.viewer.GlobalSettings
- multiTouch - Variable in class org.jmol.viewer.Viewer
- multSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- mustBeConnected - Variable in class org.jmol.modelset.MeasurementData
- mustBeConnected - Variable in class org.jmol.shape.Measures
- mustFinalizeModelSet - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- mustNotBeConnected - Variable in class org.jmol.modelset.MeasurementData
- mustNotBeConnected - Variable in class org.jmol.shape.Measures
- mustRender - Variable in class org.jmol.viewer.Viewer
- mustResumeEval - Variable in class org.jmol.script.ScriptContext
- mustResumeEval - Variable in class org.jmol.script.ScriptEval
- mutate - Static variable in class org.jmol.script.T
- mutate() - Method in class org.jmol.scriptext.CmdExt
- mutate(BS, String, String[], String, float[]) - Method in class org.jmol.modelsetbio.BioModelSet
- mutate(Viewer, BS, String, String[], String, float[]) - Method in class org.jmol.modelsetbio.BioExt
-
mutate the given group
- mutateAtom(Viewer, int, String, boolean) - Static method in class org.jmol.modelsetbio.BioExt
- mutateScript - Static variable in class org.jmol.modelsetbio.BioExt
- mxyz - Variable in class org.jmol.util.ModulationSet
-
the modulated magnetic spin
- myAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
- myAtoms - Variable in class org.jmol.util.ContactPair
- myBsA - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- myBsA - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
- myBsB - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- myBsB - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
- myClip - Variable in class org.jmol.util.JmolAudio
- myColorPt - Variable in class org.jmol.shapesurface.LcaoCartoon
- myColorPt - Variable in class org.jmol.shapesurface.MolecularOrbital
- MyFileFilter - Class in org.openscience.jmol.app.janocchio
- MyFileFilter(String[], String) - Constructor for class org.openscience.jmol.app.janocchio.MyFileFilter
- MyFileFilter(String, String) - Constructor for class org.openscience.jmol.app.janocchio.MyFileFilter
- myFps - Variable in class org.jmol.thread.SpinThread
- myID - Variable in class org.jmol.shapespecial.Ellipsoid
- myIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
- myKey - Variable in class org.jmol.script.SV.Sort
- myLabels - Variable in class org.jmol.symmetry.SymmetryOperation
- myMask - Variable in class org.jmol.shape.Sticks
- myName - Variable in class org.jmol.script.SV
- myName - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- myPath - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
String path, for debugging
- mySlabValue - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- myStatusListener - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- MyStatusListener(JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.MyStatusListener
- myType - Variable in class org.jmol.shape.Shape
- mytypes - Static variable in class org.jmol.modelsetbio.BioResolver
- MyUndoableEditListener() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument.MyUndoableEditListener
- myVisibilityFlag - Static variable in class org.jmol.modelset.Bond
- myVisibilityFlag - Variable in class org.jmol.render.ShapeRenderer
- myX - Variable in class org.jmol.quantum.QMAtom
- myX2 - Variable in class org.jmol.quantum.QMAtom
- myY - Variable in class org.jmol.quantum.QMAtom
- myY2 - Variable in class org.jmol.quantum.QMAtom
- myZ - Variable in class org.jmol.quantum.QMAtom
- myZ2 - Variable in class org.jmol.quantum.QMAtom
N
- n - Static variable in class org.jmol.adapter.smarter.Resolver
- n - Variable in class org.jmol.jvxl.data.MeshData.SSet
- n - Variable in class org.jmol.quantum.NMRNoeMatrix
- n - Variable in class org.jmol.smiles.SmilesRing
- n(int, int) - Static method in class org.jmol.script.T
- N - Static variable in class org.jmol.modelsetbio.AminoMonomer
- n0 - Variable in class org.jmol.jvxl.readers.MapFileReader
- n1 - Variable in class org.jmol.jvxl.readers.MapFileReader
- N1 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- n2 - Variable in class org.jmol.jvxl.readers.MapFileReader
- N2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- N3 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- N4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- N6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- N7 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- N9 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- na - Variable in class org.jmol.jvxl.readers.MapFileReader
- na - Variable in class org.jmol.util.SimpleUnitCell
- nada - Static variable in class org.jmol.script.T
- NADA - Enum constant in enum org.jmol.c.VDW
- NADA - Enum constant in enum org.jmol.modelsetbio.AlphaPolymer.Code
- name - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- name - Variable in class org.jmol.adapter.readers.xml.XmlReader.NVPair
- name - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
- name - Variable in class org.jmol.awtjs.swing.Component
- name - Variable in class org.jmol.awtjs2d.JSFile
- name - Variable in enum org.jmol.c.PAL
- name - Variable in enum org.jmol.c.STER
- name - Variable in class org.jmol.export._MayaExporter
- name - Variable in class org.jmol.minimize.forcefield.ForceField
- name - Variable in class org.jmol.script.ScriptFunction
- name - Static variable in class org.jmol.script.T
- name - Variable in enum org.jmol.shapespecial.Draw.EnumDrawType
- name - Variable in class org.jmol.symmetry.PointGroup
- name - Variable in class org.jmol.symmetry.SpaceGroup
- name - Variable in class org.jmol.symmetry.SpaceGroupFinder.SGAtom
- name - Variable in class org.jmol.symmetry.UnitCell
- name - Variable in class org.jmol.thread.JmolThread
- name - Variable in enum org.jmol.util.Edge.EnumBondOrder
- name - Variable in class org.jmol.viewer.binding.Binding
- name - Variable in class org.jmol.viewer.MouseState
- name - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- name - Variable in class org.openscience.jmol.app.webexport.Widgets.Widget
- NAME - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- NAME_HALL - Static variable in class org.jmol.symmetry.SpaceGroup
- NAME_HM - Static variable in class org.jmol.symmetry.SpaceGroup
- NAME_UNK - Static variable in class org.jmol.symmetry.SpaceGroup
- name0 - Variable in class org.jmol.script.ContextToken
- nameAsGiven - Variable in class org.jmol.viewer.FileManager
- nameAsGivenIn - Variable in class org.jmol.io.FileReader
- namedSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
- nameList - Static variable in enum org.jmol.c.CBK
- nameOf(int) - Static method in class org.jmol.script.T
-
note: nameOf is a very inefficient mechanism for getting the name of a token.
- nameRequired - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- names - Variable in class org.jmol.adapter.writers.PWMATWriter
- names - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- names - Variable in class org.jmol.script.ScriptFunction
- namesAsGivenIn - Variable in class org.jmol.io.FilesReader
- nameToGroup - Static variable in class org.jmol.symmetry.SpaceGroup
- NamfisReader - Class in org.openscience.jmol.app.janocchio
- NamfisReader(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NamfisReader
- NamfisSaver - Class in org.openscience.jmol.app.janocchio
- NamfisSaver(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NamfisSaver
- nan - Static variable in class org.jmol.scriptext.MathExt
- naNoH - Static variable in class org.jmol.modelsetbio.BioExt
- nAOs - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- natCharges - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- nativeLanguage - Variable in class org.jmol.i18n.Language
- nAtom - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
- nAtoms - Variable in class org.jmol.adapter.readers.cif.CifReader
- nAtoms - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
- nAtoms - Variable in class org.jmol.adapter.readers.more.MdTopReader
- nAtoms - Variable in class org.jmol.adapter.readers.more.Mol2Reader
- nAtoms - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- nAtoms - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
- nAtoms - Variable in class org.jmol.adapter.readers.xtal.PWmatReader
-
The format of pwmat config file specification is now clear, would like to adjust PWmatReader accordingly.
- nAtoms - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
- nAtoms - Variable in class org.jmol.minimize.MMConstraint
- nAtoms - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
number of substituent atoms (non-null atoms[] entries)
- nAtoms - Variable in class org.jmol.symmetry.PointGroup
- nAtoms - Variable in class org.jmol.symmetry.SpaceGroupFinder
- nAtoms - Variable in class org.jmol.symmetry.UnitCellIterator
- nAtoms0 - Variable in class org.jmol.adapter.readers.cif.CifReader
- natomsPerModel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- natomsPerModel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- naturalIsotopes - Static variable in class org.jmol.util.Elements
- nav - Variable in class org.jmol.viewer.TransformManager
- NAV_MODE_IGNORE - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_NEWXY - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_NEWXYZ - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_NEWZ - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_NONE - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_RESET - Static variable in class org.jmol.viewer.TransformManager
- NAV_MODE_ZOOMED - Static variable in class org.jmol.viewer.TransformManager
- navCenter - Variable in class org.jmol.modelset.Orientation
- navCenter - Variable in class org.jmol.thread.MoveToThread
- navDepth - Variable in class org.jmol.modelset.Orientation
- navDepth - Variable in class org.jmol.thread.MoveToThread
- navfps - Static variable in class org.jmol.script.T
- navFps - Variable in class org.jmol.viewer.TransformManager
- navigate - Static variable in class org.jmol.script.T
- navigate() - Method in class org.jmol.scriptext.CmdExt
- navigate(float, P3[][], P3[], float[], int, int) - Method in class org.jmol.navigate.Navigator
- navigate(int, int) - Method in class org.jmol.viewer.Viewer
- navigateAxis(V3, float) - Method in interface org.jmol.api.JmolNavigatorInterface
- navigateAxis(V3, float) - Method in class org.jmol.navigate.Navigator
- navigateAxis(V3, float) - Method in class org.jmol.viewer.TransformManager
-
scripted entry point for navigation
- navigateAxis(V3, float) - Method in class org.jmol.viewer.Viewer
- navigateKey(int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
- navigateKey(int, int) - Method in class org.jmol.navigate.Navigator
- navigateKey(int, int) - Method in class org.jmol.viewer.TransformManager
-
entry point for keyboard-based navigation
- navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in interface org.jmol.api.JmolNavigatorInterface
- navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.navigate.Navigator
- navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.viewer.TransformManager
- navigatePt(P3) - Method in class org.jmol.viewer.Viewer
- navigatesurface - Static variable in class org.jmol.script.T
- navigateTo(float, V3, float, P3, float, float, float) - Method in class org.jmol.navigate.Navigator
- navigating - Variable in class org.jmol.viewer.TransformManager
- navigationCenter - Variable in class org.jmol.viewer.TransformManager
- navigationdepth - Static variable in class org.jmol.script.T
- navigationDepthPercent - Variable in class org.jmol.viewer.TransformManager
- navigationList - Variable in class org.jmol.navigate.Navigator
- navigationmode - Static variable in class org.jmol.script.T
- navigationMode - Variable in class org.jmol.modelset.Orientation
- navigationMode - Variable in class org.jmol.viewer.GlobalSettings
- navigationOffset - Variable in class org.jmol.viewer.TransformManager
- navigationperiodic - Static variable in class org.jmol.script.T
- navigationPeriodic - Variable in class org.jmol.viewer.GlobalSettings
- navigationShiftXY - Variable in class org.jmol.viewer.TransformManager
- navigationslab - Static variable in class org.jmol.script.T
- navigationSlabOffset - Variable in class org.jmol.viewer.TransformManager
- navigationspeed - Static variable in class org.jmol.script.T
- navigationSpeed - Variable in class org.jmol.viewer.GlobalSettings
- Navigator - Class in org.jmol.navigate
-
Navigator is a user input mechanism that utilizes the keypad to drive through the model.
- Navigator() - Constructor for class org.jmol.navigate.Navigator
- navInterrupt() - Method in class org.jmol.viewer.TransformManager
- navMinMax - Variable in class org.jmol.viewer.ShapeManager
- navMode - Variable in class org.jmol.viewer.TransformManager
- navOn - Variable in class org.jmol.viewer.TransformManager
- navTranslatePercent(float, float) - Method in class org.jmol.viewer.Viewer
- navTranslatePercentOrTo(float, float, float) - Method in interface org.jmol.api.JmolNavigatorInterface
- navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.navigate.Navigator
- navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.viewer.TransformManager
-
seconds < 0 means "to (x,y)"; >= 0 mean "to (x%, y%)"
- navx - Static variable in class org.jmol.script.T
- navX - Variable in class org.jmol.viewer.TransformManager
- navy - Static variable in class org.jmol.script.T
- navY - Variable in class org.jmol.viewer.TransformManager
- NAVY - Static variable in class org.jmol.util.C
- navz - Static variable in class org.jmol.script.T
- navZ - Variable in class org.jmol.viewer.TransformManager
- nAxes - Variable in class org.jmol.symmetry.PointGroup
- nb - Variable in class org.jmol.jvxl.readers.MapFileReader
- nb - Variable in class org.jmol.util.SimpleUnitCell
- nb_spheres_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- nb_spheres_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- nb_spheres_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- nBackbonesDisplayed - Variable in class org.jmol.modelset.Atom
- nBalls - Variable in class org.jmol.export._MayaExporter
- nBasis - Variable in class org.jmol.adapter.readers.quantum.QchemReader
- nBasisFunctions - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
- nBF - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
- nBits - Variable in class org.jmol.g3d.LineRenderer
- nBlock - Variable in class org.jmol.jvxl.readers.XplorReader
- nbo - Static variable in class org.jmol.script.T
- NBO - Class in org.jmol.shapesurface
- NBO() - Constructor for class org.jmol.shapesurface.NBO
- NBO_CONFIG - Static variable in class org.jmol.viewer.JC
- NBO_MODEL - Static variable in class org.jmol.viewer.JC
- NBO_RUN - Static variable in class org.jmol.viewer.JC
- NBO_SEARCH - Static variable in class org.jmol.viewer.JC
- NBO_TYPES - Static variable in class org.jmol.viewer.JC
- NBO_VIEW - Static variable in class org.jmol.viewer.JC
- nbocharges - Static variable in class org.jmol.script.T
- nboCharges - Variable in class org.jmol.viewer.GlobalSettings
- nBonds - Variable in class org.jmol.minimize.MinAtom
- nBondsDisplayed - Variable in class org.jmol.modelset.Atom
- nBondsOr - Variable in class org.jmol.smiles.SmilesBond
- nboOptions - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- nboParser - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- nboParser - Variable in class org.jmol.viewer.Viewer
- NBOParser - Class in org.jmol.adapter.readers.quantum
- NBOParser() - Constructor for class org.jmol.adapter.readers.quantum.NBOParser
- NBORenderer - Class in org.jmol.rendersurface
- NBORenderer() - Constructor for class org.jmol.rendersurface.NBORenderer
- nboType - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- nboType - Variable in class org.jmol.shapesurface.MolecularOrbital
- nBrickX - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
- nBrickY - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
- nBytes - Variable in class org.jmol.jvxl.data.JvxlData
- nBytes - Variable in class org.jmol.jvxl.readers.SurfaceReader
- nc - Variable in class org.jmol.jvxl.readers.MapFileReader
- nc - Variable in class org.jmol.util.SimpleUnitCell
- nCharNewLine(int) - Method in class org.jmol.script.ScriptCompiler
-
Check for line ending at this point in script.
- nci - Static variable in class org.jmol.script.T
- NciCalculation - Class in org.jmol.quantum
- NciCalculation() - Constructor for class org.jmol.quantum.NciCalculation
- nCoef - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- nCoefficients - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- ncols - Variable in class org.jmol.awtjs.swing.Grid
- nContourMax - Static variable in class org.jmol.jvxl.calc.MarchingSquares
- nContourMax - Static variable in class org.jmol.jvxl.readers.Parameters
- nContours - Variable in class org.jmol.jvxl.data.JvxlData
- nContours - Variable in class org.jmol.jvxl.readers.Parameters
- nContourSegments - Variable in class org.jmol.jvxl.calc.MarchingSquares
- ncsoperFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- nCyl - Variable in class org.jmol.export._MayaExporter
- nData - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- nDataPoints - Variable in class org.jmol.jvxl.readers.SurfaceReader
- nDegrees - Variable in class org.jmol.thread.SpinThread
- ndim() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- NDIM - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- ndims - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- ndots - Static variable in class org.jmol.render.FontLineShapeRenderer
- nDots - Variable in class org.jmol.jvxl.readers.KinemageReader
- nDouble - Variable in class org.jmol.smiles.SmilesSearch
- ne - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
- nearbyAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
- nEdges - Variable in class org.jmol.jvxl.data.JvxlData
- needAromatic - Variable in class org.jmol.smiles.SmilesSearch
- needRightParen - Variable in class org.jmol.script.ScriptCompiler
- needRingData - Variable in class org.jmol.smiles.SmilesSearch
- needRingMemberships - Variable in class org.jmol.smiles.SmilesSearch
- needSelections() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- needToFill - Variable in class org.jmol.g3d.HermiteRenderer
- needTranslucent - Variable in class org.jmol.render.MeshRenderer
- needTranslucent - Variable in class org.jmol.renderbio.BioShapeRenderer
- negativeAtomCount - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- negCorner - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- neighbor_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- neighborCenters - Variable in class org.jmol.geodesic.EnvelopeCalculation
- neighborCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
- neighborIndices - Variable in class org.jmol.geodesic.EnvelopeCalculation
- neighborPlusProbeRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
- neighborRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
- neighborVertexesArrays - Static variable in class org.jmol.util.Geodesic
- neighborVertexesArrays - Static variable in class org.jmol.util.Normix
- neighborVertexesIcosahedron - Static variable in class org.jmol.util.Geodesic
- nElements - Variable in class org.jmol.awtjs.swing.JPanel
- nElements - Variable in class org.jmol.util.JmolMolecule
- nError - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- nestedBond - Variable in class org.jmol.smiles.SmilesSearch
- net - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- net - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- net - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- netCount - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- netID - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- netID - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- netLabel - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- netNotes - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- nets - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
list of TOPOL_NET loop or single data item data
- newA(float[]) - Static method in class org.jmol.util.SimpleUnitCell
- newAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- newAction(int, String, String) - Static method in class org.jmol.viewer.ActionManager
- NewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
- NewAction(String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
- newAndSetBit(int) - Static method in class org.jmol.util.BSUtil
- newAntialiasing - Variable in class org.jmol.util.GData
- newAtomSet() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- newAtomSet() - Method in class org.jmol.adapter.readers.xtal.DmolReader
- newAtomSet() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- newAtomSet() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- newAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Create a new atoms set, clearing the atom map
- newAtomSet(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
- newAtomSet(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- newAtomSetClear(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Create a new atom set, optionally clearing the atom map.
- newBinaryDocument() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- newBinding(Viewer, String) - Static method in class org.jmol.viewer.binding.Binding
- newBitSet2(int, int) - Static method in class org.jmol.util.BSUtil
- newBS(BS, int[]) - Static method in class org.jmol.modelset.BondSet
- newBufferedImage(int, int) - Static method in class org.jmol.awt.Image
- newBufferedImage(Object, int, int) - Method in interface org.jmol.api.GenericPlatform
- newBufferedImage(Object, int, int) - Static method in class org.jmol.awt.Image
- newBufferedImage(Object, int, int) - Method in class org.jmol.awt.Platform
- newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs.Platform
- newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs2d.Platform
- newBZ(int) - Method in class org.jmol.util.BZone
-
initialize a new Brillouin zone
- newChain - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- newCloneAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- newCmd(int, Object) - Static method in class org.jmol.script.ContextToken
- newContext(boolean) - Static method in class org.jmol.script.ContextToken
- newContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
- newDataReader(Viewer, Object) - Static method in class org.jmol.viewer.FileManager
- newEcho(Viewer, Font, String, short, int, int, float) - Static method in class org.jmol.modelset.Text
- newF(float) - Static method in class org.jmol.script.SV
- newFile(String) - Method in interface org.jmol.api.GenericPlatform
- newFile(String) - Method in class org.jmol.awt.Platform
- newFile(String) - Static method in class org.jmol.awtjs2d.JSFile
- newFile(String) - Method in class org.jmol.awtjs2d.Platform
- newFileName - Variable in class org.jmol.shapesurface.Isosurface
- newFilesReader(String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
- newFont(String, boolean, boolean, float) - Method in interface org.jmol.api.FontManager
- newFont(String, boolean, boolean, float) - Static method in class org.jmol.awt.AwtFont
- newFont(String, boolean, boolean, float) - Method in class org.jmol.awt.Platform
- newFont(String, boolean, boolean, float) - Method in class org.jmol.awtjs2d.Platform
- newFont(String, boolean, boolean, float, String) - Static method in class org.jmol.awtjs2d.JSFont
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in interface org.jmol.api.GenericGraphics
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awt.AwtG2D
- newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awtjs2d.JsG2D
- newI(int) - Static method in class org.jmol.script.SV
- newI(int) - Static method in class org.jmol.util.Rgb16
- newID(String) - Static method in class org.jmol.awtjs.swing.Component
- newJButton(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJCheckBox(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJCheckBoxMenuItem(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJMenu(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
- newJMenu(String) - Method in class org.jmol.console.JmolConsole
- newJMenu(String) - Method in class org.jmol.consolejs.AppletConsole
- newJMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJMenuItem(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
- newJMenuItem(String) - Method in class org.jmol.console.JmolConsole
- newJMenuItem(String) - Method in class org.jmol.consolejs.AppletConsole
- newJMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJniInchiStructure(Viewer, String) - Static method in class org.jmol.inchi.InChIJNI
-
Jmol addition to create a JniInchiStructure from MOL data.
- newJniInchiStructure(Viewer, BS) - Static method in class org.jmol.inchi.InChIJNI
-
Jmol addition to create a JniInchiStructure from Jmol atoms.
- newJRadioButtonMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- newJSVar(Object) - Static method in class org.jmol.script.SV
-
Conversion to Jmol variables of JavaScript variables using y = javascript("x")
- newLabel(Viewer, Font, String, short, short, int, float) - Static method in class org.jmol.modelset.Text
- newLattice(boolean) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- newLatticePts - Variable in class org.jmol.util.BZone
- newMeasure(Viewer, Font, short) - Static method in class org.jmol.modelset.Text
- newMeasurementData(String, Lst<Object>) - Method in class org.jmol.viewer.Viewer
- newMenuItem(SC, SC, String, String, String) - Method in class org.jmol.popup.GenericPopup
- newMesh(boolean, T3[], int, int[][], T3[], int) - Static method in class org.jmol.util.MeshSurface
- newModel(int) - Method in class org.jmol.adapter.readers.cif.CifReader
- newNavigationCenter() - Method in class org.jmol.navigate.Navigator
-
We do not want the fixed navigation offset to change, but we need a new model-based equivalent position.
- newOffScreenImage(int, int) - Method in interface org.jmol.api.GenericPlatform
- newOffScreenImage(int, int) - Method in class org.jmol.awt.Platform
- newOffScreenImage(int, int) - Method in class org.jmol.awtjs.Platform
- newOffScreenImage(int, int) - Method in class org.jmol.awtjs2d.Platform
- newPlanePts - Variable in class org.jmol.util.BZone
- newPlanes - Variable in class org.jmol.util.BZone
- newPoint(int, int, int, P3) - Method in class org.jmol.util.BZone
- newPoint(M4, P3, int, int, int, P3) - Static method in class org.jmol.symmetry.Symmetry
- newReader(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- newReaderBr(String, BufferedReader) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- newRegion(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
-
Add a new region to the list of regions.
- newS(String) - Static method in class org.jmol.script.SV
- newScale - Variable in class org.jmol.shapecgo.CGO
- newScale - Variable in class org.jmol.shapespecial.Draw
- newScriptEvaluator() - Method in class org.jmol.script.ScriptManager
- newSearch(String, boolean, boolean) - Static method in class org.jmol.smiles.SmilesParser
- newSet() - Method in class org.jmol.geodesic.EnvelopeCalculation
- newSg() - Method in class org.jmol.shapesurface.Isosurface
- newSlider(float, float) - Method in class org.jmol.thread.MoveToThread
- newSpaceGroupPoint(P3, int, M4, int, int, int, P3) - Method in interface org.jmol.api.SymmetryInterface
- newSpaceGroupPoint(P3, int, M4, int, int, int, P3) - Method in class org.jmol.symmetry.Symmetry
- newStereo(SmilesSearch) - Static method in class org.jmol.smiles.SmilesStereo
- newSubZone(BZone, String, int) - Method in class org.jmol.util.BZone
- newSurface(int, ContactPair, BS, BS, RadiusData, float[], Object, boolean, VolumeData, float) - Method in class org.jmol.shapesurface.Contact
- newSV(int, int, Object) - Static method in class org.jmol.script.SV
- newT(T) - Static method in class org.jmol.script.SV
- newTensorType(V3[], float[], String, String) - Method in class org.jmol.util.Tensor
-
common processing of eigenvectors.
- newTextLabel(String, float[], int, int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- newToolbar(String[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- newTrajectory(ModelSet, Lst<P3[]>) - Method in class org.jmol.modelset.ModelLoader
- newUnits - Variable in class org.jmol.modelset.Measurement
- newV(int, Object) - Static method in class org.jmol.script.SV
- newVertex(P3, V3, float) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- newVertexBitSet() - Static method in class org.jmol.util.Normix
- newVoxelDataCube() - Method in class org.jmol.jvxl.readers.SurfaceReader
- newwinAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- NewwinAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
- newWindowHeight - Variable in class org.jmol.util.GData
- newWindowWidth - Variable in class org.jmol.util.GData
- next - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- next - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
- next - Static variable in class org.jmol.script.T
- next - Variable in class org.jmol.util.Int2IntHashEntry
- next - Variable in class org.jmol.util.MeshCapper.CapVertex
- next() - Method in interface org.jmol.api.AtomIndexIterator
- next() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- next() - Method in interface org.jmol.modelset.BondIterator
- next() - Method in class org.jmol.modelset.BondIteratorSelected
- next() - Method in class org.jmol.symmetry.UnitCellIterator
- NEXT - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- nextAtomSet() - Method in class org.jmol.adapter.readers.cif.CifReader
- nextCell() - Method in class org.jmol.symmetry.UnitCellIterator
- nextChiralBranch - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
points to next branching point that has two or more chiral branches
- nextCommand - Variable in class org.jmol.util.CommandHistory
-
Position of the next command.
- nextElement() - Method in class org.jmol.bspt.CubeIterator
-
normal iterator method
- nextFileName(String, int) - Method in class org.jmol.console.GenericConsole
- nextFileName(String, int) - Method in class org.jmol.console.JmolConsole
- nextFileName(String, int) - Method in class org.jmol.consolejs.AppletConsole
- nextIndex() - Method in interface org.jmol.modelset.BondIterator
- nextIndex() - Method in class org.jmol.modelset.BondIteratorSelected
- nextList(Object[], P3) - Method in class org.jmol.navigate.Navigator
- nextMeasure(int, int, Measurement, int) - Method in class org.jmol.modelset.MeasurementData
-
iterator for measurements
- nextPatternAtom(int, int, boolean, int) - Method in class org.jmol.smiles.SmilesSearch
- nextRandom8Bit() - Method in class org.jmol.util.Shader
-
Implements RANDU algorithm for random noise in lighting/shading.
- nextSP2 - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
first =X= atom in a string of =X=X=X=...
- nextTargetAtom(SmilesAtom, Node, int, int, boolean, int) - Method in class org.jmol.smiles.SmilesSearch
-
Check for a specific match of a model set atom with a pattern position
- nextToken() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
- nextToken() - Method in class org.jmol.jvxl.readers.PmeshReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.BCifDensityReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.MrcBinaryReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.UhbdReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.VaspChgcarReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.VolumeFileReader
- nextVoxel() - Method in class org.jmol.jvxl.readers.XplorReader
- nf - Static variable in class org.jmol.quantum.NMRNoeMatrix
- nFaces - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- nFast - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- NffReader - Class in org.jmol.jvxl.readers
- NffReader() - Constructor for class org.jmol.jvxl.readers.NffReader
- nFilePoints - Variable in class org.jmol.jvxl.readers.CastepDensityReader
- nFiltered - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- nFound - Variable in class org.jmol.symmetry.UnitCellIterator
- nFrankList - Variable in class org.jmol.popup.JmolGenericPopup
- nFree - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
- nGaussians - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- nGaussians - Variable in class org.jmol.quantum.MOCalculation
- nHallOperators - Variable in class org.jmol.symmetry.SpaceGroup
- nHAtoms - Variable in class org.jmol.quantum.NMRNoeMatrix
- nhChecked - Variable in class org.jmol.modelsetbio.AminoMonomer
- nHits - Variable in class org.jmol.navigate.Navigator
- nihresolverformat - Static variable in class org.jmol.script.T
- nihResolverFormat - Variable in class org.jmol.viewer.GlobalSettings
- nImage - Variable in class org.jmol.export.___Exporter
- nIn - Variable in class org.jmol.util.Shader
- nInvalid - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- nioClosed(JsonNioServer) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- nioClosed(JsonNioServer) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
- nioSync(Viewer, Map<String, Object>) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
-
process touch or gesture commands driven by hardware.
- nitrogenHydrogenPoint - Variable in class org.jmol.modelsetbio.AlphaMonomer
- nLatticeTypes - Static variable in class org.jmol.symmetry.HallTranslation
- nLatticeVectors - Variable in class org.jmol.adapter.readers.xtal.AimsReader
- nLCAO - Variable in class org.jmol.shapesurface.Isosurface
- nLinks - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- nList - Variable in class org.jmol.shapecgo.CGOMesh
- nMatrixElements - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- nModels - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
- nModels - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- nMolecular - Variable in class org.jmol.adapter.readers.cif.CifReader
- nMolecules - Variable in class org.jmol.quantum.NciCalculation
- nmr - Static variable in class org.jmol.script.T
- nmr - Variable in class org.openscience.jmol.app.janocchio.NmrReaderThread
- Nmr - Class in org.openscience.jmol.app.janocchio
- Nmr(String[]) - Constructor for class org.openscience.jmol.app.janocchio.Nmr
- Nmr(String[], NmrPlugin) - Constructor for class org.openscience.jmol.app.janocchio.Nmr
- NMR_DC - Static variable in class org.jmol.modelset.Measurement
- NMR_DisplayPanel - Class in org.openscience.jmol.app.janocchio
- NMR_DisplayPanel(JmolPanel) - Constructor for class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- NMR_DisplayPanel.DeselectallAction - Class in org.openscience.jmol.app.janocchio
- NMR_DisplayPanel.FrameDeltaDisplayAction - Class in org.openscience.jmol.app.janocchio
- NMR_DisplayPanel.PickAction - Class in org.openscience.jmol.app.janocchio
- NMR_DisplayPanel.PopulationDisplayAction - Class in org.openscience.jmol.app.janocchio
- NMR_DisplayPanel.RotateAction - Class in org.openscience.jmol.app.janocchio
- NMR_DisplayPanel.SelectallAction - Class in org.openscience.jmol.app.janocchio
- NMR_JC - Static variable in class org.jmol.modelset.Measurement
- NMR_JmolPanel - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel(JmolApp, Splash, JFrame, Jmol, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- NMR_JmolPanel.AtomSetChooserAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.DetachAppletAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.JumpBestFrameAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.LabelNmrAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.MoleculeDependentAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.MyStatusListener - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ReadNamfisAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ReadNmrAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ReattachAppletAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.SaveNmrAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ViewCoupleTableAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.ViewNoeTableAction - Class in org.openscience.jmol.app.janocchio
- NMR_JmolPanel.WriteNamfisAction - Class in org.openscience.jmol.app.janocchio
- NMR_NOE_OR_J - Static variable in class org.jmol.modelset.Measurement
- NMR_NOT - Static variable in class org.jmol.modelset.Measurement
- NMR_Viewer - Class in org.openscience.jmol.app.janocchio
-
Implements some lost interfaces.
- NMR_Viewer(Map<String, Object>) - Constructor for class org.openscience.jmol.app.janocchio.NMR_Viewer
- nmrApp - Variable in class org.openscience.jmol.app.janocchio.NmrPlugin
- nmrApplet - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- NmrApplet - Class in org.openscience.jmol.app.janocchio
- NmrApplet() - Constructor for class org.openscience.jmol.app.janocchio.NmrApplet
- nmrCalculation - Variable in class org.jmol.viewer.Viewer
- NMRCalculation - Class in org.jmol.quantum
- NMRCalculation() - Constructor for class org.jmol.quantum.NMRCalculation
- nmrDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- nmrguimap - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- NmrGuiMap - Class in org.openscience.jmol.app.janocchio
- NmrGuiMap() - Constructor for class org.openscience.jmol.app.janocchio.NmrGuiMap
- NmrMolecule - Class in org.openscience.jmol.app.janocchio
- NmrMolecule(NMR_JmolPanel, BS, String[], boolean) - Constructor for class org.openscience.jmol.app.janocchio.NmrMolecule
- NmrMolecule.DihedralCouple - Class in org.openscience.jmol.app.janocchio
- NMRNoeMatrix - Class in org.jmol.quantum
-
Class for calculating NOE intensities by full matrix relaxation approach.
- NMRNoeMatrix() - Constructor for class org.jmol.quantum.NMRNoeMatrix
- NMRNoeMatrix(NMRNoeMatrix.NOEParams) - Constructor for class org.jmol.quantum.NMRNoeMatrix
- NMRNoeMatrix.NOEAtom - Class in org.jmol.quantum
- NMRNoeMatrix.NOEParams - Class in org.jmol.quantum
- nmrPanel - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- nmrPanel - Variable in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- nmrPanel - Variable in class org.openscience.jmol.app.janocchio.Nmr
- nmrPanel - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- nmrPanel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- NmrPlugin - Class in org.openscience.jmol.app.janocchio
- NmrPlugin() - Constructor for class org.openscience.jmol.app.janocchio.NmrPlugin
- nmrpredictformat - Static variable in class org.jmol.script.T
- nmrPredictFormat - Variable in class org.jmol.viewer.GlobalSettings
- NmrReader - Class in org.openscience.jmol.app.janocchio
- NmrReader(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NmrReader
- NmrReaderThread - Class in org.openscience.jmol.app.janocchio
- NmrReaderThread(File, NMR_JmolPanel) - Constructor for class org.openscience.jmol.app.janocchio.NmrReaderThread
- NmrResourceHandler - Class in org.openscience.jmol.app.janocchio
-
Provides access to resources (for example, strings and images).
- NmrResourceHandler() - Constructor for class org.openscience.jmol.app.janocchio.NmrResourceHandler
- NmrSaver - Class in org.openscience.jmol.app.janocchio
- NmrSaver(JFileChooser) - Constructor for class org.openscience.jmol.app.janocchio.NmrSaver
- NMRTableCellRenderer - Class in org.openscience.jmol.app.janocchio
- NMRTableCellRenderer() - Constructor for class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- nmrType(String) - Static method in class org.jmol.modelset.Measurement
- nmrurlformat - Static variable in class org.jmol.script.T
- nmrUrlFormat - Variable in class org.jmol.viewer.GlobalSettings
- nMtlBytes - Variable in class org.jmol.export._ObjExporter
-
Bytes written to the .mtl file.
- nNested - Variable in class org.jmol.smiles.SmilesSearch
- nNodes - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- nNOs - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- NO_ANISOTROPY - Static variable in class org.jmol.jvxl.readers.Parameters
- NO_AUTOPLAY - Static variable in interface org.jmol.api.JmolScriptManager
- NO_CHIRALITY - Static variable in class org.jmol.symmetry.CIPChirality
- no_idle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- NO_SCRIPT - Static variable in interface org.jmol.api.JmolScriptManager
- NO_VALUE - Static variable in class org.jmol.quantum.NciCalculation
- noArgs - Static variable in class org.jmol.script.T
- noAromatic - Variable in class org.jmol.smiles.SmilesSearch
- noAtoms - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- noAutoBond - Variable in class org.jmol.modelset.ModelLoader
- nobackshell - Static variable in class org.jmol.script.T
- NOBASIS_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- noBioComment - Variable in class org.jmol.smiles.SmilesGenerator
- noBondSym - Variable in class org.jmol.adapter.readers.xtal.CgdReader
- noColor - Variable in class org.jmol.export.__CartesianExporter
- noColor - Variable in class org.jmol.shapesurface.PMeshWriter
- nocontourlines - Static variable in class org.jmol.script.T
- noCopy(int, int) - Method in class org.jmol.script.ScriptExpr
- nocross - Static variable in class org.jmol.script.T
- noCross - Variable in class org.jmol.renderspecial.DipolesRenderer
- noCross - Variable in class org.jmol.shapespecial.Dipole
- Node - Class in org.jmol.bspt
-
Nodes of the bspt.
- Node - Interface in org.jmol.util
- Node(Bspt, int, Leaf) - Constructor for class org.jmol.bspt.Node
- nodebug - Static variable in class org.jmol.script.T
- nodeID - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- nodeIds - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- nodeLabels - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- nodelay - Static variable in class org.jmol.script.T
- noDelay - Variable in class org.jmol.viewer.GlobalSettings
-
ensures that ScriptManager.allowJSThreads is false so that ScriptManager.useThreads() returns false; Jmol 14.21.1
- nodes - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
list of TOPOL_NODE loop data
- nodes - Variable in class org.jmol.symmetry.CIPDataSmiles
- nodes - Variable in class org.jmol.util.JmolMolecule
- nodes - Variable in class org.jmol.viewer.Gesture
- nodots - Static variable in class org.jmol.script.T
- NOEAtom() - Constructor for class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- noeColourSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- NoeColourSelectionPanel - Class in org.openscience.jmol.app.janocchio
- NoeColourSelectionPanel(NoeTable) - Constructor for class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- noedeleteAllButton - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- noedeleteButton - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- noedges - Static variable in class org.jmol.script.T
- noeExprefValue - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- noeHeaders - Variable in class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- NoeListWindowListener() - Constructor for class org.openscience.jmol.app.janocchio.NoeTable.NoeListWindowListener
- noeM - Variable in class org.jmol.quantum.NMRNoeMatrix
- noeMatrix - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- noeNPrefIndices - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- noeNPrefValue - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- noeParameterSelectionPanel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- NoeParameterSelectionPanel - Class in org.openscience.jmol.app.janocchio
- NoeParameterSelectionPanel(NoeTable) - Constructor for class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- NOEParams() - Constructor for class org.jmol.quantum.NMRNoeMatrix.NOEParams
- noeSelection - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- noesetRefButton - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- noesy - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- noesy - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- noesyComboBox - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- noesyComboBoxActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- noesyLabel - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- noeTable - Variable in class org.openscience.jmol.app.janocchio.LabelSetter
- noeTable - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- noeTable - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- noeTable - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- noeTable - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- NoeTable - Class in org.openscience.jmol.app.janocchio
- NoeTable(NMR_JmolPanel, JFrame) - Constructor for class org.openscience.jmol.app.janocchio.NoeTable
-
Constructor
- NoeTable.NoeListWindowListener - Class in org.openscience.jmol.app.janocchio
- NoeTable.NoeTableModel - Class in org.openscience.jmol.app.janocchio
- noeTableModel - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- NoeTableModel() - Constructor for class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- noeWeight - Variable in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- noeWeightField - Variable in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- noFaceSpheres - Variable in class org.jmol.jvxl.readers.AtomDataReader
- nofill - Static variable in class org.jmol.script.T
- noFrankEcho - Variable in class org.jmol.viewer.Viewer
- noGraphicsAllowed - Variable in class org.jmol.viewer.Viewer
- nohead - Static variable in class org.jmol.script.T
- noHead - Variable in class org.jmol.shapespecial.Draw
- noHead - Variable in class org.jmol.shapespecial.DrawMesh
- NOHISTORYATALL_FLAG - Static variable in class org.jmol.util.CommandHistory
- NOHISTORYLINE_FLAG - Static variable in class org.jmol.util.CommandHistory
- NOJMOL - Enum constant in enum org.jmol.c.VDW
- noload - Static variable in class org.jmol.script.T
- nomesh - Static variable in class org.jmol.script.T
- nonbonded_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- nonbonded_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- nonbonded_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- nonbonded_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- nonbondedSize - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- nonbondedTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- none - Static variable in class org.jmol.modelkit.ModelKit
- none - Static variable in class org.jmol.script.T
- NONE - Enum constant in enum org.jmol.c.PAL
- NONE - Enum constant in enum org.jmol.c.STER
- NONE - Enum constant in enum org.jmol.c.STR
- NONE - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- NONE - Enum constant in enum org.jmol.viewer.Viewer.ACCESS
- NONE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- NONE - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- NONE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- NONE - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
- noneSelected - Variable in class org.jmol.viewer.SelectionManager
-
a flag to indicate that labels and fonts should be set to default values; set only by SELECT NONE;
- nonhydrogenDegree - Variable in class org.jmol.smiles.SmilesAtom
- nonNull(int[][], int) - Static method in class org.jmol.shape.Mesh
- nonNullBS(BS, int[][], int) - Static method in class org.jmol.shape.Mesh
- noPack - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- noplane - Static variable in class org.jmol.script.T
- noPrefs - Variable in class org.jmol.console.ScriptEditor
- noPrefs - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- nOps - Variable in class org.jmol.adapter.readers.cif.MSRdr
- nOps - Variable in class org.jmol.symmetry.PointGroup
- nOps - Variable in class org.jmol.util.ModulationSet
-
the number of operators in this space group -- needed for occupancy calculation
- nOrbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- nOrbitals0 - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- norm - Variable in class org.jmol.renderbio.BioMeshRenderer
- norm - Variable in class org.jmol.util.MeshSlicer
- NORM_NBO - Static variable in class org.jmol.quantum.MOCalculation
- NORM_NONE - Static variable in class org.jmol.quantum.MOCalculation
- NORM_NWCHEM - Static variable in class org.jmol.quantum.MOCalculation
- NORM_STANDARD - Static variable in class org.jmol.quantum.MOCalculation
- normal - Static variable in class org.jmol.script.T
- NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
- NORMAL_MODE - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- normal_workaround - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- normalCount - Variable in class org.jmol.util.MeshSurface
- normalize(V3) - Method in class org.jmol.symmetry.UnitCell
- normalize_ccp4_maps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- normalize_grd_maps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- normalize_o_maps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- normalizeAromaticity(BS) - Method in class org.jmol.smiles.SmilesSearch
-
create a temporary object to generate the aromaticity in a SMILES pattern for which there is no explicit aromaticity (Kekule) Not applicable to SMARTS
- normalizeClass(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
-
re-order bonds to match standard @ and @@ types
- normalizeOperationToCentroid(int, M4, P3[], int, int) - Static method in class org.jmol.symmetry.SymmetryOperation
-
Adjust the translation for this operator so that it moves the center of mass of the full set of atoms into the cell.
- normalizeTwelfths(float, int, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- normalizeUV - Variable in class org.jmol.export._ObjExporter
-
Whether to normalize UV texture coordinates.
- normalizeXRnd(float) - Static method in class org.jmol.util.SimpleUnitCell
- normalOrAxis - Variable in class org.jmol.symmetry.PointGroup.Operation
- normals - Variable in class org.jmol.shapespecial.Polyhedron
- normals - Variable in class org.jmol.util.MeshSurface
- normalsInverted - Variable in class org.jmol.shape.Mesh
- normalsT - Variable in class org.jmol.shapespecial.Polyhedra
- normalsTemp - Variable in class org.jmol.util.MeshSurface
- normAnglePanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- normDispl - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
- normix - Variable in class org.jmol.rendercgo.CGORenderer
- Normix - Class in org.jmol.util
-
Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
- Normix() - Constructor for class org.jmol.util.Normix
- NORMIX_GEODESIC_LEVEL - Static variable in class org.jmol.util.Normix
- NORMIX_NULL - Static variable in class org.jmol.util.Normix
- normix0 - Variable in class org.jmol.rendercgo.CGORenderer
- normix1 - Variable in class org.jmol.rendercgo.CGORenderer
- normix2 - Variable in class org.jmol.rendercgo.CGORenderer
- normixCount - Static variable in class org.jmol.util.GData
- normixCount - Variable in class org.jmol.util.MeshSurface
- normixCount - Static variable in class org.jmol.util.Normix
- normixes - Variable in class org.jmol.render.MeshRenderer
- normixes - Variable in class org.jmol.shape.Mesh
- normixes - Variable in class org.jmol.shapespecial.Polyhedron
- norml - Variable in class org.jmol.renderbio.BioMeshRenderer
- normType - Variable in class org.jmol.quantum.MOCalculation
- NORTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
- noSlab - Variable in class org.jmol.adapter.readers.xtal.OptimadeReader
- noStereo - Variable in class org.jmol.smiles.SmilesGenerator
- noSymmetryCount - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- not - Variable in class org.jmol.smiles.SmilesAtom
- NOT - Enum constant in enum org.jmol.c.HB
- NOT - Enum constant in enum org.jmol.c.STR
- NOT_LOADED - Enum constant in enum org.jmol.c.FIL
- NOT_SORTED - Static variable in class org.openscience.jmol.app.janocchio.TableSorter
- notBondedIndex - Variable in class org.jmol.smiles.SmilesAtom
- notCrossLinked - Variable in class org.jmol.smiles.SmilesAtom
- note - Static variable in class org.jmol.adapter.readers.simple.FAHReader
- note - Variable in class org.jmol.modelset.MeasurementData
- NOTE_SCRIPT_FILE - Static variable in class org.jmol.viewer.JC
- notfrontonly - Static variable in class org.jmol.script.T
- notHelixOrSheet(int) - Method in class org.jmol.modelsetbio.Sheet
- notification - Static variable in class org.openscience.jmol.app.janocchio.NmrPlugin
- notify(int, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
- notify(int, Object[]) - Method in class org.jmol.console.ScriptEditor
- notifyAtomPicked(int, String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.MyStatusListener
- notifyAtomPicked(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- notifyAtomPositionsChanged(int, BS, M4) - Method in class org.jmol.viewer.ShapeManager
- notifyAudioEnded(Object) - Method in interface org.jmol.api.JmolAppletInterface
- notifyAudioEnded(Object) - Method in class org.jmol.util.GenericApplet
- notifyAudioStatus(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
-
called from JmolAudio
- notifyCallback(CBK, Object[]) - Method in interface org.jmol.api.JmolCallbackListener
- notifyCallback(CBK, Object[]) - Method in class org.jmol.console.GenericConsole
- notifyCallback(CBK, Object[]) - Method in class org.jmol.util.GenericApplet
- notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.MyStatusListener
- notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- notifyCallback(CBK, Object[]) - Method in interface org.openscience.jmol.app.JmolPlugin
- notifyContext(ScriptContext, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
- notifyContext(ScriptContext, Object[]) - Method in class org.jmol.console.ScriptEditor
- notifyDone() - Method in class org.jmol.console.ScriptEditor
- notifyEnabled(CBK) - Method in interface org.jmol.api.JmolCallbackListener
- notifyEnabled(CBK) - Method in class org.jmol.console.GenericConsole
- notifyEnabled(CBK) - Method in class org.jmol.util.GenericApplet
- notifyEnabled(CBK) - Method in class org.jmol.viewer.StatusManager
- notifyEnabled(CBK) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- notifyEndOfRendering() - Method in interface org.jmol.api.GenericPlatform
- notifyEndOfRendering() - Method in class org.jmol.awt.Platform
- notifyEndOfRendering() - Method in class org.jmol.awtjs2d.Platform
- notifyEndOfRendering() - Method in class org.jmol.g3d.Platform3D
- notifyError(String, String, String) - Method in class org.jmol.viewer.StatusManager
- notifyError(String, String, String) - Method in class org.jmol.viewer.Viewer
- notifyFileLoaded(String, String, String, String, Boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.MyStatusListener
- notifyFileLoaded(String, String, String, String, Boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- notifyFileOpen(String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
" (*)" appended to a file name indicates that this file was loaded asynchronously
- notifyFileOpen(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- notifyFont(int) - Method in class org.jmol.console.ScriptEditor
- notifyFrameChanged(int) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.MyStatusListener
- notifyMinimizationStatus() - Method in class org.jmol.viewer.Viewer
- notifyMinimizationStatus(String, Integer, Float, Float, String) - Method in class org.jmol.viewer.StatusManager
- notifyMouseClicked(int, int, int, int) - Method in class org.jmol.viewer.Viewer
- notifyResumeStatus() - Method in interface org.jmol.api.JmolScriptEvaluator
- notifyResumeStatus() - Method in class org.jmol.script.ScriptEval
- notifyScriptCallback(String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- notifyScriptEditor(int) - Method in class org.jmol.script.ScriptEval
- notifyScriptEditor(int, Object[]) - Method in class org.jmol.viewer.Viewer
- notifyScriptStart() - Method in class org.jmol.console.ScriptEditor
- notifyScriptTermination(String) - Method in class org.jmol.console.ScriptEditor
- notifyStatusReady(boolean) - Method in class org.jmol.api.JmolViewer
- notifyStatusReady(boolean) - Method in class org.jmol.viewer.Viewer
- notifyStructureModified() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.MyStatusListener
- notifyStructureModified(int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- notifySurfaceGenerationCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
- notifySurfaceGenerationCompleted() - Method in class org.jmol.shapesurface.Isosurface
- notifySurfaceMappingCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
- notifySurfaceMappingCompleted() - Method in class org.jmol.shapesurface.Isosurface
- notifySync(String, String) - Method in class org.jmol.util.GenericApplet
- notifyThisCommand(int, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor
- notifyViewerRepaintDone() - Method in class org.jmol.api.JmolViewer
- notifyViewerRepaintDone() - Method in class org.jmol.viewer.Viewer
- notImplemented(String) - Static method in class org.jmol.modelkit.ModelKit
- notInCentroid(ModelSet, BS, int[]) - Method in interface org.jmol.api.SymmetryInterface
- notInCentroid(ModelSet, BS, int[]) - Method in class org.jmol.symmetry.Symmetry
- NotPDB - Variable in class org.jmol.popup.JmolPopup
- notriangles - Static variable in class org.jmol.script.T
- nOut - Variable in class org.jmol.util.Shader
- noValuesAtAll - Variable in class org.jmol.quantum.NciCalculation
- now - Static variable in class org.jmol.script.T
- noZapped - Variable in class org.jmol.popup.JmolPopup
- NP - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- nPairs - Variable in class org.jmol.smiles.SmilesGenerator
- nPairsMax - Variable in class org.jmol.smiles.SmilesGenerator
- nParameters - Variable in class org.jmol.script.ScriptFunction
- nPeaks - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- nPerLine - Variable in class org.jmol.jvxl.readers.VaspChgcarReader
- nPoints - Variable in class org.jmol.jvxl.data.VolumeData
- nPoints - Variable in class org.jmol.shapespecial.Draw
- nPoints - Variable in class org.jmol.shapespecial.Polyhedra
- nPoints - Variable in class org.jmol.smiles.SmilesMeasure
- nPoints - Variable in class org.jmol.util.MeshCapper
- nPointsX - Variable in class org.jmol.jvxl.data.JvxlData
- nPointsX - Variable in class org.jmol.jvxl.readers.SurfaceReader
- nPointsY - Variable in class org.jmol.jvxl.data.JvxlData
- nPointsY - Variable in class org.jmol.jvxl.readers.SurfaceReader
- nPointsZ - Variable in class org.jmol.jvxl.data.JvxlData
- nPointsZ - Variable in class org.jmol.jvxl.readers.SurfaceReader
- nPolygons - Variable in class org.jmol.jvxl.readers.NffReader
- nPolygons - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
- nPolygons - Variable in class org.jmol.jvxl.readers.PmeshReader
- nPolygons - Variable in class org.jmol.jvxl.readers.Ras3DReader
- npqd - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- nPrimitives - Variable in class org.jmol.smiles.SmilesBond
- nPriorities - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
the number of distinct priorities determined for this atom for the current rule; 0-4 for the root atom; 0-3 for all others
- nProcessors - Static variable in class org.jmol.viewer.Viewer
- nRead - Variable in class org.jmol.jvxl.readers.XplorReader
- nRegions - Variable in class org.jmol.util.MeshCapper
-
informational only
- nRes - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- nRes - Variable in class org.jmol.modelsetbio.ProteinStructure
- nRootDuplicates - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
number of root-duplicate atoms (root atom only
- nRotations - Variable in class org.jmol.symmetry.HallInfo
- nrows - Variable in class org.jmol.awtjs.swing.Grid
- nSemiSkip - Variable in class org.jmol.script.ScriptCompiler
- nSets - Variable in class org.jmol.util.MeshSurface
- nSFO - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
- nSkip - Variable in class org.jmol.jvxl.readers.CastepDensityReader
- nSkipX - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- nSkipY - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- nSkipZ - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- nSlaters - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- nSPDF - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- nStructures - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- nSubAtoms - Variable in class org.jmol.smiles.SmilesAtom
- nSurfaceAtoms - Variable in class org.jmol.modelset.AtomCollection
- nSurfaceInts - Variable in class org.jmol.jvxl.data.JvxlData
- nSurfaces - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- nTab - Variable in class org.jmol.console.GenericConsole
- nTest - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- nText - Variable in class org.jmol.export.___Exporter
- nTokens - Variable in class org.jmol.script.ScriptTokenParser
- nTri - Variable in class org.jmol.export._StlExporter
- nTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
- nTriangles - Variable in class org.jmol.jvxl.readers.PolygonFileReader
- nTriangles - Variable in class org.jmol.util.MeshCapper
-
informational only
- nTries - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- nType - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
- nuclearCharges - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- nucleic - Static variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- nucleic - Static variable in class org.jmol.script.T
- NUCLEIC - Enum constant in enum org.jmol.c.PAL
- NUCLEIC - Static variable in class org.jmol.util.ColorEncoder
- NucleicMonomer - Class in org.jmol.modelsetbio
- NucleicMonomer() - Constructor for class org.jmol.modelsetbio.NucleicMonomer
- NucleicPolymer - Class in org.jmol.modelsetbio
- NucleicPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.NucleicPolymer
- nucleicRenderer - Variable in class org.jmol.renderbio.CartoonRenderer
- NucleicRenderer - Class in org.jmol.renderbio
-
extends CartoonRenderer for nucleics
- NucleicRenderer() - Constructor for class org.jmol.renderbio.NucleicRenderer
- nucleus - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- nullDeletedAtoms - Static variable in class org.jmol.viewer.Viewer
- nullDesc - Static variable in class org.jmol.symmetry.Symmetry
- nullGroup - Variable in class org.jmol.modelset.ModelLoader
- nullModelSetName - Variable in class org.jmol.popup.JmolPopup
- nullReturn(int) - Static method in class org.jmol.symmetry.SymmetryDesc
- nullShadeIndex - Static variable in class org.jmol.g3d.Graphics3D
- nullToken - Static variable in class org.jmol.shape.Labels
- number - Variable in class org.jmol.symmetry.SymmetryOperation
- number - Variable in enum org.jmol.util.Edge.EnumBondOrder
- numberOutOfRange(float, float) - Method in class org.jmol.script.ScriptError
- numCached - Variable in class org.jmol.modelset.BondCollection
- numSet - Variable in class org.jmol.modelset.MeasurementPending
- numWindows - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- nUnique - Static variable in class org.jmol.symmetry.PointGroup
- nUNK - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- nUnnamed - Variable in class org.jmol.shape.MeshCollection
- nValue(T) - Static method in class org.jmol.script.SV
- nVertexColors - Variable in class org.jmol.jvxl.data.JvxlData
- nVertices - Variable in class org.jmol.jvxl.readers.PolygonFileReader
- nVertices - Variable in class org.jmol.shapespecial.Polyhedra
- nVertices - Variable in class org.jmol.shapespecial.Polyhedron
- nVib - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- nVibrations - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- nvidia_bugs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- NVPair() - Constructor for class org.jmol.adapter.readers.xml.XmlReader.NVPair
- nwchemContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- NWChemReader - Class in org.jmol.adapter.readers.quantum
-
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
- NWChemReader() - Constructor for class org.jmol.adapter.readers.quantum.NWChemReader
- nWidgets - Variable in class org.openscience.jmol.app.webexport.WebPanel
- nX - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
- nX - Variable in class org.jmol.quantum.QuantumCalculation
- nXX - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- nY - Variable in class org.jmol.jvxl.calc.MarchingCubes
- nY - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
- nY - Variable in class org.jmol.quantum.QuantumCalculation
- nZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
- nZ - Variable in class org.jmol.quantum.QuantumCalculation
O
- o(int, Object) - Static method in class org.jmol.script.T
- o(String, Object) - Static method in class org.jmol.i18n.GT
- O - Static variable in class org.jmol.modelsetbio.AminoMonomer
- O1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- O2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- O2P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- O2Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- O3P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- O4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- O4P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- O5P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- O6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- oabc - Variable in class org.jmol.jvxl.data.VolumeData
- oabc - Variable in class org.jmol.util.MeshSurface
- obj - Static variable in class org.jmol.script.T
- OBJ - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- OBJ_AXIS1 - Static variable in class org.jmol.viewer.StateManager
- OBJ_AXIS2 - Static variable in class org.jmol.viewer.StateManager
- OBJ_AXIS3 - Static variable in class org.jmol.viewer.StateManager
- OBJ_BACKGROUND - Static variable in class org.jmol.viewer.StateManager
- OBJ_BOUNDBOX - Static variable in class org.jmol.viewer.StateManager
- OBJ_FRANK - Static variable in class org.jmol.viewer.StateManager
- OBJ_MAX - Static variable in class org.jmol.viewer.StateManager
- OBJ_UNITCELL - Static variable in class org.jmol.viewer.StateManager
- objCls1 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- objCls2 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- objColors - Variable in class org.jmol.viewer.GlobalSettings
- object - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- object - Static variable in class org.jmol.script.T
- OBJECT_ALIGNMENT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_CALCULATOR - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_CALLBACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_CGO - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_GADGET - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_GROUP - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_MAPDATA - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_MAPDATA - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- OBJECT_MAPMESH - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_MAPMESH - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- OBJECT_MEASURE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_MOLECULE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_SELECTION - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_SLICE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OBJECT_SURFACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- objectHidden - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- objectInfo - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- objectJmolName - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- objectName - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- objectName - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- objectNameID - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- objectNameID - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- objectNameList - Static variable in class org.jmol.viewer.StateManager
- objectNameParameter(int) - Method in class org.jmol.script.ScriptParam
- objectOf(DefaultListModel<?>, Object) - Static method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- objects - Variable in class org.jmol.shape.TextShape
- objectSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- objectsPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- objectType - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- objFileRootName - Variable in class org.jmol.export._ObjExporter
-
Path of the OBJ file without the extension.
- objID1 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- objID2 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- objMad10 - Variable in class org.jmol.viewer.GlobalSettings
- ObjReader - Class in org.jmol.jvxl.readers
- ObjReader() - Constructor for class org.jmol.jvxl.readers.ObjReader
- objStateOn - Variable in class org.jmol.viewer.GlobalSettings
- oc - Variable in class org.jmol.adapter.writers.CIFWriter
- oc - Variable in class org.jmol.adapter.writers.CMLWriter
- oc - Variable in class org.jmol.adapter.writers.PDBWriter
- oc - Variable in class org.jmol.adapter.writers.PWMATWriter
- oc - Variable in class org.jmol.adapter.writers.XSFWriter
- oc - Variable in class org.jmol.export._StlExporter
- oc - Variable in class org.jmol.shapesurface.PMeshWriter
- oc - Variable in class org.jmol.util.JSONWriter
- OCC_CRENEL_C - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- OCC_CRENEL_W - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- OCC_SPECIAL_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- occAbsolute - Variable in class org.jmol.util.ModulationSet
-
for Crenels (simple occupational modulation or Legendre displacement modulation, the value determined here is absolute (0 or 1), not an adjustment; set in calculate() by one of the modulations
- occluded - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- occludedObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- occParams - Variable in class org.jmol.util.ModulationSet
- occSiteMultiplicity - Variable in class org.jmol.util.ModulationSet
- occupancies - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- occupancies - Variable in class org.jmol.modelset.AtomCollection
- occupancy - Static variable in class org.jmol.script.T
- OCCUPANCY - Static variable in class org.jmol.adapter.readers.cif.CifReader
- OCCUPANCY - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- occValue - Variable in class org.jmol.util.ModulationSet
-
final occupancy value -- absolute; in range [0,1]
- OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
- octants - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- OdysseyReader - Class in org.jmol.adapter.readers.spartan
- OdysseyReader() - Constructor for class org.jmol.adapter.readers.spartan.OdysseyReader
- off - Static variable in class org.jmol.script.T
- officialRelease - Static variable in class org.jmol.viewer.JC
- offscreen_rendering_for_antialiasing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- offscreen_rendering_multiplier - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- offscreenImage - Variable in class org.jmol.g3d.Platform3D
- offset - Variable in class org.jmol.jvxl.calc.MarchingCubes
- offset - Variable in class org.jmol.modelkit.ModelKit.Constraint
- offset - Variable in class org.jmol.render.LabelsRenderer
- offset - Variable in class org.jmol.render.UccageRenderer
- offset - Variable in class org.jmol.renderspecial.DipolesRenderer
- offset - Static variable in class org.jmol.script.T
- offset - Variable in class org.jmol.shapespecial.Draw
- offset - Variable in class org.jmol.shapespecial.Polyhedron
- offset - Variable in class org.jmol.util.BZone
- offset - Variable in class org.jmol.util.MeshSurface
- offset(int, int) - Method in class org.jmol.adapter.readers.pymol.JmolObject
-
offset is carried out in ModelLoader when the "script" is processed to move the bits to skip the base atom index.
- offset(BS, int, int) - Static method in class org.jmol.util.BSUtil
-
offset the bitset in place by the specified number of bits starting at a given position
- offset(V3) - Method in class org.jmol.shapespecial.DrawMesh
- OFFSET - Enum constant in enum org.jmol.atomdata.RadiusData.EnumType
- offsetAfterPrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- offsetAngstroms - Variable in class org.jmol.shapespecial.Dipole
- offsetCenter(P3) - Method in class org.jmol.jvxl.data.VolumeData
- offsetObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- offsetPbufBeginLine - Variable in class org.jmol.g3d.SphereRenderer
- offsetPercent - Variable in class org.jmol.shapespecial.Dipole
- offsetPolyhedra(P3) - Method in class org.jmol.shapespecial.Polyhedra
- offsetPt - Variable in class org.jmol.shapespecial.Dipole
- offsets - Variable in class org.jmol.modelsetbio.Monomer
- offsets - Variable in class org.jmol.shape.Labels
- offsetside - Static variable in class org.jmol.script.T
- offsetSide - Variable in class org.jmol.renderspecial.DipolesRenderer
- offsetSide - Variable in class org.jmol.shapespecial.Dipole
- offsetT - Variable in class org.jmol.render.UccageRenderer
- offsetX - Variable in class org.jmol.modelset.Text
- offsetY - Variable in class org.jmol.modelset.Text
- ok() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- OK - Static variable in interface org.jmol.api.JmolGestureServerInterface
- OK - Static variable in class org.jmol.script.ScriptCompiler
- OK2 - Static variable in class org.jmol.script.ScriptCompiler
- okButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- okButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- okMF - Variable in class org.jmol.smiles.SmilesMatcher
- OKPressed() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
- oldFileName - Variable in class org.jmol.shapesurface.Isosurface
- oldNPriorities - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
the number of distinct priorities determined for this atom for the current rule; 0-4 for the root atom; 0-3 for all others
- oldPriorities - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
priorities associated with each subsituent from high (0) to low (3); due to equivaliencies at a given rule level, these numbers may duplicate and have gaps - for example, [0 2 0 3]
- oldType - Variable in class org.jmol.util.ContactPair
- OLIVE - Static variable in class org.jmol.util.C
- omega - Variable in class org.jmol.modelsetbio.Monomer
- omega - Static variable in class org.jmol.script.T
- on - Static variable in class org.jmol.script.T
- once - Static variable in class org.jmol.script.T
- ONE_OVER_D - Static variable in class org.jmol.quantum.MepCalculation
- ONE_OVER_ONE_PLUS_D - Static variable in class org.jmol.quantum.MepCalculation
- oneFace - Variable in class org.jmol.export._VrmlExporter
- oneFifth - Static variable in class org.jmol.util.Geodesic
- onePerLine - Variable in class org.jmol.jvxl.readers.PmeshReader
- oneTenth - Static variable in class org.jmol.util.Geodesic
- only - Static variable in class org.jmol.script.T
- onlySelectedDots - Variable in class org.jmol.geodesic.EnvelopeCalculation
- oopCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- oopCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
- oops(Exception) - Method in class org.jmol.minimize.MinimizationThread
- oops(Exception) - Method in class org.jmol.navigate.Navigator
- oops(Exception) - Method in class org.jmol.thread.JmolThread
- OP_COUNT - Static variable in class org.jmol.symmetry.SpaceGroupFinder
- opacity - Variable in class org.jmol.awt.AwtColor
- opacityFractionalFromArgb(int) - Static method in class org.jmol.export.___Exporter
- opacityFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
- opAnd - Static variable in class org.jmol.script.T
- opAND - Static variable in class org.jmol.script.T
- opaque - Static variable in class org.jmol.script.T
- opaque_background - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OPAQUE_MASK - Static variable in class org.jmol.util.C
- opCount - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- open() - Method in class org.jmol.console.ScriptEditor
- openAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OpenAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
- openBufferedReader(String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
- openBufferedReader(String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
- openBufferedReader(String, String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
- openButton - Variable in class org.jmol.console.ScriptEditor
- openChooser - Static variable in class org.jmol.dialog.Dialog
- openChooser - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- openDOM(Object) - Method in class org.jmol.api.JmolViewer
- openDOM(Object) - Method in class org.jmol.viewer.Viewer
-
applet DOM method -- does not preserve state
- openExportChannel(double, String, boolean) - Method in class org.jmol.viewer.Viewer
- openFile() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- openFile(String) - Method in class org.jmol.api.JmolViewer
- openFile(String) - Method in class org.jmol.util.GenericApplet
-
possibly called from JSmolApplet.js upon start up
- openFile(String) - Method in class org.jmol.viewer.Viewer
-
for JmolSimpleViewer -- external applications only (and no-script JavaScript)
- openFileAsync(String) - Method in class org.jmol.api.JmolViewer
- openFileAsync(String, int, String) - Method in interface org.jmol.api.JmolScriptManager
- openFileAsync(String, int, String) - Method in class org.jmol.script.ScriptManager
-
From file dropping.
- openFileAsyncSpecial(String, int) - Method in class org.jmol.api.JmolViewer
- openFileAsyncSpecial(String, int) - Method in class org.jmol.util.GenericApplet
- openFileAsyncSpecial(String, int) - Method in class org.jmol.viewer.Viewer
-
opens a file as a model, a script, or a surface via the creation of a script that is queued.
- openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.api.JmolViewer
- openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.util.GenericApplet
- openFileAsyncSpecialType(String, int, String) - Method in class org.jmol.viewer.Viewer
- openFileFull(String, boolean, Map<String, Object>, SB) - Method in class org.jmol.viewer.Viewer
-
does NOT repaint
- openFilePreview - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- openFiles(String[]) - Method in class org.jmol.api.JmolViewer
- openFiles(String[]) - Method in class org.jmol.viewer.Viewer
-
for JmolSimpleViewer -- external applications only
- openmolAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OpenMolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
- openOutputChannel(double, String, boolean, boolean) - Method in class org.jmol.viewer.OutputManager
- openOutputChannel(double, String, boolean, boolean) - Method in class org.jmol.viewer.OutputManagerAwt
- openOutputChannel(double, String, boolean, boolean) - Method in class org.jmol.viewer.OutputManagerJS
- openpdbAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OpenPdbAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
- openPreview - Variable in class org.jmol.dialog.Dialog
- openReader(String, Object) - Method in class org.jmol.api.JmolViewer
-
Opens the file and creates the model set, given the reader.
- openReader(String, String, Object) - Method in class org.jmol.api.JmolViewer
-
Opens the file and creates the model set, given the reader.
- openReader(String, String, Object) - Method in class org.jmol.viewer.Viewer
-
Opens the file, given an already-created reader.
- openSchema() - Method in class org.jmol.adapter.writers.QCJSONWriter
- openSMILES - Variable in class org.jmol.smiles.SmilesGenerator
- openStringInline(String) - Method in class org.jmol.api.JmolViewer
- openStringInline(String) - Method in class org.jmol.viewer.Viewer
-
only used by file dropper.
- openStringInlineParamsAppend(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
-
Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.
- openStringsInlineParamsAppend(String[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
-
opens multiple files inline; does NOT repaint
- openTag(SB, String) - Static method in class org.jmol.adapter.writers.CMLWriter
- openurlAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OpenUrlAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
- opEQ - Static variable in class org.jmol.script.T
- OPER_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- OPER_XYZ - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- operate() - Method in class org.jmol.script.ScriptMathProcessor
- Operation() - Constructor for class org.jmol.symmetry.PointGroup.Operation
- Operation(V3) - Constructor for class org.jmol.symmetry.PointGroup.Operation
- Operation(V3, int) - Constructor for class org.jmol.symmetry.PointGroup.Operation
- OPERATION_IMPROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
- OPERATION_INVERSION_CENTER - Static variable in class org.jmol.symmetry.PointGroup
- OPERATION_PLANE - Static variable in class org.jmol.symmetry.PointGroup
- OPERATION_PROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
- operationCount - Variable in class org.jmol.symmetry.SpaceGroup
- operations - Variable in class org.jmol.symmetry.SpaceGroup
- operFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- opGE - Static variable in class org.jmol.script.T
- opGT - Static variable in class org.jmol.script.T
- opId - Variable in class org.jmol.symmetry.SymmetryOperation
- opIf - Static variable in class org.jmol.script.T
- opLE - Static variable in class org.jmol.script.T
- opLIKE - Static variable in class org.jmol.script.T
- opLT - Static variable in class org.jmol.script.T
- opNE - Static variable in class org.jmol.script.T
- opNot - Static variable in class org.jmol.script.T
- opOr - Static variable in class org.jmol.script.T
- ops - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
symmetry operations for this space group
- ops - Static variable in class org.jmol.symmetry.SpaceGroupFinder
- oPt - Variable in class org.jmol.script.ScriptMathProcessor
- OPT_ARCS - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- OPT_ARROWS - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- OPT_AXES - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- OPT_BALL - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- OPT_COUNT - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- OPT_DOTS - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- OPT_FILL - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- OPT_WIREFRAME - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- optimadeContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- OptimadeReader - Class in org.jmol.adapter.readers.xtal
-
A (preliminary) reader for OPTIMADE resources.
- OptimadeReader() - Constructor for class org.jmol.adapter.readers.xtal.OptimadeReader
- optimize2d - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- optimize2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- optimize2D - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- options - Static variable in class org.jmol.script.T
- options - Variable in class org.jmol.shapespecial.Ellipsoid
- OPTIONS_MODE - Static variable in class org.jmol.modelkit.ModelKit
- opToggle - Static variable in class org.jmol.script.T
- opTokenFor(int) - Method in class org.jmol.scriptext.MathExt
- optOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- optParameterAsString(int) - Method in class org.jmol.script.ScriptParam
- OPTS - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- optsField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- OptSort() - Constructor for class org.openscience.jmol.app.JmolApp.OptSort
- opXor - Static variable in class org.jmol.script.T
- opXYZ - Static variable in class org.jmol.symmetry.SpaceGroupFinder
- ORANGE - Static variable in class org.jmol.util.C
- orbEnergy - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- orbital - Static variable in class org.jmol.script.T
- orbitalData - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- orbitalInfo - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- orbitalMaps - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- orbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- orbitals - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
- Orbitals - Class in org.openscience.jmol.app.webexport
- Orbitals() - Constructor for class org.openscience.jmol.app.webexport.Orbitals
- OrbitalSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
- orbitalsRead - Variable in class org.jmol.adapter.readers.quantum.MOReader
- orbitalType - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- orbOcc - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- orcaContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- orcaInputLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- OrcaReader - Class in org.jmol.adapter.readers.quantum
-
Reads ORCA input and output files
- OrcaReader - Class in org.jmol.adapter.readers.simple
-
Reads ORCA input and output files
- OrcaReader() - Constructor for class org.jmol.adapter.readers.quantum.OrcaReader
- OrcaReader() - Constructor for class org.jmol.adapter.readers.simple.OrcaReader
- order - Variable in class org.jmol.adapter.smarter.Bond
- order - Variable in class org.jmol.minimize.MinBond
- order - Variable in class org.jmol.symmetry.HallRotationTerm
- order - Variable in class org.jmol.symmetry.PointGroup.Operation
- order - Variable in class org.jmol.util.Edge
- order - Variable in class org.jmol.util.Modulation
- order - Variable in class org.jmol.viewer.Connection
- ORDER_AROMATIC - Static variable in class org.jmol.api.JmolAdapter
- ORDER_AROMATIC_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_AROMATIC_SINGLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_HEX - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_QUAD - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_QUINT - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_SINGLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_COVALENT_TRIPLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_HBOND - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PARTIAL01 - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PARTIAL12 - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PARTIAL23 - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PARTIAL32 - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PYMOL_MULT - Static variable in class org.jmol.api.JmolAdapter
- ORDER_PYMOL_SINGLE - Static variable in class org.jmol.api.JmolAdapter
- ORDER_STEREO_FAR - Static variable in class org.jmol.api.JmolAdapter
- ORDER_STEREO_NEAR - Static variable in class org.jmol.api.JmolAdapter
- ORDER_UNSPECIFIED - Static variable in class org.jmol.api.JmolAdapter
- orderList(int[]) - Static method in class org.jmol.inchi.InChIJNI
- org.jmol.adapter.readers.cif - package org.jmol.adapter.readers.cif
- org.jmol.adapter.readers.molxyz - package org.jmol.adapter.readers.molxyz
- org.jmol.adapter.readers.more - package org.jmol.adapter.readers.more
- org.jmol.adapter.readers.pdb - package org.jmol.adapter.readers.pdb
- org.jmol.adapter.readers.pymol - package org.jmol.adapter.readers.pymol
- org.jmol.adapter.readers.quantum - package org.jmol.adapter.readers.quantum
- org.jmol.adapter.readers.simple - package org.jmol.adapter.readers.simple
- org.jmol.adapter.readers.spartan - package org.jmol.adapter.readers.spartan
- org.jmol.adapter.readers.xml - package org.jmol.adapter.readers.xml
- org.jmol.adapter.readers.xtal - package org.jmol.adapter.readers.xtal
- org.jmol.adapter.smarter - package org.jmol.adapter.smarter
- org.jmol.adapter.writers - package org.jmol.adapter.writers
- org.jmol.api - package org.jmol.api
- org.jmol.api.js - package org.jmol.api.js
- org.jmol.appletjs - package org.jmol.appletjs
- org.jmol.atomdata - package org.jmol.atomdata
- org.jmol.awt - package org.jmol.awt
- org.jmol.awtjs - package org.jmol.awtjs
- org.jmol.awtjs.swing - package org.jmol.awtjs.swing
- org.jmol.awtjs2d - package org.jmol.awtjs2d
- org.jmol.bspt - package org.jmol.bspt
-
Provides Binary Space Partitioning Functionality to spacially separate data structures in n-dimensions
- org.jmol.c - package org.jmol.c
- org.jmol.console - package org.jmol.console
- org.jmol.consolejs - package org.jmol.consolejs
- org.jmol.dialog - package org.jmol.dialog
- org.jmol.dssx - package org.jmol.dssx
- org.jmol.export - package org.jmol.export
- org.jmol.g3d - package org.jmol.g3d
-
Provides a software implementation of complete 3D graphics engine for rendering molecules and associated shapes.
- org.jmol.geodesic - package org.jmol.geodesic
- org.jmol.i18n - package org.jmol.i18n
- org.jmol.image - package org.jmol.image
- org.jmol.inchi - package org.jmol.inchi
- org.jmol.io - package org.jmol.io
- org.jmol.jsv - package org.jmol.jsv
- org.jmol.jvxl.api - package org.jmol.jvxl.api
- org.jmol.jvxl.calc - package org.jmol.jvxl.calc
- org.jmol.jvxl.data - package org.jmol.jvxl.data
- org.jmol.jvxl.readers - package org.jmol.jvxl.readers
- org.jmol.minimize - package org.jmol.minimize
- org.jmol.minimize.forcefield - package org.jmol.minimize.forcefield
- org.jmol.modelkit - package org.jmol.modelkit
- org.jmol.modelset - package org.jmol.modelset
- org.jmol.modelsetbio - package org.jmol.modelsetbio
- org.jmol.multitouch - package org.jmol.multitouch
- org.jmol.multitouch.jni - package org.jmol.multitouch.jni
- org.jmol.multitouch.sparshui - package org.jmol.multitouch.sparshui
- org.jmol.navigate - package org.jmol.navigate
- org.jmol.popup - package org.jmol.popup
- org.jmol.quantum - package org.jmol.quantum
- org.jmol.quantum.mo - package org.jmol.quantum.mo
- org.jmol.render - package org.jmol.render
- org.jmol.renderbio - package org.jmol.renderbio
- org.jmol.rendercgo - package org.jmol.rendercgo
- org.jmol.renderspecial - package org.jmol.renderspecial
- org.jmol.rendersurface - package org.jmol.rendersurface
- org.jmol.script - package org.jmol.script
- org.jmol.scriptext - package org.jmol.scriptext
- org.jmol.shape - package org.jmol.shape
- org.jmol.shapebio - package org.jmol.shapebio
- org.jmol.shapecgo - package org.jmol.shapecgo
- org.jmol.shapespecial - package org.jmol.shapespecial
- org.jmol.shapesurface - package org.jmol.shapesurface
- org.jmol.smiles - package org.jmol.smiles
-
Jmol SMILES, Jmol SMARTS, Jmol bioSMILES, and Jmol bioSMARTS
- org.jmol.symmetry - package org.jmol.symmetry
- org.jmol.thread - package org.jmol.thread
- org.jmol.translation - package org.jmol.translation
- org.jmol.util - package org.jmol.util
- org.jmol.viewer - package org.jmol.viewer
- org.jmol.viewer.binding - package org.jmol.viewer.binding
- org.openscience.jmol.app - package org.openscience.jmol.app
- org.openscience.jmol.app.janocchio - package org.openscience.jmol.app.janocchio
- org.openscience.jmol.app.jmolpanel - package org.openscience.jmol.app.jmolpanel
- org.openscience.jmol.app.jmolpanel.console - package org.openscience.jmol.app.jmolpanel.console
- org.openscience.jmol.app.jsonkiosk - package org.openscience.jmol.app.jsonkiosk
- org.openscience.jmol.app.surfacetool - package org.openscience.jmol.app.surfacetool
- org.openscience.jmol.app.webexport - package org.openscience.jmol.app.webexport
- org.openscience.jvxl - package org.openscience.jvxl
- org.openscience.jvxl.simplewriter - package org.openscience.jvxl.simplewriter
- orientation - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
- orientation - Variable in class org.jmol.modelset.Model
- orientation - Static variable in class org.jmol.script.T
- Orientation - Class in org.jmol.modelset
- Orientation(Viewer, boolean, float[]) - Constructor for class org.jmol.modelset.Orientation
- orientationInput - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
- origin - Variable in class org.jmol.jvxl.data.VolumeData
- origin - Variable in class org.jmol.jvxl.readers.MapFileReader
- origin - Variable in class org.jmol.jvxl.readers.Parameters
- origin - Static variable in class org.jmol.script.T
- origin - Variable in class org.jmol.shapespecial.Dipole
- originBohr - Variable in class org.jmol.quantum.QuantumCalculation
- originPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- originPoint - Variable in class org.jmol.shape.Axes
- originScreen - Variable in class org.jmol.render.AxesRenderer
- orthoscopic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- OS_PI_COUNTS - Static variable in class org.jmol.smiles.SmilesAromatic
-
Index to inner array is covalent bond count (b) + valence (v) + charge (c, carbon only) - 4.
- oStack - Variable in class org.jmol.script.ScriptMathProcessor
- OT - Static variable in class org.jmol.modelsetbio.AminoMonomer
- otherAtoms - Variable in class org.jmol.shapespecial.Polyhedra
- out - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- out - Variable in class org.jmol.export.___Exporter
- out - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
- out - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- out - Static variable in class org.jmol.script.T
- output - Variable in class org.jmol.console.GenericConsole
- output(String) - Method in class org.jmol.console.ScriptEditor
- output(String) - Method in class org.jmol.export.___Exporter
- output(String) - Method in class org.jmol.export._StlExporter
- output(String) - Method in class org.jmol.util.GenericApplet
- output(T3) - Method in class org.jmol.export.___Exporter
- output(T3) - Method in class org.jmol.export._IdtfExporter
- output(T3) - Method in class org.jmol.export._MayaExporter
- output(T3) - Method in class org.jmol.export._ObjExporter
- output(T3) - Method in class org.jmol.export._PovrayExporter
- output(T3) - Method in class org.jmol.export._TachyonExporter
- output(T3) - Method in class org.jmol.export._VrmlExporter
- output(T3) - Method in class org.jmol.export.JSExporter
- output(T3, SB, boolean) - Method in class org.jmol.export._IdtfExporter
- output80CharWrap(SB, String, int) - Method in class org.jmol.adapter.writers.MOLWriter
- outputAlphaCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- outputAppearance(short, boolean) - Method in class org.jmol.export._VrmlExporter
- outputAppearance(short, boolean) - Method in class org.jmol.export._X3dExporter
- outputAttr(String, float, float, float) - Method in class org.jmol.export._StlExporter
- outputAttr(String, float, float, float) - Method in class org.jmol.export._VrmlExporter
- outputAttr(String, float, float, float) - Method in class org.jmol.export._X3dExporter
- outputAttrPt(String, T3) - Method in class org.jmol.export._StlExporter
- outputAttrPt(String, T3) - Method in class org.jmol.export._VrmlExporter
- outputAttrPt(String, T3) - Method in class org.jmol.export._X3dExporter
- outputBeforePrompt(String, SimpleAttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- outputBuffer - Variable in class org.jmol.script.ScriptContext
- outputBuffer - Variable in class org.jmol.script.ScriptEval
- outputBuffer - Variable in class org.jmol.util.GenericApplet
- outputChildClose() - Method in class org.jmol.export._StlExporter
- outputChildClose() - Method in class org.jmol.export._VrmlExporter
- outputChildClose() - Method in class org.jmol.export._X3dExporter
- outputChildShapeClose() - Method in class org.jmol.export._VrmlExporter
- outputChildShapeClose() - Method in class org.jmol.export._X3dExporter
- outputChildShapeStart() - Method in class org.jmol.export._VrmlExporter
- outputChildShapeStart() - Method in class org.jmol.export._X3dExporter
- outputChildStart() - Method in class org.jmol.export._StlExporter
- outputChildStart() - Method in class org.jmol.export._VrmlExporter
- outputChildStart() - Method in class org.jmol.export._X3dExporter
- outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
- outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
- outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._StlExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._X3dExporter
- outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
- outputCircle(P3, P3, short, float) - Method in class org.jmol.export._IdtfExporter
- outputCircle1(P3, P3, short, float) - Method in class org.jmol.export._ObjExporter
-
Local implementation of outputCircle.
- outputCloseTag() - Method in class org.jmol.export._VrmlExporter
- outputCloseTag() - Method in class org.jmol.export._X3dExporter
- outputColorIndices(int[][], int, BS, int, Map<Short, Integer>, short[], short[]) - Method in class org.jmol.export._VrmlExporter
- outputColors(Lst<Short>) - Method in class org.jmol.export._VrmlExporter
- outputComment(String) - Method in class org.jmol.export.___Exporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export.__CartesianExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export._IdtfExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export._MayaExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export._ObjExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export._VrmlExporter
- outputCone(P3, P3, float, short) - Method in class org.jmol.export.JSExporter
- outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
- outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
- outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
- outputCone1(P3, P3, float, short) - Method in class org.jmol.export._ObjExporter
-
Local implementation of outputCone.
- outputConeGeometry(boolean) - Method in class org.jmol.export._VrmlExporter
- outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
- outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
- outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._IdtfExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._MayaExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._ObjExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._VrmlExporter
- outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.JSExporter
- outputCylinder1(P3, P3, P3, short, byte, float, P3, P3) - Method in class org.jmol.export._ObjExporter
-
Local implementation of outputCylinder.
- outputCylinderChildScaled(short, byte) - Method in class org.jmol.export._VrmlExporter
- outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export.__RayTracerExporter
- outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._PovrayExporter
- outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._TachyonExporter
- outputCylinderGeometry(int) - Method in class org.jmol.export._VrmlExporter
- outputDefChildFaceSet(String) - Method in class org.jmol.export._VrmlExporter
- outputDefChildFaceSet(String) - Method in class org.jmol.export._X3dExporter
- outputDocument - Variable in class org.jmol.console.AppletConsole.GenericTextPane
- outputEcho(String) - Method in class org.jmol.console.ScriptEditor.EditorDocument
- outputEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- outputEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- outputEdge(int, int, int) - Method in class org.jmol.shapesurface.PMeshWriter
- outputEllipse(P3, P3, P3, P3, short) - Method in class org.jmol.export._IdtfExporter
- outputEllipse1(P3, P3, P3, P3, short) - Method in class org.jmol.export._ObjExporter
-
Local implementation of outputEllipse.
- outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export.__RayTracerExporter
- outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._PovrayExporter
- outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._TachyonExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.__CartesianExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._IdtfExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._MayaExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._ObjExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._VrmlExporter
- outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.JSExporter
- outputEllipsoid(T3, M4, short) - Method in class org.jmol.export._IdtfExporter
- outputEllipsoid1(T3, float, float, float, A4, short) - Method in class org.jmol.export._ObjExporter
-
Local implementation of outputEllipsoid.
- outputError(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- outputError(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- outputErrorForeground(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- outputErrorForeground(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- outputExtension - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- outputFace(int[], int[], int) - Method in class org.jmol.export.__CartesianExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export._IdtfExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export._MayaExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export._ObjExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export._VrmlExporter
- outputFace(int[], int[], int) - Method in class org.jmol.export.JSExporter
- outputFace1(int[], int[], int[]) - Method in class org.jmol.export._ObjExporter
-
Local implementation of outputFace used for no texture coordinates.
- outputFace2(int[], int, int[], int[]) - Method in class org.jmol.export._ObjExporter
-
Local implementation of outputFace used with texture coordinates.
- outputFaceSetClose() - Method in class org.jmol.export._VrmlExporter
- outputFaceSetClose() - Method in class org.jmol.export._X3dExporter
- outputFaceSetStart() - Method in class org.jmol.export._VrmlExporter
- outputFaceSetStart() - Method in class org.jmol.export._X3dExporter
- outputFileName - Variable in class org.jmol.dialog.Dialog
- outputFileType - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- outputFooter() - Method in class org.jmol.export.___Exporter
- outputFooter() - Method in class org.jmol.export._IdtfExporter
- outputFooter() - Method in class org.jmol.export._TachyonExporter
- outputFooter() - Method in class org.jmol.export._VrmlExporter
- outputFooter() - Method in class org.jmol.export._X3dExporter
- outputFooter() - Method in class org.jmol.export.JSExporter
- outputFormatChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Called when the OutputFormat check box is modified
- outputFormatCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- outputFormatCombo - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._StlExporter
- outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._VrmlExporter
- outputGeometry(T3[], T3[], short[], int[][], short[], int, int, BS, int, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._X3dExporter
- outputHeader() - Method in class org.jmol.export.___Exporter
- outputHeader() - Method in class org.jmol.export._IdtfExporter
- outputHeader() - Method in class org.jmol.export._MayaExporter
- outputHeader() - Method in class org.jmol.export._ObjExporter
- outputHeader() - Method in class org.jmol.export._PovrayExporter
- outputHeader() - Method in class org.jmol.export._StlExporter
- outputHeader() - Method in class org.jmol.export._TachyonExporter
- outputHeader() - Method in class org.jmol.export._VrmlExporter
- outputHeader() - Method in class org.jmol.export._X3dExporter
- outputHeader() - Method in class org.jmol.export.JSExporter
- outputHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- outputIndices(int[][], int[], int, BS, int) - Method in class org.jmol.export.__CartesianExporter
- outputInitialTransform() - Method in class org.jmol.export._VrmlExporter
- outputInt(int) - Method in class org.jmol.shapesurface.PMeshWriter
- outputJmolPerspective() - Method in class org.jmol.export.___Exporter
- outputLines(SB, String, int) - Method in class org.jmol.adapter.writers.MOLWriter
- outputList(T3[], int, M4, String, BS) - Method in class org.jmol.export._ObjExporter
-
create the v or vn list
- outputManager - Variable in class org.jmol.viewer.Viewer
- OutputManager - Class in org.jmol.viewer
- OutputManager() - Constructor for class org.jmol.viewer.OutputManager
- OutputManagerAwt - Class in org.jmol.viewer
- OutputManagerAwt() - Constructor for class org.jmol.viewer.OutputManagerAwt
- OutputManagerJS - Class in org.jmol.viewer
- OutputManagerJS() - Constructor for class org.jmol.viewer.OutputManagerJS
- outputMsg(String) - Method in class org.jmol.console.GenericConsole
- outputMtl(String) - Method in class org.jmol.export._ObjExporter
-
Write to the .mtl file and keep track of the bytes written.
- outputNodes() - Method in class org.jmol.export._IdtfExporter
- outputNormals(Lst<String>) - Method in class org.jmol.export._VrmlExporter
- outputPoint(int, int) - Method in class org.jmol.shapesurface.PMeshWriter
- outputPoints(BS) - Method in class org.jmol.shapesurface.PMeshWriter
- outputQuaternionFrame(P3, P3, P3, P3, float, float, float) - Method in class org.jmol.export._VrmlExporter
- outputRing(int, int, int, V3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
- outputRotation(A4) - Method in class org.jmol.export._StlExporter
- outputRotation(A4) - Method in class org.jmol.export._VrmlExporter
- outputRotation(A4) - Method in class org.jmol.export._X3dExporter
- outputShapeClose() - Method in class org.jmol.export._VrmlExporter
- outputShapeClose() - Method in class org.jmol.export._X3dExporter
- outputShapeStart() - Method in class org.jmol.export._VrmlExporter
- outputShapeStart() - Method in class org.jmol.export._X3dExporter
- outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export.__CartesianExporter
- outputSolidPlate(P3, P3, P3, short) - Method in class org.jmol.export._VrmlExporter
- outputSphere(float, float, float, float, short) - Method in class org.jmol.export.__RayTracerExporter
- outputSphere(float, float, float, float, short) - Method in class org.jmol.export._PovrayExporter
- outputSphere(float, float, float, float, short) - Method in class org.jmol.export._TachyonExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
- outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
- outputSphereChildScaled(P3, float, P3[], short) - Method in class org.jmol.export._VrmlExporter
- outputSphereGeometry() - Method in class org.jmol.export._VrmlExporter
- outputStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- outputStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.___Exporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._IdtfExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._MayaExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._PovrayExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._TachyonExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._VrmlExporter
- outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.JSExporter
- outputTextPixel(int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
- outputTextPixel(int, int, int, int) - Method in class org.jmol.export._PovrayExporter
- outputTextPixel(int, int, int, int) - Method in class org.jmol.export._TachyonExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export.__CartesianExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._IdtfExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._MayaExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._ObjExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._VrmlExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export._X3dExporter
- outputTextPixel(P3, int) - Method in class org.jmol.export.JSExporter
- outputTexture(int, boolean) - Method in class org.jmol.export._TachyonExporter
- outputTexture(short, boolean) - Method in class org.jmol.export._TachyonExporter
- outputTexture2(String, String, boolean) - Method in class org.jmol.export._TachyonExporter
- outputTextureCode() - Method in class org.jmol.export._TachyonExporter
- outputToFile(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
- outputToFile(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
- outputToFile(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- outputTransRot(P3, P3, int, int, int) - Method in class org.jmol.export._VrmlExporter
- outputTriangle(int, int, int) - Method in class org.jmol.util.MeshCapper
-
Export triangle to MeshSlicer
- outputTriangle(int, int, int, int, int) - Method in class org.jmol.shapesurface.PMeshWriter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.__CartesianExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.__RayTracerExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._IdtfExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._MayaExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._ObjExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._PovrayExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._TachyonExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._VrmlExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._X3dExporter
- outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.JSExporter
- outputTriangle1(T3, T3, T3, short) - Method in class org.jmol.export._ObjExporter
-
Local implementation of outputCylinder.
- outputTriangleGeometry(T3, T3, T3, short) - Method in class org.jmol.export._VrmlExporter
- outputTriangles(boolean, BS, BS) - Method in class org.jmol.shapesurface.PMeshWriter
- outputUseChildClose(String) - Method in class org.jmol.export._VrmlExporter
- outputUseChildClose(String) - Method in class org.jmol.export._X3dExporter
- outputVertex(T3, T3) - Method in class org.jmol.export.___Exporter
- outputVertex(T3, T3) - Method in class org.jmol.export.__RayTracerExporter
- outputVertices(T3[], int, T3) - Method in class org.jmol.export.___Exporter
- outputWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- outputXYZ(T3) - Method in class org.jmol.shapesurface.PMeshWriter
- outSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- OUTSOCKET - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- OUTSOCKET - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- oValue(Object) - Static method in class org.jmol.script.SV
- overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- overlay_lines - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
P
- p - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- p - Variable in class org.jmol.minimize.Minimizer
- p - Variable in class org.jmol.quantum.NMRNoeMatrix
- p - Variable in class org.jmol.render.MeasuresRenderer
- p - Variable in class org.jmol.symmetry.UnitCellIterator
- P - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
- P - Static variable in class org.jmol.quantum.QS
- P_CHECK - Static variable in class org.jmol.util.MeshSurface
- P_CONTOUR - Static variable in class org.jmol.util.MeshSurface
- P_EXPLICIT_COLOR - Static variable in class org.jmol.util.MeshSurface
- P_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- P_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
- p0 - Variable in class org.jmol.g3d.Pixelator
- p0 - Variable in class org.jmol.quantum.NciCalculation
- p1 - Variable in class org.jmol.quantum.NciCalculation
- p1 - Variable in class org.jmol.render.SticksRenderer
- p2 - Variable in class org.jmol.quantum.NciCalculation
- p2 - Variable in class org.jmol.render.SticksRenderer
- P2nReader - Class in org.jmol.adapter.readers.pdb
-
P2N file reader.
- P2nReader() - Constructor for class org.jmol.adapter.readers.pdb.P2nReader
- p2nStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- p3 - Variable in class org.jmol.jvxl.readers.MapFileReader
- p3Screens - Variable in class org.jmol.render.CageRenderer
- p3Screens - Variable in class org.jmol.render.MeshRenderer
- p4 - Variable in class org.jmol.viewer.TransformManager4D
- pack() - Method in class org.jmol.awtjs.swing.JDialog
- packageReadable(String, String, String) - Static method in class org.jmol.util.Escape
- packageReadableSb(String, String, SB) - Static method in class org.jmol.util.Escape
- packed - Static variable in class org.jmol.script.T
- packingError - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- packingError - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- pageAuthorName - Static variable in class org.openscience.jmol.app.webexport.WebExport
- pageAuthorName - Variable in class org.openscience.jmol.app.webexport.WebPanel
- PageLoader(URL, Cursor) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
- pageUpBuffer - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- paint(Graphics) - Method in class org.jmol.dialog.FilePreview.FPPanel
- paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.Splash
- paintComponent(Graphics) - Method in class org.jmol.console.ImageDialog.ImageCanvas
- paintIcon(Component, Graphics, int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter.Arrow
- pairSearch(Lst<Object[]>, Calculation, Lst<Object[]>, Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
- PAL - Enum in org.jmol.c
-
Enum for animation mode.
- PAL(String, int) - Constructor for enum org.jmol.c.PAL
- PALETTE_ALTLOC - Static variable in enum org.jmol.c.PAL
- PALETTE_AMINO - Static variable in enum org.jmol.c.PAL
- PALETTE_CHAIN - Static variable in enum org.jmol.c.PAL
- PALETTE_CPK - Static variable in enum org.jmol.c.PAL
- PALETTE_ENERGY - Static variable in enum org.jmol.c.PAL
- PALETTE_FIXEDTEMP - Static variable in enum org.jmol.c.PAL
- PALETTE_FORMAL_CHARGE - Static variable in enum org.jmol.c.PAL
- PALETTE_GROUP - Static variable in enum org.jmol.c.PAL
- PALETTE_INSERTION - Static variable in enum org.jmol.c.PAL
- PALETTE_JMOL - Static variable in enum org.jmol.c.PAL
- PALETTE_MOLECULE - Static variable in enum org.jmol.c.PAL
- PALETTE_MONOMER - Static variable in enum org.jmol.c.PAL
- PALETTE_NONE - Static variable in enum org.jmol.c.PAL
- PALETTE_NUCLEIC - Static variable in enum org.jmol.c.PAL
- PALETTE_PARTIAL_CHARGE - Static variable in enum org.jmol.c.PAL
- PALETTE_POLYMER - Static variable in enum org.jmol.c.PAL
- PALETTE_PROPERTY - Static variable in enum org.jmol.c.PAL
- PALETTE_RASMOL - Static variable in enum org.jmol.c.PAL
- PALETTE_SHAPELY - Static variable in enum org.jmol.c.PAL
- PALETTE_STRAIGHTNESS - Static variable in enum org.jmol.c.PAL
- PALETTE_STRUCTURE - Static variable in enum org.jmol.c.PAL
- PALETTE_SURFACE - Static variable in enum org.jmol.c.PAL
- PALETTE_TEMP - Static variable in enum org.jmol.c.PAL
- PALETTE_TYPE - Static variable in enum org.jmol.c.PAL
- PALETTE_VARIABLE - Static variable in enum org.jmol.c.PAL
- PALETTE_VOLATILE - Static variable in enum org.jmol.c.PAL
- paletteBW - Variable in class org.jmol.util.ColorEncoder
- paletteFriendly - Variable in class org.jmol.util.ColorEncoder
- paletteID - Variable in class org.jmol.modelset.Atom
- paletteIDs - Variable in class org.jmol.shape.AtomShape
- paletteWB - Variable in class org.jmol.util.ColorEncoder
- palindrome - Static variable in class org.jmol.script.T
- pAltona - Static variable in class org.jmol.quantum.NMRCalculation
- panel() - Method in class org.openscience.jmol.app.webexport.Test
- panelIndex - Variable in class org.openscience.jmol.app.webexport.WebPanel
- panelName - Variable in class org.openscience.jmol.app.webexport.WebPanel
- PAR_D - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_HARD - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_R - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_RADIUS - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_THETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_U - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_V - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_X - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_XI - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_Z - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- PAR_ZETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
- parA - Variable in class org.jmol.minimize.forcefield.Calculations
- parallel - Static variable in class org.jmol.script.T
- parallelProcessor - Variable in class org.jmol.script.ScriptContext
- parallelProcessor - Variable in class org.jmol.script.ScriptEval
- parallelProcessor - Variable in class org.jmol.script.ScriptProcessRunnable
- PARAM_COUNT - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_M4 - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_SCALE - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_STD - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_SUPERCELL - Static variable in class org.jmol.util.SimpleUnitCell
- PARAM_VABC - Static variable in class org.jmol.util.SimpleUnitCell
- paramAsStr(int) - Method in class org.jmol.script.ScriptParam
- paramAsStr(int) - Method in class org.jmol.scriptext.ScriptExt
- parameterExpression(int, int, String, boolean, boolean, int, boolean, Map<String, SV>, String, boolean) - Method in class org.jmol.script.ScriptExpr
-
This is the primary driver of the RPN (reverse Polish notation) expression processor.
- parameterExpressionBoolean(int, int) - Method in class org.jmol.script.ScriptExpr
- parameterExpressionList(int, int, boolean) - Method in class org.jmol.script.ScriptExpr
- parameterExpressionSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptExpr
- parameterExpressionString(int, int) - Method in class org.jmol.script.ScriptExpr
- parameterExpressionToken(int) - Method in class org.jmol.script.ScriptExpr
- parameterIndex(String) - Static method in class org.jmol.adapter.readers.xtal.GulpReader
- parameters - Variable in class org.jmol.jvxl.readers.Parameters
- parameters - Static variable in class org.jmol.script.T
- Parameters - Class in org.jmol.jvxl.readers
- Parameters() - Constructor for class org.jmol.jvxl.readers.Parameters
- params - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- params - Variable in class org.jmol.jvxl.readers.SurfaceReader
- params - Variable in class org.jmol.quantum.NMRNoeMatrix
- params - Variable in class org.jmol.util.JmolAudio
- params - Variable in class org.jmol.util.Modulation
- params - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- paramsCentroid - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- paramsLattice - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- paramsPacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- paramTypes - Static variable in class org.jmol.script.T
- parB - Variable in class org.jmol.minimize.forcefield.Calculations
- parBorU - Variable in class org.jmol.util.Tensor
- parC - Variable in class org.jmol.minimize.forcefield.Calculations
- parenCount - Variable in class org.jmol.script.ScriptCompiler
- parenCount - Variable in class org.jmol.script.ScriptMathProcessor
- parent - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- parent - Variable in class org.jmol.adapter.readers.xml.XmlReader
- parent - Variable in class org.jmol.awt.AwtSwingComponent
- parent - Variable in class org.jmol.awtjs.swing.Component
- parent - Variable in class org.jmol.script.ScriptFlowContext
- parent - Variable in class org.jmol.smiles.SmilesAtom
- parent - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
direct ancestor of this atom
- parentContext - Variable in class org.jmol.script.ScriptContext
- parse(String) - Method in class org.jmol.smiles.SmilesParser
-
Parses a SMILES String
- parseAtom(SmilesSearch, SmilesAtom, String, SmilesAtom, SmilesBond, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
-
Parses an atom definition
- parseAtomTokens(Atom, String) - Method in class org.jmol.adapter.readers.simple.InputReader
- parseBond(SmilesSearch, SmilesBond, String, SmilesBond, SmilesAtom, boolean, boolean, int, int[]) - Method in class org.jmol.smiles.SmilesParser
- parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
- parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
- parseCommandLine(String[]) - Method in class org.openscience.jmol.app.JmolApp
- parseCommandParameter(short, boolean) - Method in class org.jmol.script.ScriptCompiler
- parseConnection(SmilesSearch, int, SmilesAtom, SmilesBond) - Method in class org.jmol.smiles.SmilesParser
-
Parses a ring definition
- parseDataArray(String, boolean) - Method in class org.jmol.scriptext.CmdExt
- parsedContext - Variable in class org.jmol.console.ScriptEditor
- parsedData - Variable in class org.jmol.console.ScriptEditor
- parseDouble(String) - Method in class org.jmol.adapter.readers.cif.MSCifParser
- parseEPSData(String, Lst<Object>) - Static method in class org.jmol.shapecgo.CGOMesh
- parseFloat() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseFloat() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- parseFloat(String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- parseFloatArrayBsData(String[], BS, float[]) - Static method in class org.jmol.util.Parser
- parseFloatArrayFromMatchAndField(String, BS, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
-
the major lifter here.
- parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- parseFloatRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- parseFloatStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseFloatStr(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- parseInt() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseInt() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- parseInt(String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- parseIntAt(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseIntNext(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- parseIntRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseIntStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseIntStr(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- parseJSON(String) - Method in class org.jmol.viewer.Viewer
- parseJSONArray(String) - Method in class org.jmol.viewer.Viewer
- parseJSONMap(String) - Method in class org.jmol.viewer.Viewer
- parseKnownToken() - Method in class org.jmol.script.ScriptCompiler
- parseLattRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- parseLineParameters(String[], byte[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cif.CifReader
-
sets up arrays and variables for tokenizer.getData()
- parseLoopParametersFor(String, String[]) - Method in class org.jmol.adapter.readers.cif.CifReader
- parseM40Floats() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- parseMeasure(SmilesSearch, String, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
- parseNested(SmilesSearch, String, String) - Method in class org.jmol.smiles.SmilesParser
- Parser - Class in org.jmol.util
- Parser() - Constructor for class org.jmol.util.Parser
- parseScript(String, int) - Method in class org.jmol.console.ScriptEditor
- parseSfacCoefficients(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- parseSfacElementSymbols(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- parseSfacRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- parseSmiles(SmilesSearch, String, SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesParser
-
Parses a part of a SMILES String
- parseStringInfestedFloatArray(String, BS, float[]) - Static method in class org.jmol.util.Parser
-
parses a "dirty" string for floats.
- parseSymmRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- parseToken() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseTokenNext(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseTokenRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseTokenStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- parseVariableLength(String) - Method in class org.jmol.smiles.SmilesParser
- parseVariables(String) - Method in class org.jmol.smiles.SmilesParser
-
variables can be defined, as in select within(SMARTS,'$R1="[CH3, NH2]";$R2="[$([$R1]),OH]"; {a}[$R2]') select within(SMARTS,'$R1="[CH3,NH2]";$R2="[OH]"; {a}[$([$R1]),$([$R2])]') "select aromatic atoms bearing CH3, NH2, or OH"
- parseXML() - Method in class org.jmol.adapter.readers.xml.XmlReader
- parseXML(XmlReader, Object, BufferedReader) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- PARTIAL_CHARGE - Enum constant in enum org.jmol.c.PAL
- PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
- PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JC
- PARTIAL01 - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- PARTIAL12 - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- PARTIAL23 - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- PARTIAL32 - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- partialcharge - Static variable in class org.jmol.script.T
- partialCharge - Variable in class org.jmol.adapter.smarter.Atom
- partialCharge - Variable in class org.jmol.minimize.MinAtom
- PARTIALCHARGE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- partialCharges - Variable in class org.jmol.adapter.readers.simple.AmpacReader
- partialCharges - Variable in class org.jmol.minimize.Minimizer
- partialCharges - Variable in class org.jmol.modelset.AtomCollection
- partialdots - Static variable in class org.jmol.script.T
- partialDots - Variable in class org.jmol.viewer.GlobalSettings
- PARTICLE_CHAIN - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
- PARTICLE_NONE - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
- PARTICLE_SYMOP - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
- particleradius - Static variable in class org.jmol.script.T
- particleRadius - Variable in class org.jmol.viewer.GlobalSettings
- pass2Flag01 - Variable in class org.jmol.g3d.Graphics3D
- pasteClipboardAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PasteClipboardAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
- pasteClipboardActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- path - Variable in class org.jmol.awt.AwtG2D
- path - Static variable in class org.jmol.script.T
- path - Static variable in class org.openscience.jmol.app.janocchio.Nmr
- path() - Method in class org.jmol.script.ScriptFlowContext
- PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
AtomSetCollectionReader.readData() will close any BufferedReader
- PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
- PathButton - Variable in class org.openscience.jmol.app.webexport.Test
- pathforallfiles - Static variable in class org.jmol.script.T
- pathForAllFiles - Variable in class org.jmol.viewer.FileManager
- pattern - Variable in class org.jmol.smiles.SmilesAtom
- pattern - Variable in class org.jmol.smiles.SmilesSearch
- patternAromatic - Variable in class org.jmol.smiles.SmilesSearch
-
Set in set() to indicate to SmilesMatcher that the string already has aromatic atoms indicated and so no aromaticity model should be applied.
- patternAtoms - Variable in class org.jmol.smiles.SmilesSearch
- patternBioSequence - Variable in class org.jmol.smiles.SmilesSearch
- patternIndex - Variable in class org.jmol.smiles.SmilesAtom
- PatternMatcher - Class in org.jmol.util
- PatternMatcher() - Constructor for class org.jmol.util.PatternMatcher
- pause - Static variable in class org.jmol.script.T
- PAUSE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- PAUSE_DELAY - Static variable in class org.jmol.script.ScriptDelayThread
- pauseAnimation() - Method in class org.jmol.viewer.AnimationManager
- pauseButton - Variable in class org.jmol.console.ScriptEditor
- pauseExecution(boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- pauseExecution(boolean) - Method in class org.jmol.script.ScriptEval
- pauseScript(Viewer, boolean) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- pauseScriptExecution() - Method in class org.jmol.viewer.Viewer
- pb - Variable in class org.jmol.g3d.Pixelator
- pBotLeft - Variable in class org.jmol.g3d.HermiteRenderer
- pBotRight - Variable in class org.jmol.g3d.HermiteRenderer
- pbuf - Variable in class org.jmol.g3d.Graphics3D
- pBuffer - Variable in class org.jmol.g3d.Platform3D
- pBufferT - Variable in class org.jmol.g3d.Platform3D
- pbufT - Variable in class org.jmol.g3d.Graphics3D
- pButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- pc - Variable in class org.jmol.script.ScriptContext
- pc - Variable in class org.jmol.script.ScriptEval
- pc - Variable in class org.jmol.util.MeshSurface
-
polygon count
- pc0 - Variable in class org.jmol.script.ScriptContext
- pcEnd - Variable in class org.jmol.script.ScriptContext
- pcEnd - Variable in class org.jmol.script.ScriptEval
- PCHRG - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- pcl - Variable in class org.jmol.awt.FileDropper
- pcResume - Variable in class org.jmol.script.ScriptEval
- pcs - Variable in class org.jmol.util.MeshSurface
-
polygon color index "colix" array
- pcs - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- pdb - Static variable in class org.jmol.script.T
- PDB_ANNOTATIONS - Static variable in class org.jmol.viewer.JC
- PDB_CARTOONS - Static variable in interface org.jmol.api.JmolScriptManager
- pdb_conect_all - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_discrete_chains - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_echo_tags - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_formal_charges - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_hetatm_guess_valences - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_hetatm_sort - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_honor_model_number - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_ignore_conect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_insertions_go_first - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_insure_orthogonal - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_literal_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_no_end_record - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_reformat_names_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_retain_ids - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_standard_order - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_truncate_residue_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_unbond_cations - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdb_use_ter_records - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pdbaddhydrogens - Static variable in class org.jmol.script.T
- pdbAddHydrogens - Variable in class org.jmol.viewer.GlobalSettings
- pdbAtomForH - Static variable in class org.jmol.dssx.AnnotationParser
- pdbBondInfo - Static variable in class org.jmol.modelsetbio.BioResolver
-
pdbBondInfo describes in a compact way what the hydrogen atom names are for each standard amino acid.
- pdbCartoonChecked - Static variable in class org.jmol.dialog.FilePreview
- pdbgetheader - Static variable in class org.jmol.script.T
- pdbGetHeader - Variable in class org.jmol.viewer.GlobalSettings
- pdbheader - Static variable in class org.jmol.script.T
- pdbHeader - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- pdbHydrogenCount - Static variable in class org.jmol.modelsetbio.BioResolver
- pdbID - Variable in class org.jmol.adapter.readers.cif.CifReader
- pdbID - Variable in class org.jmol.adapter.readers.cif.MMTFReader
- pdbID - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- pdbID - Variable in class org.jmol.modelset.Model
- pdbKey(int) - Method in class org.jmol.adapter.writers.PDBWriter
- pdbLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- pdbLoadFormat - Variable in class org.jmol.viewer.GlobalSettings
- pdbLoadLigandFormat - Variable in class org.jmol.viewer.GlobalSettings
- PDBOnly - Variable in class org.jmol.popup.JmolPopup
- PdbReader - Class in org.jmol.adapter.readers.pdb
-
PDB file reader.
- PdbReader() - Constructor for class org.jmol.adapter.readers.pdb.PdbReader
- pdbRecords - Static variable in class org.jmol.modelsetbio.BioExt
- pdbsequential - Static variable in class org.jmol.script.T
- pdbSequential - Variable in class org.jmol.viewer.GlobalSettings
- PDBWriter - Class in org.jmol.adapter.writers
-
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
- PDBWriter() - Constructor for class org.jmol.adapter.writers.PDBWriter
- peakData - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- peakFilePath - Variable in class org.jmol.jsv.JDXMOLParser
- peakIndex - Variable in class org.jmol.jsv.JDXMOLParser
- peek() - Method in class org.jmol.adapter.readers.pymol.PickleReader
- per - Static variable in class org.jmol.script.T
- percent - Static variable in class org.jmol.script.T
- percent - Variable in class org.jmol.shapespecial.Ellipsoid
- percentToPixels(char, float) - Method in class org.jmol.viewer.TransformManager
- percentvdwatom - Static variable in class org.jmol.script.T
- percentVdwAtom - Variable in class org.jmol.viewer.GlobalSettings
- percentVdwAtom - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- period - Static variable in class org.jmol.script.T
- PERIOD_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Maximum value for the vibration period in seconds.
- PERIOD_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Precision of the vibration period slider in seconds.
- PERIOD_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Initial value for the vibration period in seconds.
- PeriodicVolumeFileReader - Class in org.jmol.jvxl.readers
- PeriodicVolumeFileReader() - Constructor for class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- periodSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- PERM_OCT - Static variable in class org.jmol.smiles.SmilesStereo
- PERM_SS - Static variable in class org.jmol.smiles.SmilesStereo
- PERM_TB - Static variable in class org.jmol.smiles.SmilesStereo
- permutation - Variable in class org.jmol.adapter.readers.xtal.OptimadeReader
-
values 0, 1, or 2 indicate how to permute the lattice vectors to be of the form [1,0,0] for polymers or [1,1,0] for slabs
- perpendicular - Static variable in class org.jmol.script.T
- perper - Static variable in class org.jmol.script.T
- perspectiveAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- perspectivedepth - Static variable in class org.jmol.script.T
- perspectiveDepth - Variable in class org.jmol.viewer.TransformManager
- perspectiveDepth - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- perspectiveFactor - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- perspectivemodel - Static variable in class org.jmol.script.T
- perspectiveModel - Variable in class org.jmol.viewer.TransformManager
- perspectiveOffset - Variable in class org.jmol.viewer.TransformManager
- perspectiveShiftXY - Variable in class org.jmol.viewer.TransformManager
- pfaatBinding - Variable in class org.jmol.viewer.ActionManager
- PfaatBinding - Class in org.jmol.viewer.binding
- PfaatBinding() - Constructor for class org.jmol.viewer.binding.PfaatBinding
- pfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- pFF - Variable in class org.jmol.minimize.Minimizer
- phase - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
- phase - Static variable in class org.jmol.script.T
- phi - Variable in class org.jmol.modelsetbio.Monomer
- phi - Static variable in class org.jmol.script.T
- phong - Variable in class org.jmol.export._TachyonExporter
- phongexponent - Static variable in class org.jmol.script.T
- phongExponent - Variable in class org.jmol.util.Shader
- PhosphorusMonomer - Class in org.jmol.modelsetbio
- PhosphorusMonomer() - Constructor for class org.jmol.modelsetbio.PhosphorusMonomer
- phosphorusOffsets - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
- PhosphorusPolymer - Class in org.jmol.modelsetbio
- PhosphorusPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.PhosphorusPolymer
- PI_OVER_2 - Static variable in class org.jmol.minimize.forcefield.Calculations
- PICK - Enum constant in enum org.jmol.c.CBK
- PICK_COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
- pickable - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- PickAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.PickAction
- pickAtomAssignType - Variable in class org.jmol.modelkit.ModelKit
- pickBondAssignType - Variable in class org.jmol.modelkit.ModelKit
- pickedAtom - Variable in class org.jmol.shape.Labels
- pickedMesh - Variable in class org.jmol.shape.MeshCollection
- pickedModel - Variable in class org.jmol.shape.MeshCollection
- pickedOffset - Variable in class org.jmol.shape.Labels
- pickedPt - Variable in class org.jmol.shape.MeshCollection
- pickedVertex - Variable in class org.jmol.shape.MeshCollection
- pickedX - Variable in class org.jmol.shape.Labels
- pickedY - Variable in class org.jmol.shape.Labels
- picking - Static variable in class org.jmol.script.T
- PICKING_ASSIGN_ATOM - Static variable in class org.jmol.viewer.ActionManager
- PICKING_ASSIGN_BOND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_CENTER - Static variable in class org.jmol.viewer.ActionManager
- PICKING_CONNECT - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DELETE_ATOM - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DELETE_BOND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_ATOM - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_LIGAND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_MINIMIZE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_MINIMIZE_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_MODEL - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAG_SELECTED - Static variable in class org.jmol.viewer.ActionManager
- PICKING_DRAW - Static variable in class org.jmol.viewer.ActionManager
- PICKING_IDENTIFY - Static variable in class org.jmol.viewer.ActionManager
- PICKING_IDENTIFY_BOND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_INVERT_STEREO - Static variable in class org.jmol.viewer.ActionManager
- PICKING_LABEL - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE_ANGLE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE_DISTANCE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE_SEQUENCE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MEASURE_TORSION - Static variable in class org.jmol.viewer.ActionManager
- PICKING_MK_RESET - Static variable in class org.jmol.viewer.ActionManager
- PICKING_NAVIGATE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_OFF - Static variable in class org.jmol.viewer.ActionManager
- PICKING_ROTATE_BOND - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_ATOM - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_CHAIN - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_ELEMENT - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_GROUP - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_MODEL - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_POLYMER - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_SITE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SELECT_STRUCTURE - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SPIN - Static variable in class org.jmol.viewer.ActionManager
- PICKING_STRUTS - Static variable in class org.jmol.viewer.ActionManager
- PICKING_SYMMETRY - Static variable in class org.jmol.viewer.ActionManager
- pickingModeNames - Static variable in class org.jmol.viewer.ActionManager
- pickingspinrate - Static variable in class org.jmol.script.T
- pickingSpinRate - Variable in class org.jmol.viewer.GlobalSettings
- pickingstyle - Static variable in class org.jmol.script.T
- pickingStyle - Variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_MEASURE_OFF - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_MEASURE_ON - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_SELECT_CHIME - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_SELECT_DRAG - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_SELECT_JMOL - Static variable in class org.jmol.viewer.ActionManager
-
picking styles
- PICKINGSTYLE_SELECT_PFAAT - Static variable in class org.jmol.viewer.ActionManager
- PICKINGSTYLE_SELECT_RASMOL - Static variable in class org.jmol.viewer.ActionManager
- pickingStyleMeasure - Variable in class org.jmol.viewer.ActionManager
- pickingStyleNames - Static variable in class org.jmol.viewer.ActionManager
- pickingStyleSelect - Variable in class org.jmol.viewer.ActionManager
- picklabel - Static variable in class org.jmol.script.T
- pickLabel - Variable in class org.jmol.viewer.GlobalSettings
- pickLabel(int) - Method in class org.jmol.viewer.ActionManager
- PickleReader - Class in org.jmol.adapter.readers.pymol
-
generic Python Pickle file reader only utilizing records needed for PyMOL.
- PickleReader(GenericBinaryDocument, Viewer) - Constructor for class org.jmol.adapter.readers.pymol.PickleReader
- pictFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- pictIsScratchFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- pid - Variable in class org.jmol.shapespecial.Ellipsoid
- pidOf(Object) - Static method in enum org.jmol.c.PAL
- pilp - Variable in class org.jmol.minimize.forcefield.AtomType
-
MMFF pi lone pair type, i.e.
- PINK - Static variable in class org.jmol.util.C
- pipedIS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
- pipedOS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
- pis - Variable in class org.jmol.util.MeshSurface
-
polygon indexes
- piUnitsX - Variable in class org.jmol.jsv.JDXMOLParser
- piUnitsY - Variable in class org.jmol.jsv.JDXMOLParser
- pivot - Static variable in class org.jmol.script.T
- pivot2 - Static variable in class org.jmol.script.T
- pixel - Variable in class org.jmol.g3d.Graphics3D
- pixel0 - Variable in class org.jmol.g3d.Graphics3D
- Pixelator - Class in org.jmol.g3d
- Pixelator(Graphics3D) - Constructor for class org.jmol.g3d.Pixelator
- PixelatorScreened - Class in org.jmol.g3d
-
A class to create a "screened" translucent effect by discarding pixels in a checkerboard fashion.
- PixelatorScreened(Graphics3D, Pixelator) - Constructor for class org.jmol.g3d.PixelatorScreened
- PixelatorShaded - Class in org.jmol.g3d
-
A class to do Z Shading of pixels.
- PixelatorShaded(Graphics3D) - Constructor for class org.jmol.g3d.PixelatorShaded
- PixelatorT - Class in org.jmol.g3d
-
Handle pixels in Pass 2 - Translucency
- PixelatorT(Graphics3D) - Constructor for class org.jmol.g3d.PixelatorT
- pixelScale - Variable in class org.jmol.thread.MoveToThread
- pixelScreened - Variable in class org.jmol.g3d.Graphics3D
- pixelShaded - Variable in class org.jmol.g3d.Graphics3D
- pixelT0 - Variable in class org.jmol.g3d.Graphics3D
- planarparam - Static variable in class org.jmol.script.T
- planarParam - Variable in class org.jmol.shapespecial.Polyhedra
- plane - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- plane - Variable in class org.jmol.modelkit.ModelKit.Constraint
- plane - Variable in class org.jmol.modelsetbio.BioResolver
- plane - Static variable in class org.jmol.script.T
- plane - Variable in class org.jmol.shapespecial.Draw
- plane(P3, P3, float) - Method in class org.jmol.util.BZone
- PLANE - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- plane_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
- plane_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
- plane1 - Variable in class org.jmol.adapter.readers.simple.InputReader
- plane2 - Variable in class org.jmol.adapter.readers.simple.InputReader
- planeCenter - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- planeCount - Variable in class org.jmol.jvxl.readers.UhbdReader
- planeParameter(int, boolean) - Method in class org.jmol.script.ScriptParam
- planeRadius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- planes - Variable in class org.jmol.shapespecial.Polyhedron
- planes - Variable in class org.jmol.util.BZone
- planeShade - Variable in class org.jmol.g3d.SphereRenderer
- planeShades - Variable in class org.jmol.g3d.SphereRenderer
- planesT - Variable in class org.jmol.shapespecial.Polyhedra
- planesUnused - Variable in class org.jmol.util.BZone
- planeU - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- planeV - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- planeValue(T) - Method in class org.jmol.script.ScriptParam
- plateColixes - Variable in class org.jmol.export._VrmlExporter
- plateIndices - Variable in class org.jmol.export._VrmlExporter
- plateVertices - Variable in class org.jmol.export._VrmlExporter
- platform - Variable in class org.jmol.g3d.Graphics3D
- Platform - Class in org.jmol.awt
- Platform - Class in org.jmol.awtjs
-
WebGL interface
- Platform - Class in org.jmol.awtjs2d
-
JavaScript 2D canvas version requires Ajax-based URL stream processing.
- Platform() - Constructor for class org.jmol.awt.Platform
- Platform() - Constructor for class org.jmol.awtjs.Platform
- Platform() - Constructor for class org.jmol.awtjs2d.Platform
- Platform3D - Class in org.jmol.g3d
-
Specifies the API to an underlying int[] buffer of ARGB values that can be converted into an Image object and a short[] for z-buffer depth.
- Platform3D(GenericPlatform) - Constructor for class org.jmol.g3d.Platform3D
- platformspeed - Static variable in class org.jmol.script.T
- platformSpeed - Variable in class org.jmol.viewer.GlobalSettings
- PlatformViewer - Interface in org.jmol.api
- play - Static variable in class org.jmol.script.T
- PLAY - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- playAudio(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
- playAudio(JSmolAppletObject, Map<String, Object>) - Method in interface org.jmol.api.js.JmolToJSmolInterface
- playAudio(Viewer, Map<String, Object>) - Method in class org.jmol.util.JmolAudio
-
WAV only for application
- playrev - Static variable in class org.jmol.script.T
- pLeft - Variable in class org.jmol.g3d.HermiteRenderer
- plot - Static variable in class org.jmol.script.T
- plot(int, int, int, int, int, String, Font, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.TextRenderer
- plot(T[]) - Method in class org.jmol.scriptext.CmdExt
- plot3d - Static variable in class org.jmol.script.T
- Plot3D - Class in org.jmol.shapesurface
- Plot3D() - Constructor for class org.jmol.shapesurface.Plot3D
- Plot3DRenderer - Class in org.jmol.rendersurface
- Plot3DRenderer() - Constructor for class org.jmol.rendersurface.Plot3DRenderer
- plotByCharacter(int, int, int, int, int, String, Font, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.TextRenderer
- plotCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
- plotCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
- plotFilledCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
- plotFilledCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
- plotImage(int, int, int, Object, short, int, int) - Method in class org.jmol.export.___Exporter
- plotImage(int, int, int, Object, short, int, int) - Method in class org.jmol.export.__CartesianExporter
- plotImage(int, int, int, Object, short, int, int) - Method in class org.jmol.export.JSExporter
- plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.g3d.Graphics3D
- plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.util.GData
- plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in interface org.jmol.api.JmolRendererInterface
- plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.export.Export3D
- plotImagePixel(int, int, int, int, byte, int, int, int, int[], Object, int) - Method in class org.jmol.g3d.Graphics3D
- plotLineBits(int, int, P3i, P3i, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
- plotLineClippedOld(int, int, int, int, int, int, int, int, boolean, int, int) - Method in class org.jmol.g3d.LineRenderer
-
low-resolution linear z-buffer (old style)
- plotLineDeltaABitsFloat(int[], int[], int, P3, P3, int, boolean) - Method in class org.jmol.g3d.LineRenderer
- plotLineDeltaABitsInt(int[], int[], int, P3i, P3i, int, boolean) - Method in class org.jmol.g3d.LineRenderer
- plotLineDeltaAOld(int[], int[], int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
-
low-precision old-style linear z, even in perspective mode
- plotLineDeltaOld(int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
-
low-resolution linear z
- plotLineOld(int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.LineRenderer
- plotPixelClipped(int, int, int) - Method in class org.jmol.export.Export3D
- plotPixelClippedArgb(int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
- plotPixelClippedP3i(P3i) - Method in interface org.jmol.api.JmolRendererInterface
- plotPixelClippedP3i(P3i) - Method in class org.jmol.export.Export3D
- plotPixelClippedP3i(P3i) - Method in class org.jmol.g3d.Graphics3D
- plotPixelsClipped(int, int, int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.CircleRenderer
- plotPixelsClippedRaster(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
- plotPixelsClippedRasterBits(int, int, int, int, int, Rgb16, Rgb16, float, float) - Method in class org.jmol.g3d.Graphics3D
- plotPixelsUnclippedCount(int, int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
- plotPixelsUnclippedRaster(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
- plotPixelsUnclippedRasterBits(int, int, int, Rgb16, Rgb16, float, float) - Method in class org.jmol.g3d.Graphics3D
- plotPixelUnclipped(int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
- plotPoints(int, int[], int, int) - Method in class org.jmol.g3d.Graphics3D
- plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
- plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.util.GData
- plotText(int, int, int, short, String, Font) - Method in class org.jmol.export.___Exporter
- plotText(int, int, int, short, String, Font) - Method in class org.jmol.export.__CartesianExporter
- plotText(int, int, int, short, String, Font) - Method in class org.jmol.export._StlExporter
- plotText(int, int, int, short, String, Font) - Method in class org.jmol.export._VrmlExporter
- plotText(int, int, int, short, String, Font) - Method in class org.jmol.export._X3dExporter
- plotText(int, int, int, short, String, Font) - Method in class org.jmol.export.JSExporter
- PltFormattedReader - Class in org.jmol.jvxl.readers
- PltFormattedReader() - Constructor for class org.jmol.jvxl.readers.PltFormattedReader
- plugin - Variable in class org.openscience.jmol.app.janocchio.Nmr
- pluginFile - Variable in class org.openscience.jmol.app.JmolApp
- pluginFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- pluginMenu - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- plugins - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- pluginsSet - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- plus - Static variable in class org.jmol.script.T
- plusMinus(String, float, String) - Static method in class org.jmol.symmetry.SymmetryOperation
- plusPlus - Static variable in class org.jmol.script.T
- pm - Variable in class org.jmol.scriptext.MathExt
- pm - Variable in class org.jmol.viewer.Viewer
- pmesh - Static variable in class org.jmol.script.T
- Pmesh - Class in org.jmol.shapesurface
- Pmesh() - Constructor for class org.jmol.shapesurface.Pmesh
- PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.viewer.FileManager
- Pmesh4Reader - Class in org.jmol.jvxl.readers
- Pmesh4Reader() - Constructor for class org.jmol.jvxl.readers.Pmesh4Reader
- pmeshError - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
- pmeshError - Variable in class org.jmol.jvxl.readers.PmeshReader
- pmeshError - Variable in class org.jmol.jvxl.readers.Ras3DReader
- pmeshes - Variable in class org.jmol.util.BZone
- PmeshReader - Class in org.jmol.jvxl.readers
-
PMESH format created for Jmol.
- PmeshReader() - Constructor for class org.jmol.jvxl.readers.PmeshReader
- PmeshRenderer - Class in org.jmol.rendersurface
- PmeshRenderer() - Constructor for class org.jmol.rendersurface.PmeshRenderer
- PMeshWriter - Class in org.jmol.shapesurface
-
A class called by reflection from IsosurfaceMesh from the Jmol command WRITE xxxx.pmesh (ascii) or WRITE xxxx.pmb (binary)
- PMeshWriter() - Constructor for class org.jmol.shapesurface.PMeshWriter
- png_file_gamma - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- png_screen_gamma - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pngjCache - Variable in class org.jmol.viewer.FileManager
- PO - Class in org.jmol.translation
-
Just a marker for resourceClass.getClass().getResource(resourceName); Jmol now reads the PO files directly for its translations.
- PO() - Constructor for class org.jmol.translation.PO
- pocket - Variable in class org.jmol.jvxl.readers.Parameters
- pocket - Static variable in class org.jmol.script.T
- point - Variable in class org.jmol.jvxl.readers.Parameters
- point - Variable in class org.jmol.jvxl.readers.VolumeDataReader
- point - Static variable in class org.jmol.script.T
- POINT - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- point3f - Static variable in class org.jmol.script.T
- Point3fi - Class in org.jmol.util
-
the Point3fi class allows storage of critical information involving an atom, picked bond, or measurement point, including: xyz position screen position screen radius (-1 for a simple point) index (for atoms or for an associated bond that has be picked) associated modelIndex (for measurement points)
- Point3fi() - Constructor for class org.jmol.util.Point3fi
- point4f - Static variable in class org.jmol.script.T
- pointA - Variable in class org.jmol.jvxl.calc.MarchingCubes
- pointA - Variable in class org.jmol.jvxl.calc.MarchingSquares
- pointArrowHead - Variable in class org.jmol.renderspecial.VectorsRenderer
- pointAt(Lst<Object>, int, P3) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- pointB - Variable in class org.jmol.jvxl.calc.MarchingSquares
- pointer - Variable in class org.jmol.modelset.Text
- pointer - Variable in class org.jmol.render.LabelsRenderer
- pointerPt - Variable in class org.jmol.modelset.Text
- pointers - Variable in class org.jmol.script.ScriptContext
- pointFromTriad(String) - Static method in class org.jmol.modelkit.ModelKit
- pointgroup - Static variable in class org.jmol.script.T
- pointGroup - Variable in class org.jmol.modelset.AtomCollection
- pointGroup - Variable in class org.jmol.shapespecial.Polyhedron
-
includes vertices as atoms, with atomic numbers
- pointGroup - Variable in class org.jmol.symmetry.Symmetry
- PointGroup - Class in org.jmol.symmetry
- PointGroup() - Constructor for class org.jmol.symmetry.PointGroup
- PointGroup.Operation - Class in org.jmol.symmetry
- pointgroupdistancetolerance - Static variable in class org.jmol.script.T
- pointGroupDistanceTolerance - Variable in class org.jmol.viewer.GlobalSettings
- pointGroupFamily - Variable in class org.jmol.shapespecial.Polyhedron
-
includes vertices as generic points
- pointgrouplineartolerance - Static variable in class org.jmol.script.T
- pointGroupLinearTolerance - Variable in class org.jmol.viewer.GlobalSettings
- pointGuides - Variable in class org.jmol.navigate.Navigator
- PointIterator - Class in org.jmol.bspt
- PointIterator() - Constructor for class org.jmol.bspt.PointIterator
- pointPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d, boolean) - Static method in class org.jmol.minimize.Util
-
calculates angle of a to plane bcd, returning a value > pi/2 in highly distorted trigonal pyramidal situations
- points - Variable in class org.jmol.jvxl.readers.IsoMOReader
- points - Variable in class org.jmol.jvxl.readers.Parameters
- points - Variable in class org.jmol.modelkit.ModelKit.Constraint
- points - Variable in class org.jmol.modelset.MeasurementData
- points - Variable in class org.jmol.navigate.Navigator
- points - Variable in class org.jmol.quantum.QuantumCalculation
- points - Variable in class org.jmol.renderspecial.DipolesRenderer
- points - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- points - Variable in class org.jmol.smiles.SmilesMeasure
- points - Variable in class org.jmol.symmetry.PointGroup
- POINTS_ALL - Static variable in class org.jmol.jvxl.readers.KinemageReader
- POINTS_HETS - Static variable in class org.jmol.jvxl.readers.KinemageReader
- POINTS_MCMC - Static variable in class org.jmol.jvxl.readers.KinemageReader
- POINTS_MCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
- POINTS_SCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
- pointScale - Variable in class org.jmol.shapespecial.Polyhedra
- pointScale - Variable in class org.jmol.shapespecial.Polyhedron
- pointSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- pointSize - Variable in class org.jmol.jvxl.data.JvxlData
- pointSize - Variable in class org.jmol.jvxl.readers.Parameters
- pointsperangstrom - Static variable in class org.jmol.script.T
- pointsPerAngstrom - Variable in class org.jmol.jvxl.data.JvxlData
- pointsPolyhedra(BS, float) - Method in class org.jmol.shapespecial.Polyhedra
- pointT - Variable in class org.jmol.geodesic.EnvelopeCalculation
- pointT - Variable in class org.jmol.render.FontLineShapeRenderer
- pointT - Variable in class org.jmol.renderbio.BioShapeRenderer
- pointT2 - Variable in class org.jmol.render.FontLineShapeRenderer
- pointT2 - Variable in class org.jmol.viewer.TransformManager
- pointT3 - Variable in class org.jmol.render.FontLineShapeRenderer
- pointType - Variable in class org.jmol.jvxl.readers.KinemageReader
- pointVectorEnd - Variable in class org.jmol.renderspecial.VectorsRenderer
- pointVectorStart - Variable in class org.jmol.renderspecial.VectorsRenderer
- polar_neighbor_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- polyAtom - Variable in class org.jmol.smiles.SmilesSearch
- polygon - Static variable in class org.jmol.script.T
- polygon - Variable in class org.jmol.shapespecial.Draw
- POLYGON - Enum constant in enum org.jmol.shapespecial.Draw.EnumDrawType
- polygonColorData - Variable in class org.jmol.jvxl.data.MeshData
- polygonCount0 - Variable in class org.jmol.util.MeshSurface
- PolygonFileReader - Class in org.jmol.jvxl.readers
- PolygonFileReader() - Constructor for class org.jmol.jvxl.readers.PolygonFileReader
- polygonIndexes - Variable in class org.jmol.shapesurface.PMeshWriter
- polyhedra - Static variable in class org.jmol.script.T
- polyhedra() - Method in class org.jmol.scriptext.CmdExt
- Polyhedra - Class in org.jmol.shapespecial
- Polyhedra() - Constructor for class org.jmol.shapespecial.Polyhedra
- POLYHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
- polyhedralOrders - Variable in class org.jmol.smiles.SmilesStereo
- PolyhedraRenderer - Class in org.jmol.renderspecial
- PolyhedraRenderer() - Constructor for class org.jmol.renderspecial.PolyhedraRenderer
- Polyhedron - Class in org.jmol.shapespecial
- Polyhedron() - Constructor for class org.jmol.shapespecial.Polyhedron
- polyhedronCount - Variable in class org.jmol.shapespecial.Polyhedra
- polyhedrons - Variable in class org.jmol.shapespecial.Polyhedra
- polyhedronStereo - Variable in class org.jmol.smiles.SmilesSearch
-
indicates that we have [XxPHn] with no connected atoms
- PolyhedronStereoSorter - Class in org.jmol.smiles
- PolyhedronStereoSorter() - Constructor for class org.jmol.smiles.PolyhedronStereoSorter
- polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in interface org.jmol.api.SmilesMatcherInterface
- polyhedronToSmiles(Node, int[][], int, P3[], int, String) - Method in class org.jmol.smiles.SmilesMatcher
-
Generate a topological SMILES string from a set of faces
- polyid - Variable in class org.jmol.util.BZone
- polymer - Static variable in class org.jmol.script.T
- POLYMER - Enum constant in enum org.jmol.c.PAL
- polymerlength - Static variable in class org.jmol.script.T
- polymerX - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- polySmiles - Variable in class org.jmol.shapespecial.Polyhedron
- polySmilesCenter - Variable in class org.jmol.smiles.SmilesGenerator
- pop - Static variable in class org.jmol.script.T
- pop() - Method in class org.jmol.adapter.readers.pymol.PickleReader
- popContext(boolean, boolean) - Method in class org.jmol.script.ScriptEval
- popHoldRepaint(boolean, String) - Method in interface org.jmol.api.JmolRepaintManager
- popHoldRepaint(boolean, String) - Method in class org.jmol.render.RepaintManager
- popHoldRepaint(String) - Method in class org.jmol.api.JmolViewer
- popHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
- popInHeight - Static variable in class org.openscience.jmol.app.webexport.WebExport
- PopInJmol - Class in org.openscience.jmol.app.webexport
- PopInJmol(Viewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.PopInJmol
- popInWidth - Static variable in class org.openscience.jmol.app.webexport.WebExport
- popMatrix() - Method in class org.jmol.export._StlExporter
- popMatrix() - Method in class org.jmol.export._VrmlExporter
- popMatrix() - Method in class org.jmol.export._X3dExporter
- popStack(int) - Method in class org.jmol.viewer.StateManager
-
Remove the last item on the specified stack, and save the current state to the other stack provided that state is not null.
- popState() - Method in class org.jmol.util.CommandHistory
- popState() - Method in class org.jmol.viewer.Viewer
- population - Variable in class org.openscience.jmol.app.janocchio.PopulationDisplay
- populationDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- populationDisplay - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- PopulationDisplay - Class in org.openscience.jmol.app.janocchio
- PopulationDisplay(NMR_Viewer) - Constructor for class org.openscience.jmol.app.janocchio.PopulationDisplay
-
Constructor
- PopulationDisplayAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.PopulationDisplayAction
- populationFrames - Variable in class org.openscience.jmol.app.janocchio.PopulationDisplay
- populationFramesActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- popup - Variable in class org.jmol.awt.AwtPopupHelper
- popup - Variable in class org.jmol.awtjs2d.JSPopupHelper
-
used here and by SwingController to refer to the Java class being handled by this helper.
- PopupHelper - Interface in org.jmol.popup
- popupMenu - Variable in class org.jmol.awtjs.swing.AbstractButton
- popupMenu - Variable in class org.jmol.popup.GenericPopup
- popupMenu(int, int, char) - Method in class org.jmol.viewer.Viewer
- PopupResource - Class in org.jmol.popup
- PopupResource(String, Properties) - Constructor for class org.jmol.popup.PopupResource
- port - Variable in class org.openscience.jmol.app.JmolApp
-
The data model.
- port - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- posCorner - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- position - Variable in class org.openscience.jmol.app.surfacetool.Slice
- position - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- position - Variable in class org.openscience.jvxl.MonitorInputStream
- positionAfterPrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- positionBeforePrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- positionMin - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- positionSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- positionThicknessPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- postByteArray(String, byte[]) - Method in class org.jmol.viewer.FileManager
- postProcessTry(Map<String, SV>) - Method in class org.jmol.script.ScriptEval
- postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoMOReader
- postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoSolventReader
- postProcessVertices() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- postProcessVertices() - Method in class org.jmol.jvxl.readers.SurfaceReader
- potentials - Variable in class org.jmol.quantum.MepCalculation
- povrayAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PovrayAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
- povrayActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PovrayDialog - Class in org.openscience.jmol.app.jmolpanel
-
A dialog for controling the creation of a povray input file from a Chemframe and a display.
- PovrayDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Creates a dialog for getting info related to output frames in povray format.
- PovrayDialog.PovrayWindowListener - Class in org.openscience.jmol.app.jmolpanel
-
Listener for responding to dialog window events.
- povrayPathButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- povrayPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- PovrayWindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog.PovrayWindowListener
- power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- power4 - Static variable in class org.jmol.geodesic.EnvelopeCalculation
- pqr_workarounds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- PqrReader - Class in org.jmol.adapter.readers.pdb
-
PQR file reader.
- PqrReader() - Constructor for class org.jmol.adapter.readers.pdb.PqrReader
- pqrStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- precalculateVoxelData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
- precision - Variable in class org.jmol.modelset.LabelToken
- PrecisionRenderer - Class in org.jmol.g3d
-
Note added 4/2015 BH: Well, it turns out that the calculation of the intermediate pixel z value in all methods involving rasterization of lines is incorrect and has been incorrect since Jmol's inception.
- PrecisionRenderer() - Constructor for class org.jmol.g3d.PrecisionRenderer
- predefinedGroup1Names - Static variable in class org.jmol.modelsetbio.BioResolver
- predefinedGroup3Names - Static variable in class org.jmol.modelsetbio.BioResolver
- predefinedset - Static variable in class org.jmol.script.T
- predefinedStatic - Static variable in class org.jmol.viewer.JC
- predefinedVariable - Static variable in class org.jmol.viewer.JC
- preDefining - Variable in class org.jmol.script.ScriptCompiler
- predragBinding - Variable in class org.jmol.viewer.ActionManager
- preferencesDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PreferencesDialog - Class in org.openscience.jmol.app.jmolpanel
- PreferencesDialog(JmolPanel, JFrame, GuiMap, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- PreferencesDialog.PrefsAction - Class in org.openscience.jmol.app.jmolpanel
- preFilterAtomList(SimpleNode[], BS, BS) - Method in class org.jmol.symmetry.CIPChirality
-
Remove unnecessary atoms from the list and let us know if we have alkenes to consider.
- PREFIX_LEN - Static variable in class org.jmol.adapter.writers.PWMATWriter
- prefsAction - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- PrefsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
- prepareBinaryOutput(SV) - Method in class org.jmol.scriptext.CmdExt
- preprocessString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
initial processing; returns a string bounded by \1
- presentation - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- presentation_auto_quit - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- presentation_auto_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- presentation_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- preserve_chempy_ids - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- preservestate - Static variable in class org.jmol.script.T
- preserveState - Variable in class org.jmol.modelset.AtomCollection
- preserveState - Variable in class org.jmol.viewer.GlobalSettings
- pressAction - Variable in class org.jmol.viewer.ActionManager
- pressed - Variable in class org.jmol.viewer.ActionManager
- pressed(long, int, int, int, boolean) - Method in class org.jmol.awtjs2d.Mouse
- PRESSED - Static variable in class org.jmol.awtjs.Event
- pressedCount - Variable in class org.jmol.viewer.ActionManager
- prev - Static variable in class org.jmol.script.T
- prev - Variable in class org.jmol.util.MeshCapper.CapVertex
-
edge double links
- prevAtom - Variable in class org.jmol.smiles.SmilesGenerator
- prevBondCheckBox - Variable in class org.jmol.modelkit.ModelKitPopup
- prevCovalentVersion - Static variable in class org.jmol.script.ScriptManager
- prevFrame - Variable in class org.jmol.viewer.Viewer
- PREVIOUS - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.Mesh
- PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.MeshCollection
- previousMeshID - Variable in class org.jmol.shape.MeshCollection
- previousMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- previousScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- previousSpaceGroup - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- previousUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- previousX - Variable in class org.jmol.viewer.TransformManager
- previousY - Variable in class org.jmol.viewer.TransformManager
- prevline - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- prevMorphModel - Variable in class org.jmol.viewer.Viewer
- prevSp2Atoms - Variable in class org.jmol.smiles.SmilesGenerator
- prevZoomSetting - Variable in class org.jmol.viewer.TransformManager
- pRight - Variable in class org.jmol.g3d.HermiteRenderer
- primitiveCode - Variable in class org.jmol.symmetry.HallRotationTerm
- primitiveData - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- primitiveDensity - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- primitiveHallSymbol - Variable in class org.jmol.symmetry.HallInfo
- primitives - Variable in class org.jmol.smiles.SmilesBond
- primitiveToCrystal - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- primitiveToIndex - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- primitiveType - Variable in class org.jmol.smiles.SmilesAtom
- primitiveVolume - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- principalAxis - Variable in class org.jmol.symmetry.PointGroup
- principalPlane - Variable in class org.jmol.symmetry.PointGroup
- principalQuantumNumber - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- print - Static variable in class org.jmol.script.T
- print() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
added print command, so that it can be used by RasmolScriptHandler
- print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- printAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- PrintAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
- printActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- priorities - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
priorities associated with each subsituent from high (0) to low (3); due to equivaliencies at a given rule level, these numbers may duplicate and have gaps - for example, [0 2 0 3]
- priority - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
current priority 0-3; used for Rule 4b and 5 priority sorting
- priority - Variable in class org.openscience.jmol.app.janocchio.TableSorter.Arrow
- PRIORITY - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- privat - Static variable in class org.jmol.script.T
- privateFuncs - Variable in class org.jmol.script.ScriptContext
- privateFuncs - Variable in class org.jmol.script.ScriptExpr
- privateKey - Variable in class org.jmol.export.___Exporter
- privateKey - Variable in class org.jmol.export.Export3D
- privateKey - Variable in class org.jmol.viewer.OutputManager
- privateKey - Variable in class org.jmol.viewer.Viewer
- probe - Static variable in class org.jmol.script.T
- probes - Variable in class org.jmol.jvxl.readers.Parameters
- probeValues - Variable in class org.jmol.jvxl.readers.Parameters
- probeValues - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- proc - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- process - Variable in class org.jmol.script.ScriptProcessRunnable
- process - Static variable in class org.jmol.script.T
- process() - Method in class org.jmol.quantum.MepCalculation
- process() - Method in class org.jmol.quantum.MOCalculation
- process() - Method in class org.jmol.quantum.NciCalculation
- process() - Method in class org.jmol.quantum.QuantumCalculation
- process(int, int, float) - Method in class org.jmol.quantum.NciCalculation
-
Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point.
- process(int, int, float) - Method in class org.jmol.quantum.QuantumPlaneCalculation
-
Data mapping function to radically increase speed and reduce memory requirements of mapping data when the mapping comes from the same data set as the points, so isosurface creation and data mapping can be carried out both in the first (and only) pass.
- process(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
The main processor.
- process(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
-
Handle the point; mark as processed.
- processAssemblyGenBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processAssociations(BS, BS) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Find and process all "bonds" associated with all links and nodes.
- processAtom() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
- processAtom(Atom, String, char, String, int, int, char, boolean, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- processAtom2(Atom, int, float, float, float, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- processAtomClick(int) - Method in class org.jmol.modelkit.ModelKit
-
An atom has been clicked -- handle it.
- processAtomicCharges() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- processAtomicCharges() - Method in class org.jmol.adapter.readers.simple.MopacReader
-
Reads the section in MOPAC files with atomic charges.
- processAtomicCharges() - Method in class org.jmol.adapter.readers.simple.OrcaReader
- processAtomObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
- processAtoms() - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- processAtoms() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- processAtoms() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
- processAtoms(int, int, int, int) - Method in class org.jmol.quantum.NciCalculation
-
At each grid point we need to calculate the sum of the atom-based promolecular data.
- processAtomSiteLoopBlock(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
-
reads atom data in any order
- processAtomTypeLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
-
reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.
- processBasis() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- processBasisObject(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- processBinaryDocument() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- processBinaryDocument() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- processBinaryDocument() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- processBinaryDocument() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- processBirth(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- processBlock(String) - Method in interface org.jmol.adapter.readers.cif.CifReader.Parser
- processBlock(String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- processBondObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
- processBonds() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
- processBonds(Lst<Object[]>, Map<Object, Integer>, boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processCellParameter() - Method in class org.jmol.adapter.readers.cif.CifReader
-
unit cell parameters -- two options, so we use MOD 6
- processCGO(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create a CGO JmolObject, just passing on key information.
- processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
-
incorporates double-click gesture
- processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- processChangeSync(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- processCharges() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
- processChemCompLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
a general name definition field.
- processChemicalInfo(String) - Method in class org.jmol.adapter.readers.cif.CifReader
-
reads some of the more interesting info into specific atomSetAuxiliaryInfo elements
- processCitationListBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
- processCmdfAtoms() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- processCommand(int) - Method in class org.jmol.script.ScriptEval
- processCompBondLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processComponentKeyEvent(KeyEvent) - Method in class org.jmol.console.AppletConsole.ControlEnterTextArea
- processConnectorObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
- processCoord() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
- processCoordinates() - Method in class org.jmol.adapter.readers.simple.MopacReader
-
Reads the section in MOPAC files with cartesian coordinates.
- processCoordinates() - Method in class org.jmol.adapter.readers.simple.OrcaReader
- processCoordLines() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
Now create atoms from the coordinate lines.
- processCtab(boolean) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- processDataParameter() - Method in class org.jmol.adapter.readers.cif.CifReader
-
initialize a new atom set
- processDeath(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- processDefinitions() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create a JmolObject that will define atom sets based on PyMOL objects
- processDeletedModelAtoms(BS) - Method in class org.jmol.viewer.SelectionManager
- processDOM(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
- processDOM(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- processEnd2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
- processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
- processEndMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
- processEnergyLine() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- processEnergyLine() - Method in class org.jmol.adapter.readers.simple.OrcaReader
- processEntry() - Method in class org.jmol.adapter.readers.cif.MSCifParser
- processes - Variable in class org.jmol.script.ScriptParallelProcessor
- processEvent(int, int, int, int, long) - Method in interface org.jmol.api.GenericMouseInterface
- processEvent(int, int, int, int, long) - Method in class org.jmol.awt.Mouse
- processEvent(int, int, int, int, long) - Method in class org.jmol.awtjs2d.Mouse
- processEvent(int, Event) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
-
Translate the specialized Sparsh UI information into a format that Jmol's ActionManager can understand without any special classes.
- processGadget(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Only process _e_pot objects -- which we need for color settings
- processGeomBondLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
-
reads bond data -- N_ijk symmetry business is ignored, so we only indicate bonds within the unit cell to just the original set of atoms.
- processHeader() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
- processInfo() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
- processing - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- processInputFile() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- processInputFile() - Method in class org.jmol.adapter.readers.simple.OrcaReader
- processJob(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- processKey(int, int, boolean) - Method in class org.jmol.console.GenericConsole
- processKey(KeyEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- processKeyEvent(KeyEvent) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
- processLinks() - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- processLocalTransform() - Method in class org.jmol.adapter.readers.quantum.CsfReader
- processLock - Variable in class org.jmol.script.ScriptProcessRunnable
- processLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
-
processes loop_ blocks of interest or skips the data
- processLoopBlock() - Method in class org.jmol.adapter.readers.cif.MSCifParser
-
creates entries in htModulation with a key of the form: type_id_axis;atomLabel@model where type = W|F|D|O (wave vector, Fourier index, displacement, occupancy); id = 1|2|3|0|S (Fourier index, Crenel(0), sawtooth); axis (optional) = 0|x|y|z (0 indicates irrelevant -- occupancy); and ;atomLabel is only for D and O.
- processMap(Lst<Object>, boolean, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create mapObjects and volumeData; create an ISOSURFACE JmolObject.
- processMeasure(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create a MEASURE JmolObject.
- processMeshes() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create mesh or mep JmolObjects.
- processMessage(byte[], NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- processMKPropertyItem(String, boolean) - Method in class org.jmol.modelkit.ModelKit
- processModeClick(String) - Method in class org.jmol.modelkit.ModelKit
- processModelData(String, String, String, String, String, float, float, boolean) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- processModelData(String, String, String, String, String, float, float, boolean) - Method in interface org.jmol.api.JmolJDXMOLReader
- processMol() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
- processMolCryst(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Pick up the crystal data.
- processMolecularOrbitalObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
- processMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.OrcaReader
- processMolecule() - Method in class org.jmol.adapter.readers.more.Mol2Reader
- processMolecule(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create everything necessary to generate a molecule in Jmol.
- processMolSdHeader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
- processMonotonic(MeshCapper.CapVertex, boolean) - Method in class org.jmol.util.MeshCapper
-
Process a standard monotonic region, cleaving off as many triangles as possible.
- processMouseEvent(int, int, int, int, long) - Method in class org.jmol.util.GenericApplet
- processMouseEvent(int, int, int, int, long) - Method in class org.jmol.viewer.Viewer
- processMove(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- processMovie(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create a JmolObject that will represent the movie.
- processMultiFrameOutput(String, BS, int, Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
- processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.multitouch.ActionManagerMT
- processMultitouchEvent(int, int, int, int, P3, long) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
- processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.viewer.ActionManager
-
Specific to ActionManagerMT -- for processing SparshUI gestures
- processName - Variable in class org.jmol.script.ScriptProcess
- processNets() - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Process all nets.
- processNextCriticalPoint() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- processNextMeasure(Measurement) - Method in interface org.jmol.api.JmolMeasurementClient
- processNextMeasure(Measurement) - Method in class org.jmol.modelset.MeasurementData
-
if this is the client, then this method is called by MeasurementData when a measurement is ready
- processNextMeasure(Measurement) - Method in class org.jmol.shape.Measures
- processNioMessage(byte[]) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- processNioMessage(byte[]) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
- processNodes() - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- processObject(Lst<Object>, boolean, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
The main object processor.
- processOneCubical(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- processPeakData() - Method in class org.jmol.adapter.readers.more.JcampdxReader
-
integrate the
records into the associated models, and delete unreferenced n.m models - processPeakSelectAtom(int, String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- processPeakSelectModel(int, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- processPoints() - Method in class org.jmol.quantum.MOCalculation
- processPoints() - Method in class org.jmol.quantum.QuantumCalculation
- processPosition(String, Atom, boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
We process the Pos#n record here.
- processPt(T3) - Method in class org.jmol.quantum.QuantumCalculation
- processQuotedString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
Handle all forms of quotation, including '...', "...", '''...''', """...""", and ;...\n...\n;
- ProcessRecord(String, String) - Method in interface org.jmol.adapter.readers.cif.CifReader.Parser
- ProcessRecord(String, String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
process _topol_node.id 1
- processScript(Object[]) - Method in class org.jmol.viewer.StatusManager
- processSelClick(String) - Method in class org.jmol.modelkit.ModelKit
- processSelection(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
process the selection sets (sele), (...)
- processSelectionsAndScenes(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
A PyMOL scene consists of one or more of: view frame visibilities, by object colors, by color reps, by type currently just extracts viewpoint
- processSelOpClick(String) - Method in class org.jmol.modelkit.ModelKit
- processSemiString() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
Sets a multiline semicolon-eclipsed string to be parsed from the beginning, allowing for CIF 2.0-type prefixed text lines and removing line folding.
- processSequence() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
get canonical 1-letter DNA/RNA sequence code from 3-letter code.
- processService(Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
-
service is expected to return a value in the "ret" key
- processShapeCommand(int) - Method in class org.jmol.script.ScriptEval
- processShell(int) - Method in class org.jmol.quantum.MOCalculation
- processSlater(int) - Method in class org.jmol.quantum.MOCalculation
- processSplit(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
-
Process what M3O refer to as a "split" vertex, which we handle differently here, cloning the "helper" point and the "split" point, creating a new region if necessary, and then swapping pointers.
- processStart2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
- processStartElement(String, String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
- processStartMO(String) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
- processState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- processStructConfLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
identifies ranges for HELIX and TURN
- processStructConnLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processStructOperListBlock(boolean) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processStructSheetRangeLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
identifies sheet ranges
- processStructSiteBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
identifies structure sites
- processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
- processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.CifReader
- processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
- processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- processSubsystemLoopBlock() - Method in class org.jmol.adapter.readers.cif.MSCifParser
- processSupportedRecord(int) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
- processSymClick(String) - Method in class org.jmol.modelkit.ModelKit
- processSymmetryOperationsLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
-
retrieves symmetry operations
- processSymmetrySpaceGroupName() - Method in class org.jmol.adapter.readers.cif.CifReader
-
done by AtomSetCollectionReader
- processSymop(String, boolean) - Method in class org.jmol.modelkit.ModelKit
- processSync(String, int) - Method in interface org.jmol.api.JmolJSpecView
- processSync(String, int) - Method in class org.jmol.jsv.JSpecView
- processTokenList(short, boolean) - Method in class org.jmol.script.ScriptCompiler
- processTotalEnergy() - Method in class org.jmol.adapter.readers.simple.MopacReader
- processTranslation(int, int[], String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- processTriangles(int) - Method in class org.jmol.jvxl.calc.MarchingCubes
- processTriangles(int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- processTwoPointGesture(float[][][]) - Method in interface org.jmol.api.GenericMouseInterface
- processTwoPointGesture(float[][][]) - Method in class org.jmol.awt.Mouse
- processTwoPointGesture(float[][][]) - Method in class org.jmol.awtjs2d.Mouse
-
called by JSmol as processTwoPointGesture(canvas.touches);
- processTwoPointGesture(float[][][]) - Method in class org.jmol.util.GenericApplet
- processTwoPointGesture(float[][][]) - Method in class org.jmol.viewer.Viewer
- processType() - Method in class org.jmol.util.Tensor
-
Sets typeFactor, altType, isIsotropic, forThermalEllipsoid; type "iso" changed to "" here.
- processUCClick(String) - Method in class org.jmol.modelkit.ModelKit
- processUnitCellTransform() - Method in class org.jmol.adapter.readers.cif.CifReader
-
(magnetic CIF only) Process the unit cell transformation as indicated by _parent_space_group or _space_group_magn (or older _magentic_space_group)
- processUnitCellTransformMatrix() - Method in class org.jmol.adapter.readers.cif.CifReader
-
the PDB transformation matrix cartesian --> fractional
- processUpdate(String) - Method in class org.jmol.util.JmolAudio
- processVibrationObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
- processWriteOrCapture(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
- processWriteOrCapture(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
-
from eval write command only includes option to write set of files
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
-
the current state
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMOReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
- processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
- processXml2(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
- processXtalClick(String, String) - Method in class org.jmol.modelkit.ModelKit
- procSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- programInfo - Variable in class org.jmol.atomdata.AtomData
- prompt - Static variable in class org.jmol.script.T
- prompt - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
- prompt(String, String, String[], boolean) - Method in interface org.jmol.api.GenericPlatform
- prompt(String, String, String[], boolean) - Static method in class org.jmol.awt.Display
- prompt(String, String, String[], boolean) - Method in class org.jmol.awt.Platform
- prompt(String, String, String[], boolean) - Static method in class org.jmol.awtjs2d.Display
- prompt(String, String, String[], boolean) - Method in class org.jmol.awtjs2d.Platform
- prompt(String, String, String[], boolean) - Method in class org.jmol.viewer.Viewer
- promptUser(String, String) - Method in class org.jmol.modelkit.ModelKit
- prop - Static variable in class org.openscience.jmol.app.webexport.WebExport
- PROP_ANIMATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_APPLET_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_ATOM_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_AUXILIARY_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_BOND_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_BOUNDBOX_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_CENTER_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_CHAIN_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_CIF_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_CONSOLE_TEXT - Static variable in class org.jmol.viewer.PropertyManager
- PROP_COUNT - Static variable in class org.jmol.viewer.PropertyManager
- PROP_DATA_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_DOM_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_ERROR_MESSAGE - Static variable in class org.jmol.viewer.PropertyManager
- PROP_EVALUATE - Static variable in class org.jmol.viewer.PropertyManager
- PROP_EXTRACT_MODEL - Static variable in class org.jmol.viewer.PropertyManager
- PROP_FILE_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_FILECONTENTS - Static variable in class org.jmol.viewer.PropertyManager
- PROP_FILECONTENTS_PATH - Static variable in class org.jmol.viewer.PropertyManager
- PROP_FILEHEADER - Static variable in class org.jmol.viewer.PropertyManager
- PROP_FILENAME - Static variable in class org.jmol.viewer.PropertyManager
- PROP_IMAGE - Static variable in class org.jmol.viewer.PropertyManager
- PROP_ISOSURFACE_DATA - Static variable in class org.jmol.viewer.PropertyManager
- PROP_ISOSURFACE_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_JMOL_STATUS - Static variable in class org.jmol.viewer.PropertyManager
- PROP_JMOL_VIEWER - Static variable in class org.jmol.viewer.PropertyManager
- PROP_JSPECVIEW - Static variable in class org.jmol.viewer.PropertyManager
- PROP_LIGAND_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_MEASUREMENT_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_MENU - Static variable in class org.jmol.viewer.PropertyManager
- PROP_MESSAGE_QUEUE - Static variable in class org.jmol.viewer.PropertyManager
- PROP_MINIMIZATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_MODEL_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_MODELKIT_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_MOLECULE_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_MOUSE_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_NMR_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_ORIENTATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_POINTGROUP_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_POLYMER_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_SCRIPT_QUEUE_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_SERVICE - Static variable in class org.jmol.viewer.PropertyManager
- PROP_SHAPE_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_STATE_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_TRANSFORM_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_UNITCELL_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_VAL_INFO - Static variable in class org.jmol.viewer.PropertyManager
- PROP_VAR_INFO - Static variable in class org.jmol.viewer.PropertyManager
- properties - Variable in class org.jmol.modelset.Model
- properties - Variable in class org.openscience.jmol.app.HistoryFile
-
The data stored in the history file.
- propertiesFileName - Static variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- propertiesTextArea - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- property - Variable in class org.jmol.modelset.Measurement
- property - Variable in class org.jmol.modelset.MeasurementData
- property - Static variable in class org.jmol.script.T
- PROPERTY - Enum constant in enum org.jmol.c.PAL
- PROPERTY_MODES - Static variable in class org.jmol.shapespecial.Ellipsoids
- propertyatomnumbercolumncount - Static variable in class org.jmol.script.T
- propertyatomnumberfield - Static variable in class org.jmol.script.T
- propertyChange(PropertyChangeEvent) - Method in class org.jmol.dialog.FilePreview
- propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.MoleculeDependentAction
- propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
- propertycolorscheme - Static variable in class org.jmol.script.T
- propertyColorScheme - Variable in class org.jmol.viewer.GlobalSettings
- propertydatacolumncount - Static variable in class org.jmol.script.T
- propertydatafield - Static variable in class org.jmol.script.T
- propertyDistanceMax - Variable in class org.jmol.jvxl.readers.Parameters
- PROPERTYFLAGS - Static variable in class org.jmol.script.T
- propertyItemCounts - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- PropertyManager - Class in org.jmol.viewer
-
The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().
- PropertyManager() - Constructor for class org.jmol.viewer.PropertyManager
- propertySmoothing - Variable in class org.jmol.jvxl.readers.Parameters
- propertySmoothingPower - Variable in class org.jmol.jvxl.readers.Parameters
- propertyTypes - Static variable in class org.jmol.viewer.PropertyManager
- props - Variable in class org.jmol.adapter.readers.pdb.JmolDataReader
- props - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- propselector - Static variable in class org.jmol.script.T
- protein - Static variable in class org.jmol.script.T
- proteinStructure - Variable in class org.jmol.modelsetbio.AlphaMonomer
- ProteinStructure - Class in org.jmol.modelsetbio
- ProteinStructure() - Constructor for class org.jmol.modelsetbio.ProteinStructure
- proteinstructurePending - Variable in class org.jmol.renderbio.RocketRenderer
- proteinStructureTainted - Variable in class org.jmol.modelset.ModelSet
- PROTEKTED - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- PROTONS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pS - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
- PS_CLOSEPATH - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_LINETO - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- PS_MOVETO - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_NEWPATH - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_SETLINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_SHOWPAGE - Static variable in class org.jmol.shapecgo.CGOMesh
- PS_STROKE - Static variable in class org.jmol.shapecgo.CGOMesh
- psi - Variable in class org.jmol.modelsetbio.Monomer
- psi - Static variable in class org.jmol.script.T
- psi_l - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- psi_l - Variable in class org.jmol.jvxl.readers.Parameters
- psi_m - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- psi_m - Variable in class org.jmol.jvxl.readers.Parameters
- psi_monteCarloCount - Variable in class org.jmol.jvxl.readers.Parameters
- psi_n - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- psi_n - Variable in class org.jmol.jvxl.readers.Parameters
- psi_normalization - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- psi_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
- psi_Znuc - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- psi_Znuc - Variable in class org.jmol.jvxl.readers.Parameters
- psiContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- PsiReader - Class in org.jmol.adapter.readers.quantum
-
Reader for Psi3 output files.
- PsiReader() - Constructor for class org.jmol.adapter.readers.quantum.PsiReader
- pt - Variable in class org.jmol.adapter.readers.simple.FAHReader
- pt - Variable in enum org.jmol.c.VDW
- pt - Variable in class org.jmol.jvxl.readers.BCifDensityReader
- pt - Variable in class org.jmol.jvxl.readers.DelPhiBinaryReader
- pt - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
- pt - Variable in class org.jmol.jvxl.readers.NffReader
- pt - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- pt - Variable in class org.jmol.jvxl.readers.UhbdReader
- pt - Variable in class org.jmol.jvxl.readers.VaspChgcarReader
- pt - Variable in class org.jmol.modelkit.ModelKit.Constraint
- pt - Variable in class org.jmol.modelset.LabelToken
- pt - Variable in class org.jmol.render.CageRenderer
- pt - Variable in class org.jmol.renderbio.BioMeshRenderer
- pt - Variable in class org.jmol.script.ScriptQueueThread
- pt - Variable in class org.jmol.symmetry.SpaceGroupFinder
- pt - Variable in class org.jmol.util.ContactPair
- pt - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
- PT_BITSET - Static variable in class org.jmol.shapespecial.Draw
- PT_CHARGE - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- PT_CONNECT - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- PT_COORD - Static variable in class org.jmol.shapespecial.Draw
- PT_ELEMENT - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- PT_IDENTIFIER - Static variable in class org.jmol.shapespecial.Draw
- PT_MODEL_BASED_POINTS - Static variable in class org.jmol.shapespecial.Draw
- PT_MODEL_INDEX - Static variable in class org.jmol.shapespecial.Draw
- pt0 - Variable in class org.jmol.adapter.readers.simple.InputReader
- pt0 - Variable in class org.jmol.jvxl.calc.MarchingCubes
- pt0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
- pt0 - Variable in class org.jmol.modelsetbio.AlphaPolymer
-
Specifically for mmTF bitset setting of structures
- pt0 - Variable in class org.jmol.render.FontLineShapeRenderer
- pt0 - Variable in class org.jmol.renderspecial.DrawRenderer
- pt0 - Variable in class org.jmol.script.ScriptFlowContext
- pt0 - Variable in class org.jmol.script.ScriptFunction
-
functions are either local or global (static).
- pt0 - Static variable in class org.jmol.script.SV
- pt0 - Variable in class org.jmol.shape.Axes
- pt000 - Variable in class org.jmol.render.AxesRenderer
- Pt000 - Static variable in class org.jmol.modelkit.ModelKit
- pt0f - Variable in class org.jmol.renderspecial.DrawRenderer
- pt0i - Variable in class org.jmol.render.FontLineShapeRenderer
- pt0i - Variable in class org.jmol.renderspecial.DrawRenderer
- pt1 - Variable in class org.jmol.jvxl.readers.AtomDataReader
- pt1 - Variable in class org.jmol.render.FontLineShapeRenderer
- pt1 - Variable in class org.jmol.renderbio.BioMeshRenderer
- pt1 - Variable in class org.jmol.renderspecial.DrawRenderer
- pt1 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- pt1 - Variable in class org.jmol.shapesurface.Contact
- pt1f - Variable in class org.jmol.render.MeshRenderer
- pt1i - Variable in class org.jmol.render.MeshRenderer
- pt2 - Variable in class org.jmol.renderspecial.DrawRenderer
- pt2 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- pt2 - Variable in class org.jmol.shapesurface.Contact
- pt2f - Variable in class org.jmol.render.MeshRenderer
- pt2i - Variable in class org.jmol.render.FontLineShapeRenderer
- pt2i - Variable in class org.jmol.render.MeshRenderer
- pt3 - Variable in class org.jmol.rendercgo.CGORenderer
- pt3i - Variable in class org.jmol.render.MeshRenderer
- pt4Value(SV) - Static method in class org.jmol.script.SV
- ptA - Variable in class org.jmol.export.Export3D
- ptA0 - Variable in class org.jmol.g3d.CylinderRenderer
- pta01 - Static variable in class org.jmol.symmetry.SymmetryDesc
- pta02 - Static variable in class org.jmol.symmetry.SymmetryDesc
- ptA0i - Variable in class org.jmol.g3d.CylinderRenderer
- ptAtom - Variable in class org.jmol.smiles.SmilesGenerator
- ptB - Variable in class org.jmol.export.Export3D
- ptB0 - Variable in class org.jmol.g3d.CylinderRenderer
- ptB0i - Variable in class org.jmol.g3d.CylinderRenderer
- ptC - Variable in class org.jmol.export.Export3D
- ptC - Variable in class org.jmol.renderbio.RocketRenderer
- ptCenter - Variable in class org.jmol.shape.Mesh
- ptCenters - Variable in class org.jmol.shapespecial.DrawMesh
- ptColor - Variable in class org.jmol.rendercgo.CGORenderer
- ptCommand - Variable in class org.jmol.script.ScriptFlowContext
- ptD - Variable in class org.jmol.export.Export3D
- ptDefault - Variable in class org.jmol.script.ScriptFlowContext
- ptDefaultLattice - Variable in class org.jmol.viewer.GlobalSettings
- ptemp - Static variable in class org.jmol.symmetry.SymmetryDesc
- pTemp - Variable in class org.jmol.render.LabelsRenderer
- ptemp2 - Static variable in class org.jmol.symmetry.SymmetryDesc
- pTemp3 - Variable in class org.jmol.renderspecial.VectorsRenderer
- ptFloat - Variable in class org.jmol.adapter.readers.more.MdCrdReader
- ptid - Variable in class org.jmol.script.ScriptMathProcessor
- ptIDLogger - Variable in class org.jmol.symmetry.CIPChirality
-
incremental pointer providing a unique ID to every CIPAtom for debugging
- ptInner - Static variable in class org.jmol.util.BZone
- ptLine - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ptLine - Variable in class org.jmol.script.ScriptFlowContext
- ptLineBuf - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- ptList - Variable in class org.jmol.shapespecial.Draw
- ptMax - Variable in class org.jmol.export._IdtfExporter
- ptMin - Variable in class org.jmol.export._IdtfExporter
- ptMoveToCenter - Variable in class org.jmol.thread.MoveToThread
- ptNew - Variable in class org.jmol.viewer.Viewer
- ptNewSetModifier - Variable in class org.jmol.script.ScriptTokenParser
- ptNext - Variable in class org.jmol.renderbio.BioMeshRenderer
- ptNext - Variable in class org.jmol.viewer.Gesture
- ptNormal - Variable in class org.jmol.rendercgo.CGORenderer
- pto - Variable in class org.jmol.script.ScriptMathProcessor
- ptOffset - Variable in class org.jmol.adapter.readers.cif.CifReader
- ptOffset - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- ptOffset - Variable in class org.jmol.viewer.TransformManager
- pTopLeft - Variable in class org.jmol.g3d.HermiteRenderer
- pTopRight - Variable in class org.jmol.g3d.HermiteRenderer
- ptOriginShift - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- ptPrev - Variable in class org.jmol.renderbio.BioMeshRenderer
- ptPsi - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- ptRef - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- pts - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
- pts - Variable in class org.jmol.modelset.Measurement
- pts - Variable in class org.jmol.util.BZone
- pts - Variable in class org.jmol.util.MeshSlicer
- ptS1 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- ptS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- ptScreen - Variable in class org.jmol.viewer.Viewer
- ptScreenNew - Variable in class org.jmol.viewer.Viewer
- ptSemi - Variable in class org.jmol.script.ScriptCompiler
- ptSp2Atom0 - Variable in class org.jmol.smiles.SmilesGenerator
- ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.VolumeDataReader
- ptsUnused - Variable in class org.jmol.util.BZone
- ptSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- ptTemp - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- ptTemp - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- ptTemp - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- ptTemp - Variable in class org.jmol.adapter.writers.MOLWriter
- ptTemp - Variable in class org.jmol.export._ObjExporter
- ptTemp - Variable in class org.jmol.g3d.SphereRenderer
- ptTemp - Variable in class org.jmol.jvxl.calc.MarchingSquares
- ptTemp - Variable in class org.jmol.jvxl.data.VolumeData
- ptTemp - Variable in class org.jmol.jvxl.readers.SurfaceReader
- ptTemp - Variable in class org.jmol.modelset.ModelSet
- ptTemp - Variable in class org.jmol.modelsetbio.AminoMonomer
- ptTemp - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- ptTemp - Variable in class org.jmol.render.AxesRenderer
- ptTemp - Variable in class org.jmol.render.HoverRenderer
- ptTemp - Variable in class org.jmol.renderbio.NucleicRenderer
- ptTemp - Variable in class org.jmol.renderspecial.VectorsRenderer
- ptTemp - Variable in class org.jmol.script.ScriptExpr
- ptTemp - Variable in class org.jmol.shape.Labels
- ptTemp - Variable in class org.jmol.util.ModulationSet
- ptTemp - Variable in class org.jmol.viewer.Viewer
- ptTemp1 - Variable in class org.jmol.modelset.ModelSet
- ptTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- ptTemp2 - Variable in class org.jmol.modelset.ModelSet
- ptTemp2 - Variable in class org.jmol.renderspecial.VectorsRenderer
- ptTemp4 - Variable in class org.jmol.renderspecial.VectorsRenderer
- ptTest1 - Variable in class org.jmol.viewer.TransformManager
- ptTest2 - Variable in class org.jmol.viewer.TransformManager
- ptTest3 - Variable in class org.jmol.viewer.TransformManager
- ptTip - Variable in class org.jmol.renderbio.RocketRenderer
- ptToIJK(T3, int) - Static method in class org.jmol.util.SimpleUnitCell
-
Convert user's {3 2 1} to {1500500500, 1503502501, 0 or 1, 1500501}
- ptTrans - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- ptV - Variable in class org.jmol.jvxl.readers.AtomDataReader
- ptValue(SV) - Static method in class org.jmol.script.SV
- ptValue(SV, BS) - Method in class org.jmol.script.ScriptMathProcessor
- ptVibTemp - Variable in class org.jmol.viewer.TransformManager
- ptx - Variable in class org.jmol.script.ScriptMathProcessor
- ptXY - Variable in class org.jmol.shape.Sticks
- ptXY - Variable in class org.jmol.shapespecial.Draw
- ptXY - Variable in class org.jmol.shapespecial.Ellipsoids
- ptXY - Variable in class org.jmol.shapesurface.Isosurface
- ptXyzTemp - Variable in class org.jmol.jvxl.data.VolumeData
- ptY0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
- ptZ0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
- pubChemFormat - Variable in class org.jmol.viewer.GlobalSettings
- purging - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
- purine - Static variable in class org.jmol.script.T
- PURINE_MASK - Static variable in class org.jmol.viewer.JC
- PURPLE - Static variable in class org.jmol.util.C
- push - Static variable in class org.jmol.script.T
- push(Object) - Method in class org.jmol.adapter.readers.pymol.PickleReader
- pushContext(ContextToken, String) - Method in class org.jmol.script.ScriptEval
- pushContext(T) - Method in class org.jmol.script.ScriptCompiler
- pushContext2(ContextToken, String) - Method in class org.jmol.script.ScriptEval
- pushContextDown(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- pushContextDown(String) - Method in class org.jmol.script.ScriptEval
- pushCount - Variable in class org.jmol.script.ScriptCompiler
- pushHoldRepaint() - Method in class org.jmol.api.JmolViewer
- pushHoldRepaint() - Method in class org.jmol.viewer.Viewer
- pushHoldRepaint(String) - Method in interface org.jmol.api.JmolRepaintManager
- pushHoldRepaint(String) - Method in class org.jmol.render.RepaintManager
- pushHoldRepaintWhy(String) - Method in class org.jmol.viewer.Viewer
- pushMatrix() - Method in class org.jmol.export._StlExporter
- pushMatrix() - Method in class org.jmol.export._VrmlExporter
- pushMatrix() - Method in class org.jmol.export._X3dExporter
- pushPop(SV, SV) - Method in class org.jmol.script.SV
-
Script variables are pushed after cloning, because the name comes with them when we do otherwise they are not mutable anyway.
- pushState() - Method in class org.jmol.viewer.Viewer
- pushState(String) - Method in class org.jmol.util.CommandHistory
- put(int, int) - Method in class org.jmol.util.Int2IntHash
- putBox(int, float[]) - Method in class org.jmol.shape.Labels
- putCoord(V3d, double[]) - Static method in class org.jmol.minimize.Util
- putIf(char) - Method in class org.jmol.script.ScriptMathProcessor
- putLabel(int, Text) - Method in class org.jmol.shape.Labels
- putMark(int) - Method in class org.jmol.adapter.readers.pymol.PickleReader
- putMemo(int, boolean) - Method in class org.jmol.adapter.readers.pymol.PickleReader
- putOp(T) - Method in class org.jmol.script.ScriptMathProcessor
- PUTTY_AbsoluteLinear - Static variable in class org.jmol.shapebio.Trace
- PUTTY_AbsoluteNonlinear - Static variable in class org.jmol.shapebio.Trace
- PUTTY_ImpliedRMS - Static variable in class org.jmol.shapebio.Trace
- PUTTY_NormalizedLinear - Static variable in class org.jmol.shapebio.Trace
- PUTTY_NormalizedNonlinear - Static variable in class org.jmol.shapebio.Trace
- PUTTY_RelativeLinear - Static variable in class org.jmol.shapebio.Trace
- PUTTY_RelativeNonlinear - Static variable in class org.jmol.shapebio.Trace
- PUTTY_ScaledLinear - Static variable in class org.jmol.shapebio.Trace
- PUTTY_ScaledNonlinear - Static variable in class org.jmol.shapebio.Trace
- putX(SV) - Method in class org.jmol.script.ScriptMathProcessor
- PWM_PREFIX - Static variable in class org.jmol.adapter.writers.PWMATWriter
- PWmatReader - Class in org.jmol.adapter.readers.xtal
-
crude PWmat atom.config reader http://pwmatus.com/manual
- PWmatReader() - Constructor for class org.jmol.adapter.readers.xtal.PWmatReader
- PWMATWriter - Class in org.jmol.adapter.writers
-
A writer for PWMAT atom.config files.
- PWMATWriter() - Constructor for class org.jmol.adapter.writers.PWMATWriter
- Pwr2 - Static variable in class org.jmol.util.TriangleData
- pymol - Static variable in class org.jmol.script.T
- PyMOL - Class in org.jmol.adapter.readers.pymol
-
PyMOL settings and constants.
- PyMOL() - Constructor for class org.jmol.adapter.readers.pymol.PyMOL
- pymol_space_max_blue - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pymol_space_max_green - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pymol_space_max_red - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- pymol_space_min_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- PymolAtomReader - Interface in org.jmol.api
- pymolFrame - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- PyMOLGroup - Class in org.jmol.adapter.readers.pymol
- PyMOLGroup(String) - Constructor for class org.jmol.adapter.readers.pymol.PyMOLGroup
- PyMOLMeshReader - Class in org.jmol.jvxl.readers
-
PyMOL surface/mesh reader.
- PyMOLMeshReader() - Constructor for class org.jmol.jvxl.readers.PyMOLMeshReader
- pymolOffset - Variable in class org.jmol.modelset.Text
- PyMOLReader - Class in org.jmol.adapter.readers.pymol
-
PyMOL PSE (binary Python session) file reader.
- PyMOLReader() - Constructor for class org.jmol.adapter.readers.pymol.PyMOLReader
- pymolScene - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- PyMOLScene - Class in org.jmol.adapter.readers.pymol
-
A class to allow manipulation of scenes dissociated from file loading.
- PyMOLScene(PymolAtomReader, Viewer, Lst<Object>, Map<Integer, Lst<Object>>, int, boolean, int, int, boolean, String) - Constructor for class org.jmol.adapter.readers.pymol.PyMOLScene
- pymolStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- pymolType - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- pymolVersion - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- pymolVersion - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- pymolView - Variable in class org.jmol.modelset.Orientation
- pyrimidine - Static variable in class org.jmol.script.T
- PYRIMIDINE_MASK - Static variable in class org.jmol.viewer.JC
Q
- q - Variable in class org.jmol.jvxl.readers.IsoMOReader
- q - Variable in class org.jmol.quantum.NMRNoeMatrix
- Q_FACTOR - Static variable in class org.jmol.quantum.NMRCalculation
- qchemContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- QchemReader - Class in org.jmol.adapter.readers.quantum
-
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
- QchemReader() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader
- QchemReader.MOInfo - Class in org.jmol.adapter.readers.quantum
- qcJsonContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- QCJSONReader - Class in org.jmol.adapter.readers.quantum
-
A molecular structure and orbital reader for MolDen files.
- QCJSONReader() - Constructor for class org.jmol.adapter.readers.quantum.QCJSONReader
- QCJSONWriter - Class in org.jmol.adapter.writers
-
A very experimental class for writing QCJSON files.
- QCJSONWriter() - Constructor for class org.jmol.adapter.writers.QCJSONWriter
- QCJSONWriter.SparseArray - Class in org.jmol.adapter.writers
- qCoefs - Variable in class org.jmol.util.Modulation
- qColor - Static variable in class org.jmol.modelsetbio.BioExt
- QConst - Static variable in class org.jmol.modelset.HBond
- qi() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- QI - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- qicount - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- qlist100 - Variable in class org.jmol.adapter.readers.cif.MSRdr
- qm_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
- qm_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
- qm_moLinearCombination - Variable in class org.jmol.jvxl.readers.Parameters
- qm_moNumber - Variable in class org.jmol.jvxl.readers.Parameters
- qm_nAtoms - Variable in class org.jmol.jvxl.readers.Parameters
- qm_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
- QM_TYPE_GAUSSIAN - Static variable in class org.jmol.jvxl.readers.Parameters
- QM_TYPE_NCI_PRO - Static variable in class org.jmol.jvxl.readers.Parameters
- QM_TYPE_NCI_SCF - Static variable in class org.jmol.jvxl.readers.Parameters
- QM_TYPE_SLATER - Static variable in class org.jmol.jvxl.readers.Parameters
- QM_TYPE_UNKNOWN - Static variable in class org.jmol.jvxl.readers.Parameters
- QM_TYPE_VOLUME_DATA - Static variable in class org.jmol.jvxl.readers.Parameters
- QMAtom - Class in org.jmol.quantum
- QMAtom(int, T3, Atom, float[], float[], float[], float[], float[], float[], float) - Constructor for class org.jmol.quantum.QMAtom
- qmAtoms - Variable in class org.jmol.quantum.QuantumCalculation
- qMods - Static variable in class org.jmol.script.ScriptMathProcessor
- qmOrbitalCount - Variable in class org.jmol.jvxl.readers.Parameters
- qmOrbitalType - Variable in class org.jmol.jvxl.readers.Parameters
- qPanelJPEG - Variable in class org.jmol.dialog.Dialog
- qPanelPNG - Variable in class org.jmol.dialog.Dialog
- qpc - Variable in class org.jmol.jvxl.readers.SurfaceReader
- qpt2 - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- qs - Variable in class org.jmol.adapter.readers.cif.MSRdr
- QS - Class in org.jmol.quantum
-
Constants and static methods for quantum shells.
- QS() - Constructor for class org.jmol.quantum.QS
- qSetupDone - Variable in class org.jmol.jvxl.readers.IsoMOReader
- qSliderJPEG - Variable in class org.jmol.dialog.Dialog
- qSliderPNG - Variable in class org.jmol.dialog.Dialog
- qtOffset - Variable in class org.jmol.util.ModulationSet
- QUADRIC - Static variable in class org.jmol.shapecgo.CGOMesh
- quadruple(int, short[]) - Static method in class org.jmol.util.Geodesic
- QUADRUPLE - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- QUADRUPOLE_MOMENT - Static variable in class org.jmol.quantum.NMRCalculation
- qualityJ - Variable in class org.jmol.dialog.Dialog
- qualityJPG - Static variable in class org.jmol.dialog.Dialog
- qualityJPG - Variable in class org.jmol.viewer.StatusManager
- qualityJPG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- QualityListener(boolean, JSlider) - Constructor for class org.jmol.dialog.Dialog.QualityListener
- qualityP - Variable in class org.jmol.dialog.Dialog
- qualityPNG - Static variable in class org.jmol.dialog.Dialog
- qualityPNG - Variable in class org.jmol.viewer.StatusManager
- qualityPNG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- quantize(float, boolean) - Method in class org.jmol.util.ColorEncoder
-
gets the value at the color boundary for this color range fraction
- quantize4(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
- QuantumCalculation - Class in org.jmol.quantum
- QuantumCalculation() - Constructor for class org.jmol.quantum.QuantumCalculation
- QuantumPlaneCalculation - Class in org.jmol.quantum
-
Allows modification of the planes prior to isosurface creation Used by Noncovalent Interaction Calculation for progressive readers
- QuantumPlaneCalculation() - Constructor for class org.jmol.quantum.QuantumPlaneCalculation
- quaternion - Static variable in class org.jmol.script.T
- quaternionframe - Static variable in class org.jmol.script.T
- quaternionFrame - Variable in class org.jmol.viewer.GlobalSettings
- queueAtom(int, Point3fi) - Method in class org.jmol.viewer.ActionManager
- queueOnHold - Variable in class org.jmol.viewer.Viewer
- queueThreadFinished(int) - Method in interface org.jmol.api.JmolScriptManager
- queueThreadFinished(int) - Method in class org.jmol.script.ScriptManager
- queueThreads - Variable in class org.jmol.script.ScriptManager
- quiet - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- QUINTUPLE - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- quit - Static variable in class org.jmol.script.T
R
- r - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- r - Variable in class org.jmol.quantum.SlaterData
- r - Variable in class org.jmol.util.Rgb16
- r0 - Variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
- r0 - Variable in class org.jmol.minimize.forcefield.UFFDistanceCalc
- r0 - Variable in class org.jmol.util.ModulationSet
-
the unmodulated original position of this atom; note that x,y,z extended from Vibration(V3) is the current displacement modulation itself
- R3 - Static variable in class org.jmol.minimize.forcefield.ForceField
- R4 - Static variable in class org.jmol.minimize.forcefield.ForceField
- R5 - Static variable in class org.jmol.minimize.forcefield.ForceField
- rab - Variable in class org.jmol.minimize.forcefield.Calculation
- rad - Static variable in class org.jmol.script.T
- RAD_COV_BODR_2014_02_22 - Static variable in class org.jmol.util.Elements
- RAD_COV_IONIC_OB1_100_1 - Static variable in class org.jmol.util.Elements
- RAD_PER_DEG - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
- RAD_TO_DEG - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
- RAD_TO_DEG - Static variable in class org.jmol.minimize.forcefield.Calculations
- RAD_TO_DEG - Static variable in class org.jmol.minimize.Util
- radialPart(double) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- RADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- radiansPerDegree - Static variable in class org.jmol.smiles.SmilesMeasure
- radiansPerDegree - Static variable in class org.jmol.viewer.JC
- radiansXStep - Variable in class org.jmol.thread.MoveToThread
- radiansYStep - Variable in class org.jmol.thread.MoveToThread
- radiansZStep - Variable in class org.jmol.thread.MoveToThread
- radical - Static variable in class org.jmol.script.T
- radii - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- radii - Variable in class org.jmol.util.ContactPair
- radiiIP2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
- radius - Variable in class org.jmol.adapter.smarter.Atom
- radius - Variable in class org.jmol.adapter.smarter.Bond
- radius - Variable in class org.jmol.bspt.CubeIterator
- radius - Variable in class org.jmol.g3d.CylinderRenderer
- radius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- radius - Static variable in class org.jmol.script.T
- radius - Variable in class org.jmol.shapespecial.Polyhedra
- radius - Variable in class org.jmol.symmetry.PointGroup
- RADIUS_GLOBAL - Static variable in class org.jmol.modelset.Atom
- RADIUS_MAX - Static variable in class org.jmol.modelset.Atom
- RADIUS_MAX - Static variable in class org.jmol.shape.Shape
- RADIUS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Maximum value for vector radius.
- RADIUS_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Initial value of vector radius.
- radius2 - Variable in class org.jmol.g3d.CylinderRenderer
- radiusData - Variable in class org.jmol.atomdata.AtomData
- radiusData - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- radiusData - Variable in class org.jmol.modelset.MeasurementData
- radiusData - Variable in class org.jmol.shape.Measures
- RadiusData - Class in org.jmol.atomdata
- RadiusData(float[], float, RadiusData.EnumType, VDW) - Constructor for class org.jmol.atomdata.RadiusData
- RadiusData.EnumType - Enum in org.jmol.atomdata
- radiusHermites - Variable in class org.jmol.renderbio.BioMeshRenderer
- radiusI - Variable in class org.jmol.geodesic.EnvelopeCalculation
- radiusMin - Variable in class org.jmol.shapespecial.Polyhedra
- radiusP - Variable in class org.jmol.geodesic.EnvelopeCalculation
- radiusPt - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- radiusSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- radiusValue - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- raise_exceptions - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ramachandran - Static variable in class org.jmol.script.T
- ramp_blend_nearby_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- rand - Variable in class org.jmol.scriptext.MathExt
- random - Variable in class org.jmol.jvxl.readers.IsoMOReader
- random - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- random - Static variable in class org.jmol.script.T
- randomizeUnitVector(V3d) - Static method in class org.jmol.minimize.Util
- randomPoint - Static variable in class org.jmol.shapespecial.Polyhedra
- randomPoint() - Static method in class org.jmol.shapespecial.Draw
- randomSeed - Variable in class org.jmol.jvxl.readers.Parameters
- range - Static variable in class org.jmol.script.T
- range - Variable in class org.jmol.shapebio.BioShape
- range(double) - Method in class org.jmol.util.Modulation
-
Check that left < x4 < right, but allow for folding
- rangeAll - Variable in class org.jmol.jvxl.readers.Parameters
- rangeBohrOrAngstroms - Variable in class org.jmol.quantum.QuantumCalculation
- rangeDefined - Variable in class org.jmol.jvxl.readers.Parameters
- rangeselected - Static variable in class org.jmol.script.T
- rangeSelected - Variable in class org.jmol.jvxl.readers.Parameters
- rangeSelected - Variable in class org.jmol.viewer.GlobalSettings
- RANK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- rank_assisted_sorts - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- rank4bAndRead(BS) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
A thread-based sphere-ordered implementation that takes into account that lists cross the boundaries of branches.
- Raromatic - Static variable in class org.jmol.minimize.forcefield.ForceField
- rAS - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- rAS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- Ras3DReader - Class in org.jmol.jvxl.readers
- Ras3DReader() - Constructor for class org.jmol.jvxl.readers.Ras3DReader
- rasmol - Static variable in class org.jmol.script.T
- RASMOL - Enum constant in enum org.jmol.c.PAL
- RASMOL - Enum constant in enum org.jmol.c.VDW
- RASMOL - Static variable in class org.jmol.util.ColorEncoder
- rasmolBinding - Variable in class org.jmol.viewer.ActionManager
- RasmolBinding - Class in org.jmol.viewer.binding
- RasmolBinding() - Constructor for class org.jmol.viewer.binding.RasmolBinding
- rasmolDefaultsButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- rasmolHeteroSetting - Variable in class org.jmol.viewer.GlobalSettings
- rasmolHydrogenSetting - Variable in class org.jmol.viewer.GlobalSettings
- rasmolOverrides - Static variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- rasmolScale - Static variable in class org.jmol.util.ColorEncoder
- rasterCount - Variable in class org.jmol.g3d.CylinderRenderer
- RAW_RGB - Static variable in class org.jmol.util.C
- RAW_RGB_INT - Static variable in class org.jmol.util.C
- rawAtomTypes - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- rawBondCount - Variable in class org.jmol.minimize.Minimizer
- rawBondTypes - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- rawIndex - Variable in class org.jmol.minimize.MinBond
- rawMMFF94Charges - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- ray_blend_blue - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_blend_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_blend_green - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_blend_red - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_clip_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_color_ramps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_default_renderer - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_direct_shade - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_hint_camera - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_hint_shadow - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_improve_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_interior_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_interior_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_interior_reflect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_interior_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_interior_texture - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_label_specular - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_legacy_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_max_passes - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_opaque_background - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_orthoscopic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_oversample_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_pixel_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_scatter - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_shadow_decay_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_shadow_decay_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_shadow_fudge - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_spec_local - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_texture - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_texture_settings - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_depth_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_disco_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_fog - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_fog_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_frames - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_gain - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_persist_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_slope_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_trace_trans_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_transparency_contrast - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_transparency_oblique - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_transparency_oblique_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_transparency_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_transparency_spec_cut - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_transparency_specular - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_triangle_fudge - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ray_volume - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- rBS - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- rBS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- rd - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- rd - Variable in class org.jmol.shape.AtomShape
- rd - Variable in class org.jmol.viewer.Viewer
- rd() - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
- rd() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- rd() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- rd() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- rd() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
filter out unnecessary lines
- rd() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- rd() - Method in interface org.jmol.api.JmolJDXMOLReader
- rd() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- rdLast - Variable in class org.jmol.shapespecial.Dots
- rdline() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- rdLine() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- rdr - Static variable in class org.jmol.symmetry.SpaceGroupFinder
- rdSiesta() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- rdVDW - Static variable in class org.jmol.shapesurface.Contact
- read() - Method in class org.openscience.jvxl.MonitorInputStream
- read(byte[]) - Method in class org.openscience.jvxl.MonitorInputStream
- read(byte[], int, int) - Method in class org.openscience.jvxl.MonitorInputStream
- read3Vectors(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block
- readableTypes - Static variable in class org.jmol.viewer.PropertyManager
- readACDAssignments(int, boolean) - Method in interface org.jmol.api.JmolJDXMOLParser
- readACDAssignments(int, boolean) - Method in class org.jmol.jsv.JDXMOLParser
- readACDMolFile() - Method in interface org.jmol.api.JmolJDXMOLParser
- readACDMolFile() - Method in class org.jmol.jsv.JDXMOLParser
-
MOL file embedded in JDX file
- readAllData - Variable in class org.jmol.jvxl.readers.Parameters
- readAllData() - Method in class org.jmol.adapter.readers.cif.CifReader
- readAllData() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readAndSetVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- readAparam() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- readArchive() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- readArchive(String, boolean, int, boolean) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readArchiveHeader() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- readAtom() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
Allowing for BOHR units here; probably unnecessary.
- readAtom(String[], boolean) - Method in class org.jmol.adapter.readers.xtal.AimsReader
- readAtomArray(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
- readAtomCountAndOrigin() - Method in class org.jmol.adapter.readers.simple.CubeReader
- readAtomCountAndSetNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- readAtomData(float) - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readAtomicCoordinatesFormat() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- readAtomicOrbitalOrder() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- readAtomicPos(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
- readAtomNames() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
- readAtomRecord(Atom, P3, P3, boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
Read the atom or pos# record, including occupancy, various flags, and, especially, modulations.
- readAtoms() - Method in class org.jmol.adapter.readers.more.GromacsReader
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- readAtoms() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- readAtoms() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
- readAtoms() - Method in class org.jmol.adapter.readers.simple.CubeReader
- readAtoms() - Method in class org.jmol.adapter.readers.spartan.SpartanReader
- readAtoms() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- readAtoms() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- readAtoms() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- readAtoms() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- readAtoms() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
- readAtoms(boolean) - Method in class org.jmol.adapter.readers.quantum.PsiReader
- readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
- readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
- readAtoms(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
- readAtoms(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
- readAtoms(int, boolean) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
-
Lots of possibilities here: atom count is real; atom count is one less than true atom count sixth column is atom type; sixth column is first bond
- readAtoms(int, boolean) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readAtoms(String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Reads the output coordinates section into a new AtomSet.
- readAtoms(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
- readAtoms(List<Object>, List<Object>, List<Object>) - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
- readAtomsAndBonds(int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
- readAtomsAndBonds(String[]) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
- readAtomsCartGeomThenCell() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- readAtomSet(String, boolean, boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- readAtomsFromFile(File) - Method in class org.jmol.quantum.NMRNoeMatrix
- readAtomsInAngstromCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readAtomSpecies() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- readAtomValues() - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
Read all V nnn lines as string data; user can adapt as needed.
- readAtSign() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- readBasis() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- readBasis() - Method in class org.jmol.adapter.readers.quantum.PsiReader
- readBasis() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- readBasis() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readBasisInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readBasisNormalized() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- readBasisQC(String) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- readBilbaoDataFile() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- readBilbaoFormat(String, float) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- readBinaryHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
- readBlock(String) - Method in class org.jmol.adapter.readers.simple.InputReader
- readBlock(String) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- readBondArray(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
- readBonds() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readBonds() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- readBonds() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
- readBonds(int) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
- readBonds(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
- readBonds(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
- readBonds(int) - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
- readBonds(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
- readBornChargeTensors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- readBrickLayer() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
- readCalculationInfo(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readCalculationType() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- readCellParam() - Method in class org.jmol.adapter.readers.xtal.DmolReader
- readCellParam(boolean) - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- readCellParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
- readCellParams() - Method in class org.jmol.adapter.readers.xtal.MagresReader
- readCFI() - Method in class org.jmol.adapter.readers.simple.InputReader
- readCharges() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- readCifData() - Method in class org.jmol.adapter.readers.cif.CifReader
- readCifData(String, Object, String) - Method in interface org.jmol.atomdata.AtomDataServer
- readCifData(String, Object, String) - Method in class org.jmol.viewer.Viewer
- readCifData(String, String) - Method in class org.jmol.viewer.Viewer
- readCifFloats(String, float[]) - Method in class org.jmol.jvxl.readers.BCifDensityReader
- readCifFloats(String, float[]) - Method in class org.jmol.jvxl.readers.CifDensityReader
- readCifP3(String, P3) - Method in class org.jmol.jvxl.readers.BCifDensityReader
- readCifP3(String, P3) - Method in class org.jmol.jvxl.readers.CifDensityReader
- readColor() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
- readColorData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readColorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
- readComments() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- readConFile() - Method in class org.jmol.adapter.readers.simple.InputReader
- readConstraints() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
- readControlInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readCoord() - Method in class org.jmol.adapter.readers.xtal.DmolReader
- readCoordinates() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- readCoordinates() - Method in class org.jmol.adapter.readers.more.MdCrdReader
- readCoordinates() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
Reads a set of coordinates
- readCoordinates() - Method in class org.jmol.adapter.readers.quantum.DgridReader
-
Reads a set of coordinates
- readCoordinates() - Method in class org.jmol.adapter.readers.simple.AmpacReader
-
Reads a set of coordinates
- readCoordinates() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
- readCoordinates() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- readCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- readCoordinates() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
- readCoordLines() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
Read coordinates, either input or crystallographic, just saving their lines in a vector for now.
- readCouplings() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- readCrystalInfo() - Method in class org.jmol.adapter.readers.more.Mol2Reader
- readCSATensors() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- readData() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- readData(String, int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
For spin and magnetic moment data, read the data block and save it as property_spin or propert_magneticMoment.
- readData31(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- readData46(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
read labels and not proper number of NOs, nNOs, for this nboType
- readData47() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- readDataBlock(String) - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- readDataObject(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- readDimensionality() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- readDipole() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- readDisplacements(float) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- readDots() - Method in class org.jmol.jvxl.readers.KinemageReader
- readDoubleArray() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- readEFPInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readElementLabelsOnly() - Method in class org.jmol.adapter.readers.more.AFLOWReader
-
scan the AFLOWReader PRE structure for elements in coord section
- readElementNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- readEmbeddedScript() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
- readEnergy() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readEnergy() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- readEnergy() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
- readEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- readEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- readEnergy() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- readEnergy(int, String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
- reader - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
- reader - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
reader will be null if filter includes TOPOS_IGNORE
- reader - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- reader - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- reader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- READER_NOT_FOUND - Static variable in class org.jmol.viewer.JC
- readerClosed - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- readerData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- readerList - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- readerName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- readerOrDocument - Variable in class org.jmol.io.FileReader
- readers - Variable in class org.jmol.jvxl.readers.IsoIntersectGridReader
- readerSave - Variable in class org.jmol.adapter.readers.simple.FAHReader
- readerSets - Static variable in class org.jmol.adapter.smarter.Resolver
- readESym(boolean) - Method in class org.jmol.adapter.readers.quantum.QchemReader
- readEventCount - Variable in class org.openscience.jvxl.MonitorInputStream
- readExtents(int) - Method in class org.jmol.jvxl.readers.JaguarReader
-
read the extentx=, extenty=, extentz= lines and cache them then read the npts= line and construct the necessary data
- readFileAsMap(BufferedInputStream, Map<String, Object>, String) - Method in class org.jmol.viewer.Viewer
- readFileData() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readFinalCell() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- readFloatArray() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- readFloatArray() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
- readFreq() - Method in class org.jmol.adapter.readers.xtal.DmolReader
- readFreqFragments() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
Select only specific atoms for frequency generation.
- readFreqsAndModes() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- readFreqsAndModesQC(ArrayList<Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.AdfReader
-
Reads a set of vibrations.
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Reads the AtomSet and projected frequencies in the frequency section.
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.PsiReader
- readFrequencies() - Method in class org.jmol.adapter.readers.quantum.QchemReader
-
Interprets the Harmonic frequencies section.
- readFrequencies() - Method in class org.jmol.adapter.readers.simple.AmpacReader
-
Reads a set of vibrations.
- readFrequencies() - Method in class org.jmol.adapter.readers.simple.MopacReader
-
Interprets the Harmonic frequencies section.
- readFrequencies() - Method in class org.jmol.adapter.readers.spartan.SpartanReader
- readFrequencies() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- readFrequencies(String, boolean) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Interprets the Harmonic frequencies section.
- readFrequency() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- readGaussianBasis(String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- readGaussianBasisQC(ArrayList<Object>, ArrayList<Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- readGeometryOptimization() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- readGradient() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
Read minimization measures
- readHeader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- readHeader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- readHeader(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- readIdeal - Variable in class org.jmol.adapter.readers.cif.CifReader
- readInitialCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- readInputAtoms() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
- readInputDeck() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readInputHeader() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
- readInputRecords() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
- readIntiallattice() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- readIsotopes() - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
Read all M ISO lines.
- readItems(String, int, float[]) - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- readJaguarMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- readKeywords() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- readLattice(List<Object>) - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
- readLatticeAbc() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readLatticeCart() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readLatticeParams(boolean) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
Read the lattice parameters.
- readLatticeVector(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
- readLengthUnit(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readLine() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readLine() - Method in class org.jmol.jsv.JDXMOLParser
- readLines(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- readM40Data(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
read the M40 file, possibly as the extension of M50+M40
- readM40FloatLines(int, int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
- readM40Floats() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- readM40WaveVectors() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- readMdyn() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- readModel(Map<String, Object>) - Method in class org.jmol.adapter.readers.xtal.OptimadeReader
- readModels() - Method in interface org.jmol.api.JmolJDXMOLParser
- readModels() - Method in class org.jmol.jsv.JDXMOLParser
- readMolData(Map<String, Object>, Lst<String>) - Method in class org.jmol.adapter.readers.molxyz.MolReader
-
Read the SDF data with name in lower case
- readMolecularFormula() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
-
try various ways to read the optional atom labels.
- readMolecularObitals() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readMolecularOrbital() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- readMolecularOrbital() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.DgridReader
- readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- readMolecularOrbitals(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.MOReader
- readMolecularOrbitals(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
- readMolecularOrbitalsQC(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
-
Read basis and orbital information.
- readMOs() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- readMOs() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- readMOs(boolean, QchemReader.MOInfo[]) - Method in class org.jmol.adapter.readers.quantum.QchemReader
- readMultipole(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
- readMyTransform() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- readNamfisAction - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- ReadNamfisAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
- readNamfisChooser - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- readNamfisOutput(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNamfisAction
- readNBO37Occupancies(int) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
Read occupancies from .37 file.
- readNBOCoefficients(Map<String, Object>, String, Viewer) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
-
Called by setNBOType in IsoExt when use issues NBO TYPE xxx
- readNextLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- readNmrAction - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- ReadNmrAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReadNmrAction
- readNmrChooser - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- readNmrData(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- readNmrDataJSON(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- readNoatom() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- readNotypes() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- readOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- readOutput() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- readOutputAtomIndex() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readOutputAtoms() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readOutputBornChargeTensors() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readOutputCharges() - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
read Mulliken or Hirshfield charges
- readOutputProperties(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- readOutputUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readParameters() - Method in class org.jmol.jvxl.readers.ApbsReader
- readParameters() - Method in class org.jmol.jvxl.readers.BCifDensityReader
- readParameters() - Method in class org.jmol.jvxl.readers.CastepDensityReader
- readParameters() - Method in class org.jmol.jvxl.readers.CubeReader
- readParameters() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
-
this reader has the critical scaling information at the end, so we just load the data straight into an array.
- readParameters() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
- readParameters() - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
- readParameters() - Method in class org.jmol.jvxl.readers.JaguarReader
-
nothing much here
- readParameters() - Method in class org.jmol.jvxl.readers.JvxlReader
- readParameters() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readParameters() - Method in class org.jmol.jvxl.readers.MrcBinaryReader
- readParameters() - Method in class org.jmol.jvxl.readers.PltFormattedReader
- readParameters() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
- readParameters() - Method in class org.jmol.jvxl.readers.UhbdReader
- readParameters() - Method in class org.jmol.jvxl.readers.VaspChgcarReader
- readParameters() - Method in class org.jmol.jvxl.readers.VolumeFileReader
- readParameters() - Method in class org.jmol.jvxl.readers.XplorReader
- readParameters() - Method in class org.jmol.jvxl.readers.XsfReader
- readParams(BufferedReader, int, Map<Object, Object>) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Reads partial charges and assigns them only to the last atom set.
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Reads partial charges and assigns them only to the last atom set.
- readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- readPartialCharges() - Method in class org.jmol.adapter.readers.simple.AmpacReader
- readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- readPeaks(boolean, int) - Method in interface org.jmol.api.JmolJDXMOLParser
- readPeaks(boolean, int) - Method in class org.jmol.jsv.JDXMOLParser
- readPhononFractionalCoord() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readPhononFrequencies() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readPhononTrajectories() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readPhononUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readPolygons() - Method in class org.jmol.jvxl.readers.KinemageReader
- readPolygons() - Method in class org.jmol.jvxl.readers.MsmsReader
- readPolygons() - Method in class org.jmol.jvxl.readers.ObjReader
- readPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
- readPolygonsPM() - Method in class org.jmol.jvxl.readers.PmeshReader
- readPOSITION() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- readPositionsAbs() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readPositionsFrac() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- readPRE - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- readPrePost() - Method in class org.jmol.adapter.readers.more.AFLOWReader
- readPrimitiveLatticeVectors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
-
Read transform matrix primitive to conventional.
- readProperties() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readProperties() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- readProperty() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readPsiMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.PsiReader
- readQchemMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.QchemReader
- readRaman(Lst<String>) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- readResInfo(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
- readSCFDone() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Interprets the SCF Done: section.
- readSCFDone() - Method in class org.jmol.adapter.readers.quantum.PsiReader
-
Interprets the SCF Done: section.
- readSecondOrderData() - Method in class org.jmol.adapter.readers.quantum.MOReader
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.AdfReader
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.DgridReader
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
- readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
- readSlaterBasisQC(ArrayList<Object>) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- readSpaceGroup() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- readSpaceGroup() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- readSpecies() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- READSPT - Enum constant in enum org.jmol.viewer.Viewer.ACCESS
- readSteps() - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- readString() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
- readStringAsBytes() - Method in class org.jmol.adapter.readers.pymol.PickleReader
- readStructure(String) - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
- readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- readSurfaceDataJXR() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readSurfaceDataVDR(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
- readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- readSurfaceDataXML() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readSymmetries() - Method in class org.jmol.adapter.readers.quantum.AdfReader
- readSymmetry() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Read the symmetry information and set the property.
- readSymmetry() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
not doing anything with this -- P1 assumed
- readSymmetry() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
- readSymmetryOperators() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- readTable() - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
Read a CIF 2.0 table into either a JSON string or a java data structure
- readTensor() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
Read a tensor line.
- readTitleLines() - Method in class org.jmol.adapter.readers.simple.CubeReader
- readTlsData() - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
- readTopAtomsAndBonds() - Method in class org.jmol.adapter.readers.simple.FAHReader
- readTotal() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
-
Interpret a line starting with a line with "Total" in it.
- readTotalAtomicCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- readTransform() - Method in class org.jmol.adapter.readers.spartan.SpartanInputReader
- readTypesequence() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
- readUniqueAtoms() - Method in class org.jmol.adapter.readers.quantum.PsiReader
- readUnitCell() - Method in class org.jmol.adapter.readers.more.GromacsReader
- readUnitCell() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- readUnitCell() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
- readUnitCell() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
- readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- readUnnormalizedBasis() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
- readUserData(int) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
- readValue(String) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- readVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readVectors() - Method in class org.jmol.jvxl.readers.KinemageReader
- readVectors(String, int, boolean) - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- readVersion() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- readVertices() - Method in class org.jmol.jvxl.readers.KinemageReader
- readVertices() - Method in class org.jmol.jvxl.readers.MsmsReader
- readVertices() - Method in class org.jmol.jvxl.readers.ObjReader
- readVertices() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
- readVertices() - Method in class org.jmol.jvxl.readers.PmeshReader
- readVertices() - Method in class org.jmol.jvxl.readers.Ras3DReader
- readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.NffReader
- readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
- readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
- readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.Ras3DReader
- readVerticesPM() - Method in class org.jmol.jvxl.readers.PmeshReader
- readVFI() - Method in class org.jmol.adapter.readers.simple.InputReader
- readVibFreqs() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- readVirtual() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- readVnnCoords() - Method in class org.jmol.adapter.readers.simple.FAHReader
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
- readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectGridReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
- readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- readVolumetricHeader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
- readVoxelDataIndividually(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
- readVoxelVector(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- reallocRgb16s(Rgb16[], int) - Method in class org.jmol.g3d.TriangleRenderer
- reattachAppletAction - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- ReattachAppletAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ReattachAppletAction
- rebond() - Method in class org.jmol.api.JmolViewer
- rebond() - Method in class org.jmol.viewer.Viewer
- rebond() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- rebondState(boolean) - Method in class org.jmol.viewer.Viewer
- recachePngjBytes(String, byte[]) - Method in class org.jmol.viewer.FileManager
- recalc() - Method in class org.jmol.modelset.Text
- recalcAltVertices - Variable in class org.jmol.shape.Mesh
- reCalculate(BS, M3) - Method in class org.jmol.geodesic.EnvelopeCalculation
-
problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
- recalculateAllPolymers(BS, Group[]) - Method in class org.jmol.modelsetbio.BioModelSet
- recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioModel
- recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
- recalculateLeadMidpointsAndWingVectors(int) - Method in class org.jmol.modelset.ModelSet
- recalculatePoints(int) - Method in class org.jmol.modelsetbio.BioModelSet
- recalculatePolymers(BS) - Method in class org.jmol.modelset.ModelSet
- recalculatePositionDependentQuantities(BS, M4) - Method in class org.jmol.modelset.ModelSet
- recallCommand(boolean, boolean) - Method in class org.jmol.console.GenericConsole
- recallCommand(boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
-
Recall command history.
- recentFiles - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- recentFilesAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- RecentFilesAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
- RecentFilesDialog - Class in org.openscience.jmol.app.jmolpanel
-
Manages a list of recently opened files.
- RecentFilesDialog(Frame) - Constructor for class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
Creates a hidden recent files dialog
- recordData(float) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- records - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- recordStatus(String) - Method in class org.jmol.viewer.StatusManager
- recordTime(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- Rectangle - Class in org.jmol.util
- Rectangle() - Constructor for class org.jmol.util.Rectangle
- rectClip - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- rectRubber - Variable in class org.jmol.viewer.ActionManager
- red - Variable in class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- RED - Static variable in class org.jmol.util.C
- REDBLUE - Enum constant in enum org.jmol.c.STER
- REDCYAN - Enum constant in enum org.jmol.c.STER
- redField - Variable in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- redField - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- redFieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- redFieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- REDGREEN - Enum constant in enum org.jmol.c.STER
- redLabel - Variable in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- redLabel - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- redLevel - Variable in class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- redo - Static variable in class org.jmol.script.T
- redo() - Method in class org.jmol.console.ScriptEditor.EditorDocument
- redoButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- redomove - Static variable in class org.jmol.script.T
- redoStateStack - Variable in class org.jmol.viewer.StateManager
- REDUCE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- reducedAnisotropy() - Method in class org.jmol.util.Tensor
-
reduced anisotropy = largest difference from isotropy (may be negative)
- reduceFilename(String) - Static method in class org.jmol.viewer.ModelManager
- redValue - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- redValue - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- referance - Variable in class org.jmol.smiles.SmilesAtom
- reference - Variable in class org.jmol.modelset.TickInfo
- reference - Static variable in class org.jmol.script.T
- referenceCenter - Variable in class org.jmol.export.___Exporter
- referencePlaneOffset - Variable in class org.jmol.viewer.TransformManager
- reflect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- reflect_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- reformatDistanceIfSelected() - Method in class org.jmol.modelset.Measurement
- reformatDistances() - Method in class org.jmol.shape.Measures
- refresh - Static variable in class org.jmol.script.T
- refresh(boolean) - Method in class org.jmol.script.ScriptEval
-
Refresh the display NOW
- refresh(int, String) - Method in class org.jmol.api.JmolViewer
- refresh(int, String) - Method in class org.jmol.viewer.Viewer
-
initiate a repaint/update sequence if it has not already been requested.
- refresh(Point3fi[]) - Method in class org.jmol.modelset.Measurement
- REFRESH_REPAINT - Static variable in class org.jmol.viewer.Viewer
- REFRESH_REPAINT_NO_MOTION_ONLY - Static variable in class org.jmol.viewer.Viewer
- REFRESH_SEND_WEBGL_NEW_ORIENTATION - Static variable in class org.jmol.viewer.Viewer
- REFRESH_SYNC - Static variable in class org.jmol.viewer.Viewer
- REFRESH_SYNC_MASK - Static variable in class org.jmol.viewer.Viewer
- refreshButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- refreshing - Static variable in class org.jmol.script.T
- refreshing - Variable in class org.jmol.viewer.Viewer
- refreshMeasures(boolean) - Method in class org.jmol.viewer.Viewer
- refSingleComboBox - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- refSingleComboBoxActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- refSingleLabel - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- region - Variable in class org.jmol.util.MeshCapper.CapVertex
-
dynamic region pointers
- register(String, JmolSyncInterface) - Method in interface org.jmol.api.JmolSyncInterface
- register(String, JmolSyncInterface) - Method in class org.jmol.util.GenericApplet
- register(String, JmolSyncInterface) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- register(Component, String) - Method in interface org.jmol.awtjs.swing.SwingController
-
Set c's id to a unique identifier and add it to an associative array that will associate that id with c.
- registerAudio(String, Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
- reinitializeLightingAndColor(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- reinitShape() - Method in class org.jmol.shape.Axes
- reinstateMenu(JMenuItem, MenuElement[]) - Method in class org.jmol.awt.AwtPopupHelper
-
Cause the menu to persist in its open state.
- rejectAtomName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- RELATIVE_DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- RELATIVE_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- relaxMatrix - Variable in class org.jmol.quantum.NMRNoeMatrix
- release() - Method in interface org.jmol.api.AtomIndexIterator
- release() - Method in class org.jmol.bspt.CubeIterator
-
nulls internal references
- release() - Method in class org.jmol.modelset.AtomIteratorWithinModel
- release() - Method in class org.jmol.symmetry.UnitCellIterator
- releaseBuffers() - Method in class org.jmol.g3d.Graphics3D
- releaseBuffers() - Method in class org.jmol.g3d.Platform3D
- released(long, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
- RELEASED - Static variable in class org.jmol.awtjs.Event
- releaseModelSet() - Method in class org.jmol.modelset.ModelSet
- releaseModelSetAC() - Method in class org.jmol.modelset.AtomCollection
- releaseModelSetBC() - Method in class org.jmol.modelset.BondCollection
- releaseScreenImage() - Method in class org.jmol.api.JmolViewer
- releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
- releaseScreenImage() - Method in class org.jmol.util.GData
- releaseScreenImage() - Method in class org.jmol.viewer.Viewer
- releaseShape(int) - Method in class org.jmol.viewer.ShapeManager
- remapColors(Viewer, ColorEncoder, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
remaps colors based on a new color scheme or translucency level
- remark285() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- remark290() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- remark350() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- remarkTls() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- rememberCheckbox(String, SC) - Method in class org.jmol.popup.GenericPopup
- remoteAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
- remoteAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
- remove - Static variable in class org.jmol.script.T
- remove(int) - Method in interface org.jmol.api.SC
- remove(int) - Method in class org.jmol.awt.AwtSwingComponent
- remove(int) - Method in class org.jmol.awtjs.swing.Container
- remove(int, int) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- removeAll() - Method in interface org.jmol.api.SC
- removeAll() - Method in class org.jmol.awt.AwtSwingComponent
- removeAll() - Method in class org.jmol.awtjs.swing.Container
- removeAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
note that sets must be iterated from LAST to FIRST not a general method -- would mess up if we had unit cells
- removeBinding(Iterator<String>, String) - Method in class org.jmol.viewer.binding.Binding
- removeBridgingRings(Lst<BS>, Lst<SmilesRing>) - Static method in class org.jmol.smiles.SmilesAromatic
-
check for any two rings with more than two common atoms and remove them from the pool
- removeCommand() - Method in class org.jmol.util.CommandHistory
- removeCommand() - Method in class org.jmol.viewer.Viewer
-
Removes one command from the command history
- removeCommand(int) - Method in class org.jmol.util.CommandHistory
- removeComments() - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- removeCurrentAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- removeDuplicates(BS) - Method in class org.jmol.symmetry.SpaceGroupFinder
- removeDuplicates(ModelSet, BS, boolean) - Method in interface org.jmol.api.SymmetryInterface
- removeDuplicates(ModelSet, BS, boolean) - Method in class org.jmol.symmetry.Symmetry
- removeFunction(String) - Method in class org.jmol.viewer.Viewer
- removeLastUnselectedAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- removeMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
-
should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.
- removePacking(int, P3, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- removeParam(String) - Method in class org.jmol.viewer.GlobalSettings
- removePropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
- removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
- removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
- removeUnnecessaryBonds(Atom, boolean) - Method in class org.jmol.modelset.BondCollection
- removeUserVariable(String) - Method in class org.jmol.viewer.GlobalSettings
- removeUserVariable(String) - Method in class org.jmol.viewer.Viewer
- render() - Method in class org.jmol.render.AxesRenderer
- render() - Method in class org.jmol.render.BallsRenderer
- render() - Method in class org.jmol.render.BbcageRenderer
- render() - Method in class org.jmol.render.EchoRenderer
- render() - Method in class org.jmol.render.FrankRenderer
- render() - Method in class org.jmol.render.HalosRenderer
- render() - Method in class org.jmol.render.HoverRenderer
- render() - Method in class org.jmol.render.LabelsRenderer
- render() - Method in class org.jmol.render.MeasuresRenderer
- render() - Method in class org.jmol.render.ShapeRenderer
- render() - Method in class org.jmol.render.StarsRenderer
- render() - Method in class org.jmol.render.SticksRenderer
- render() - Method in class org.jmol.render.UccageRenderer
- render() - Method in class org.jmol.renderbio.BioMeshRenderer
- render() - Method in class org.jmol.renderbio.BioShapeRenderer
- render() - Method in class org.jmol.rendercgo.CGORenderer
- render() - Method in class org.jmol.renderspecial.DipolesRenderer
- render() - Method in class org.jmol.renderspecial.DotsRenderer
- render() - Method in class org.jmol.renderspecial.DrawRenderer
- render() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- render() - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
- render() - Method in class org.jmol.renderspecial.PolyhedraRenderer
- render() - Method in class org.jmol.renderspecial.VectorsRenderer
- render() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- render() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
- render() - Method in class org.jmol.rendersurface.PmeshRenderer
- render() - Method in class org.jmol.viewer.Viewer
- render(int[], int, int, int, int, M3, double[], M4, int, P3[]) - Method in class org.jmol.g3d.SphereRenderer
- render(GData, ModelSet, boolean, int[]) - Method in interface org.jmol.api.JmolRepaintManager
- render(GData, ModelSet, boolean, int[]) - Method in class org.jmol.render.RepaintManager
- render(TransformManager, Text, JmolRendererInterface, float, float, float[], float[], P3i, short, int, int) - Static method in class org.jmol.render.TextRenderer
- render_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- render1(int) - Method in class org.jmol.render.UccageRenderer
- render1(Atom) - Method in class org.jmol.render.HalosRenderer
- render1(Atom, short) - Method in class org.jmol.render.StarsRenderer
- render1(Axes, int, boolean, String, boolean, float, String) - Method in class org.jmol.render.AxesRenderer
- render1(Dots) - Method in class org.jmol.renderspecial.DotsRenderer
- render1(Polyhedron) - Method in class org.jmol.renderspecial.PolyhedraRenderer
- render2(boolean) - Method in class org.jmol.render.MeshRenderer
-
Overridden in DrawRenderer and IsosurfaceRenderer
- render2(boolean) - Method in class org.jmol.renderspecial.DrawRenderer
- render2(boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- render2(Mesh) - Method in class org.jmol.rendercgo.CGORenderer
- render2b(boolean) - Method in class org.jmol.render.MeshRenderer
- render2Strand(boolean, float, float) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderAllStrings(Object) - Method in interface org.jmol.api.JmolGraphicsInterface
- renderAllStrings(Object) - Method in class org.jmol.export.Export3D
- renderAllStrings(Object) - Method in class org.jmol.g3d.Graphics3D
- renderAllStrings(Object) - Method in class org.jmol.util.GData
- renderAngle(String, Point3fi, Point3fi, Point3fi) - Method in class org.jmol.render.MeasuresRenderer
- renderArc - Variable in class org.jmol.modelset.Measurement
- renderArc(int, int) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- renderArcs() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- renderArrowHead(T3, T3, float, boolean, boolean, boolean) - Method in class org.jmol.renderspecial.DrawRenderer
- renderArrowHeads - Variable in class org.jmol.renderbio.RocketRenderer
- renderArrowHeads - Variable in class org.jmol.renderbio.RocketsRenderer
- renderArrows() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- renderAxes() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- renderAxis - Variable in class org.jmol.modelset.Measurement
- renderBackground(JmolRendererInterface) - Method in interface org.jmol.api.JmolRendererInterface
- renderBackground(JmolRendererInterface) - Method in class org.jmol.export.Export3D
- renderBackground(JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
- renderBackground(JmolRendererInterface) - Method in class org.jmol.util.GData
- renderBall() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- renderBioMesh(Mesh) - Method in class org.jmol.renderbio.BioMeshRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.BackboneRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.BioShapeRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.CartoonRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.RibbonsRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.RocketsRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.StrandsRenderer
- renderBioShape(BioShape) - Method in class org.jmol.renderbio.TraceRenderer
- renderBits(short, short, int, byte, int, P3i, P3i) - Method in class org.jmol.g3d.CylinderRenderer
- renderBitsFloat(short, short, int, byte, int, P3, P3) - Method in class org.jmol.g3d.CylinderRenderer
- renderBlock(NucleicMonomer) - Method in class org.jmol.renderbio.NucleicRenderer
- renderBond() - Method in class org.jmol.render.SticksRenderer
- renderCage(int, P3[], int[][], P3[], int, int, int, float) - Method in class org.jmol.render.CageRenderer
- renderConeOld(short, byte, int, float, float, float, float, float, float, boolean, boolean) - Method in class org.jmol.g3d.CylinderRenderer
- renderContourLines() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.DotsRenderer
-
generic renderer -- dots and geosurface
- renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
- renderCrossHairs(int[], int, int, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
- renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.export.Export3D
- renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.g3d.Graphics3D
- renderCyl(P3, P3, P3, P3) - Method in class org.jmol.renderbio.NucleicRenderer
- renderDipoleVector(Dipole, BS) - Method in class org.jmol.renderspecial.DipolesRenderer
- renderDistance(String, Point3fi, Point3fi) - Method in class org.jmol.render.MeasuresRenderer
- renderDots() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- renderDots(int) - Method in class org.jmol.renderspecial.DotsRenderer
-
also called by GeoSurface when in motion
- renderEcho(Text, int) - Method in class org.jmol.render.EchoRenderer
- renderEdge(P3[], P3[], int, int) - Method in class org.jmol.renderbio.NucleicRenderer
- renderEllipsoids(Map<?, Ellipsoid>, boolean) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- renderer - Variable in class org.jmol.awtjs.swing.Grid
- renderers - Variable in class org.jmol.render.RepaintManager
- renderExport(GData, ModelSet, Map<String, Object>) - Method in interface org.jmol.api.JmolRepaintManager
- renderExport(GData, ModelSet, Map<String, Object>) - Method in class org.jmol.render.RepaintManager
- renderFlatEndcap(boolean, boolean, int[][]) - Method in class org.jmol.g3d.CylinderRenderer
- renderFrameTitle(String) - Method in class org.jmol.render.EchoRenderer
- renderHandles() - Method in class org.jmol.renderspecial.DrawRenderer
- renderHeight - Variable in class org.jmol.awtjs.swing.Component
- renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.BioShapeRenderer
- renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.BioShapeRenderer
- renderHermiteCylinder(P3[], int) - Method in class org.jmol.renderbio.BioShapeRenderer
- renderHermiteRibbon(boolean, boolean, int, P3, P3, P3, P3, P3, P3, P3, P3, int, int) - Method in class org.jmol.g3d.HermiteRenderer
- renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.BioShapeRenderer
- renderHermiteRope(boolean, int, int, int, int, P3, P3, P3, P3) - Method in class org.jmol.g3d.HermiteRenderer
- renderInfo() - Method in class org.jmol.render.UccageRenderer
- renderInfo() - Method in class org.jmol.renderspecial.DrawRenderer
- renderInfo() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderInfo() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
- rendering - Variable in class org.jmol.jvxl.data.JvxlData
- renderIso() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderLabel(String, float, float, float, float, float) - Method in class org.jmol.render.AxesRenderer
- renderLabelOrMeasure(Text, String) - Method in class org.jmol.render.LabelsRenderer
- renderLeontisWesthofEdges(NucleicMonomer) - Method in class org.jmol.renderbio.NucleicRenderer
- renderLine(P3, P3, int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
- renderLonePair(boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderLow - Variable in class org.jmol.g3d.Graphics3D
- renderLow - Variable in class org.jmol.render.MeshRenderer
- renderMeasurement(boolean) - Method in class org.jmol.render.MeasuresRenderer
- renderMesh2(Mesh) - Method in class org.jmol.render.MeshRenderer
-
overridden in BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
- renderMeshes() - Method in class org.jmol.renderbio.BioMeshRenderer
- renderMeshRibbon() - Method in class org.jmol.renderbio.MeshRibbonRenderer
- renderMeshSlab() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderNormals() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderNucleic(BioShapeRenderer) - Method in class org.jmol.renderbio.NucleicRenderer
- renderNucleicBaseStep(int, T3, T3) - Method in class org.jmol.renderbio.NucleicRenderer
- renderOld(short, short, int, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.CylinderRenderer
- renderOne(Ellipsoid) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- renderParallelPair(boolean, int, P3, P3, P3, P3, P3, P3, P3, P3) - Method in class org.jmol.g3d.HermiteRenderer
- renderPart(int[][]) - Method in class org.jmol.renderbio.RocketRenderer
- renderPass2(short) - Static method in class org.jmol.util.C
- renderPending() - Method in class org.jmol.renderbio.RocketRenderer
- renderPendingMeasurement() - Method in class org.jmol.render.MeasuresRenderer
- renderPendingRocketSegment(int, P3, P3, P3, boolean) - Method in class org.jmol.renderbio.RocketRenderer
- renderPendingSheetPlank(P3, P3, P3, boolean) - Method in class org.jmol.renderbio.RocketRenderer
- renderPoints() - Method in class org.jmol.render.MeshRenderer
- renderPoints() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderProtein() - Method in class org.jmol.renderbio.CartoonRenderer
- renderQuadrant(int, int, int, int, int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
- renderQuadrantClipped(int, int, int, int, int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
- renderQuadrantUnclipped(int, int, int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
- renderRibose() - Method in class org.jmol.renderbio.NucleicRenderer
- renderRing5() - Method in class org.jmol.renderbio.NucleicRenderer
- renderRing6() - Method in class org.jmol.renderbio.NucleicRenderer
- renderRockets() - Method in class org.jmol.renderbio.RocketRenderer
- renderRockets() - Method in class org.jmol.renderbio.RocketsRenderer
- renderScale(JmolRendererInterface, Text, float[], int, boolean) - Static method in class org.jmol.render.TextRenderer
-
Render a short |---| bar with label from ECHO "%SCALE"
- renderScreenImage(Object, int, int) - Method in class org.jmol.api.JmolViewer
- renderScreenImage(Object, int, int) - Method in class org.jmol.viewer.Viewer
-
JmolViewer interface uses this, but that is all
- renderScreenImage(Object, Object) - Method in interface org.jmol.api.GenericPlatform
-
Deprecated.
- renderScreenImage(Object, Object) - Method in class org.jmol.awt.Platform
-
legacy apps will use this
- renderScreenImage(Object, Object) - Method in class org.jmol.awtjs2d.Platform
-
legacy apps will use this
- renderScreenImage(Object, Object, Object) - Method in class org.jmol.api.JmolViewer
-
Deprecated.
- renderScreenImage(PlatformViewer, Object, Object) - Static method in class org.jmol.awt.Display
-
Deprecated.
- renderScreenImage(PlatformViewer, Object, Object) - Static method in class org.jmol.awtjs2d.Display
-
legacy apps will use this
- renderScreenImageStereo(Object, boolean, int, int) - Method in class org.jmol.viewer.Viewer
- renderShape(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
- renderShapes() - Method in class org.jmol.renderbio.BioShapeRenderer
- renderSimpleLabel(JmolRendererInterface, Font, String, short, short, float[], int, int, int, int, float, int, short, int, int) - Static method in class org.jmol.render.TextRenderer
- renderSpecialSegment(AlphaMonomer, short, short) - Method in class org.jmol.renderbio.RocketRenderer
- renderSphereClipped(int[], int, int, int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
- renderSphereUnclipped(int[], int, int, int[]) - Method in class org.jmol.g3d.SphereRenderer
- renderSphericalEndcaps() - Method in class org.jmol.g3d.CylinderRenderer
- renderSteps(NucleicMonomer, int) - Method in class org.jmol.renderbio.NucleicRenderer
- renderStrand(P3[]) - Method in class org.jmol.renderbio.StrandsRenderer
- renderStrands() - Method in class org.jmol.renderbio.StrandsRenderer
- renderStrandShape() - Method in class org.jmol.renderbio.StrandsRenderer
- renderSurface(BS) - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
- renderTorsion(String, Point3fi, Point3fi, Point3fi, Point3fi) - Method in class org.jmol.render.MeasuresRenderer
- renderTrace() - Method in class org.jmol.renderbio.TraceRenderer
- renderTriangle(P3[], P3[], int, int, int, boolean) - Method in class org.jmol.renderbio.NucleicRenderer
- renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.render.MeshRenderer
- renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- renderVector(V3, P3, P3, float, boolean) - Method in class org.jmol.renderspecial.DipolesRenderer
- renderVector(Atom, Vibration) - Method in class org.jmol.renderspecial.VectorsRenderer
- renderWidth - Variable in class org.jmol.awtjs.swing.Component
- renderXyArrow(int) - Method in class org.jmol.renderspecial.DrawRenderer
- renderXyPoint() - Method in class org.jmol.renderspecial.DrawRenderer
- REP_ANGLES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_CALLBACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_CARTOON - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_CELL - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_CGO - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_DASHES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_DIHEDRALS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_DOTS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_ELLIPSOID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_EXTENT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_JMOL_MAX - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_JMOL_PUTTY - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_JMOL_TRACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_LABELS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_LINES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_LIST - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_MAX - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_MESH - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_NBSPHERES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_NONBONDED - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_RIBBON - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_SLICE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_SPHERES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_STICKS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_SURFACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- REP_VOLUME - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- repaint() - Method in class org.jmol.awtjs.swing.Component
- repaint() - Method in class org.jmol.awtjs.swing.JDialog
- repaint(Object) - Method in interface org.jmol.api.GenericPlatform
- repaint(Object) - Static method in class org.jmol.awt.Display
- repaint(Object) - Method in class org.jmol.awt.Platform
- repaint(Object) - Method in class org.jmol.awtjs2d.Platform
- REPAINT_IGNORE - Static variable in class org.jmol.viewer.JC
- repaintDone() - Method in interface org.jmol.api.JmolRepaintManager
- repaintDone() - Method in class org.jmol.render.RepaintManager
- repaintDone() - Method in class org.jmol.viewer.AnimationManager
- repaintIfReady(String) - Method in interface org.jmol.api.JmolRepaintManager
- repaintIfReady(String) - Method in class org.jmol.render.RepaintManager
- RepaintManager - Class in org.jmol.render
- RepaintManager() - Constructor for class org.jmol.render.RepaintManager
- repaintNow(String) - Method in class org.jmol.render.RepaintManager
- repaintPending - Variable in class org.jmol.render.RepaintManager
- repaintwaitms - Static variable in class org.jmol.script.T
- repaintWaitMs - Variable in class org.jmol.viewer.GlobalSettings
- repeatCheckBox - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- repeatCount - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- replace - Static variable in class org.jmol.script.T
- replace(int, int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- replaceCommand(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
-
Replaces current command on script.
- replaceCommand(T) - Method in class org.jmol.script.ScriptCompiler
- replaceGroup(Group, Group) - Method in class org.jmol.shape.Shape
- replaceGroup(Group, Group) - Method in class org.jmol.shapebio.BioShapeCollection
- replaceGroup(Group, Group) - Method in class org.jmol.viewer.ShapeManager
- replaceMutatedMonomer(Viewer, AminoMonomer, AminoMonomer, boolean) - Static method in class org.jmol.modelsetbio.BioExt
- replaceParentSubstituent(CIPChirality.CIPAtom, CIPChirality.CIPAtom, CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Swap a substituent and the parent in preparation for reverse traversal of this path back to the root atom.
- replaceQuotedStrings(String, ArrayList<String>, ArrayList<String>) - Static method in class org.openscience.jmol.app.webexport.WebPanel
- replaceXn(String, int) - Static method in class org.jmol.symmetry.SymmetryOperation
- reply(int, Object) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- reply(int, Object) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- report(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- report(String, boolean) - Method in class org.jmol.minimize.Minimizer
- report(String, boolean) - Method in class org.jmol.script.ScriptEval
- reportAll - Variable in class org.jmol.shape.Sticks
- reportEnergy() - Method in class org.jmol.minimize.Minimizer
- reportSelection(int) - Method in class org.jmol.viewer.ChimeMessenger
-
report atom selection in Chime format
- reportSelection(int) - Method in interface org.jmol.viewer.JmolChimeMessenger
- reportSelection(String) - Method in class org.jmol.viewer.Viewer
- repositionWindow(String, Component) - Method in class org.openscience.jmol.app.HistoryFile
-
Uses the informations in the history to reposition the window.
- repositionWindow(String, Component, int, int, boolean) - Method in class org.openscience.jmol.app.HistoryFile
-
Uses the informations in the history to reposition the window.
- reps - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- requestFocusInWindow(Object) - Method in interface org.jmol.api.GenericPlatform
- requestFocusInWindow(Object) - Static method in class org.jmol.awt.Display
- requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
- requestFocusInWindow(Object) - Static method in class org.jmol.awtjs2d.Display
- requestFocusInWindow(Object) - Method in class org.jmol.awtjs2d.Platform
- requestRepaintAndWait(String) - Method in interface org.jmol.api.JmolRepaintManager
- requestRepaintAndWait(String) - Method in class org.jmol.render.RepaintManager
- requestRepaintAndWait(String) - Method in class org.jmol.viewer.Viewer
- requiresBSFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- requiresSorting - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- requireTranslucent - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
- reset - Static variable in class org.jmol.script.T
- reset() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- reset() - Method in class org.jmol.bspt.Bspt
- reset() - Method in class org.jmol.symmetry.UnitCell
- reset() - Method in class org.jmol.thread.JmolThread
- reset() - Method in class org.jmol.util.BoxInfo
- reset() - Method in class org.jmol.viewer.ActionManager
- reset() - Method in class org.openscience.jvxl.MonitorInputStream
- reset(boolean) - Method in class org.jmol.viewer.Viewer
- reset(int) - Method in class org.jmol.util.CommandHistory
-
Resets instance.
- RESET_NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
- resetAromatic() - Method in class org.jmol.modelset.BondCollection
- resetAtomPickType() - Method in class org.jmol.modelkit.ModelKit
- resetAxes() - Method in class org.jmol.modelsetbio.ProteinStructure
- resetAxisCoordinates() - Method in class org.jmol.render.SticksRenderer
- resetBioshapes(BS) - Method in class org.jmol.viewer.ShapeManager
- resetBondFields() - Method in class org.jmol.modelkit.ModelKit
- resetBoundCount() - Method in class org.jmol.modelset.Model
- resetChirality() - Method in class org.jmol.modelset.ModelSet
- resetDefaults(String[]) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- resetDF() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- resetDSSR(boolean) - Method in class org.jmol.modelset.Model
-
Something has changed; clear the DSSR cache and possibly remove DSSR entirely.
- resetError() - Method in class org.jmol.script.ScriptEval
- resetFitToScreen(boolean) - Method in class org.jmol.viewer.TransformManager
- resetFlag - Static variable in class org.openscience.jmol.app.webexport.LogPanel
- resetForMapping(boolean) - Method in class org.jmol.jvxl.readers.Parameters
-
reset some parameters at the "MAP" keyword or initially
- resetHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
- resetHydrogenPoints() - Method in class org.jmol.modelsetbio.AminoPolymer
- resetHydrogenPoints() - Method in class org.jmol.modelsetbio.BioPolymer
- resetIndexPlane(int[][]) - Method in class org.jmol.jvxl.calc.MarchingCubes
- resetIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
- resetKey - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- resetLighting() - Method in class org.jmol.viewer.StateManager
-
Reset lighting to Jmol defaults
- resetMeasurement() - Method in class org.jmol.viewer.ActionManager
- resetMolecules() - Method in class org.jmol.modelset.ModelSet
- resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager
-
something has arisen that requires resetting of the navigation point.
- resetNeeded - Variable in class org.jmol.multitouch.ActionManagerMT
- resetObjects() - Method in class org.jmol.shape.MeshCollection
- resetPartialCharges() - Method in class org.jmol.modelset.AtomCollection
- resetPlane(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
- resetRasmolBonds(BS, int) - Method in class org.jmol.modelsetbio.BioModel
-
from Trajectory.setAtomPositions base models only; not trajectories
- resetRotation() - Method in class org.jmol.viewer.TransformManager
- resetRotation() - Method in class org.jmol.viewer.TransformManager4D
- resetShapes(boolean) - Method in class org.jmol.viewer.ShapeManager
- resetShapes(boolean) - Method in class org.jmol.viewer.Viewer
- resetSlab() - Method in class org.jmol.util.MeshSurface
- resetTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- resetValue(String, GlobalSettings) - Method in class org.jmol.viewer.GlobalSettings
- resetVoxelData(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
- resetXYCenter(int, int) - Method in class org.jmol.viewer.TransformManager
- RESI - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- residue - Static variable in class org.jmol.script.T
- residueChar - Variable in class org.jmol.smiles.SmilesAtom
- residueName - Variable in class org.jmol.smiles.SmilesAtom
- residueNames - Variable in class org.jmol.adapter.readers.pdb.JmolDataReader
- residueNumber - Variable in class org.jmol.smiles.SmilesAtom
- residueSpecCodeGenerated - Variable in class org.jmol.script.ScriptTokenParser
- RESIZE - Enum constant in enum org.jmol.c.CBK
- resizeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ResizeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
- resizeDisplay(int, int) - Method in class org.jmol.util.GenericApplet
- resizeDisplay(int, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- resizeImage(int, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- resizeInnerPanel(int, int) - Method in class org.jmol.api.JmolViewer
- resizeInnerPanel(int, int) - Method in class org.jmol.viewer.StatusManager
- resizeInnerPanel(int, int) - Method in class org.jmol.viewer.Viewer
- resizeInnerPanel(String) - Method in interface org.jmol.api.JmolStatusListener
- resizeInnerPanel(String) - Method in class org.jmol.util.GenericApplet
- resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- resizeInnerPanelString(String) - Method in class org.jmol.viewer.StatusManager
-
called by file droppers
- resMap - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
- resMap - Variable in class org.jmol.modelsetbio.ProteinStructure
- RESN - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- resno - Static variable in class org.jmol.script.T
- resolution - Variable in class org.jmol.jvxl.readers.Parameters
- resolution - Static variable in class org.jmol.script.T
- resolveDataBase(String, String, String) - Static method in class org.jmol.viewer.JC
- resolveDatabaseFormat(String) - Method in class org.jmol.viewer.Viewer
- resolveEntity(String, String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- Resolver - Class in org.jmol.adapter.smarter
- Resolver() - Constructor for class org.jmol.adapter.smarter.Resolver
- resolverResolver - Variable in class org.jmol.viewer.GlobalSettings
- resource - Variable in class org.jmol.i18n.Resource
- resource - Static variable in class org.jmol.quantum.NMRCalculation
-
NOTE! Do not change this txt file! Instead, edit trunk/Jmol/_documents/nmr_data.xls and then clip its contents to org/jmol/quantum/nmr_data.txt.
- Resource - Class in org.jmol.i18n
- Resource(Object, String) - Constructor for class org.jmol.i18n.Resource
- resourceCount - Variable in class org.jmol.i18n.GT
- resourceMap - Variable in class org.jmol.i18n.Resource
- resourceName - Variable in class org.jmol.quantum.MepCalculation
- resources - Variable in class org.jmol.export._IdtfExporter
- resources - Variable in class org.jmol.i18n.GT
- RESTART - Static variable in class org.jmol.script.ScriptCompiler
- restorativeForceAndAngleRadians(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- restorativeForceAndDistance(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- restorativeForceAndOutOfPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- restorativeForceAndTorsionAngleRadians(V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
- restore - Static variable in class org.jmol.script.T
- restore() - Method in class org.jmol.viewer.Connections
- restore(float, boolean) - Method in class org.jmol.modelset.Orientation
- restore(Viewer, float) - Method in class org.jmol.viewer.Scene
- restoreBonds(String) - Method in class org.jmol.viewer.StateManager
- restoreCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
- restoreCoordinates() - Method in class org.jmol.minimize.Minimizer
- restoreFunction(JmolScriptFunction, Lst<SV>, SV) - Method in class org.jmol.script.ScriptEval
-
note that functions requiring motion cannot be run in JavaScript
- restoreModelOrientation(int) - Method in class org.jmol.viewer.Viewer
- restoreModelRotation(int) - Method in class org.jmol.viewer.Viewer
- restoreOrientation(String, float, boolean) - Method in class org.jmol.viewer.StateManager
- restoreScene(String, float) - Method in class org.jmol.viewer.StateManager
- restoreScriptContext(ScriptContext, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
- restoreSelection(String) - Method in class org.jmol.viewer.StateManager
- restoreTokens() - Method in class org.jmol.script.ScriptContext
- restrict - Static variable in class org.jmol.script.T
- restrictSelected(boolean, boolean) - Method in class org.jmol.script.ScriptEval
- restrictSelected(boolean, boolean) - Method in class org.jmol.viewer.ShapeManager
- restrictToModel(BS, int) - Method in class org.jmol.viewer.Viewer
-
Restrict this bitset to the current model or its initial atom's model.
- RESU - Static variable in class org.jmol.util.ColorEncoder
- resume - Static variable in class org.jmol.script.T
- resumeAnimation() - Method in class org.jmol.viewer.AnimationManager
- resumeButton - Variable in class org.jmol.console.ScriptEditor
- resumeEval() - Method in class org.jmol.thread.JmolThread
- resumeEval(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
- resumeEval(Object) - Method in class org.jmol.script.ScriptEval
-
From dispatchCommands and JmolThread resumeEval.
- resumePausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
- resumePausedExecution() - Method in class org.jmol.script.ScriptEval
- resumeViewer(String) - Method in class org.jmol.script.ScriptEval
- RESV - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ret - Variable in class org.jmol.export.JSExporter
- ret - Variable in class org.jmol.util.BZone
- RET_AXISVECTOR - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_CIF2 - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_COUNT - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_CTRANS - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_CTRVECTOR - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_DRAW - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_FTRANS - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_ID - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_INVARIANT - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_INVCTR - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_LABEL - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_LIST - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_MATRIX - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_PLANE - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_POINT - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_ROTANGLE - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_TIMEREV - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_TYPE - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_UNITTRANS - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_XYZ - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_XYZCANON - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_XYZNORMALIZED - Static variable in class org.jmol.symmetry.SymmetryDesc
- RET_XYZORIGINAL - Static variable in class org.jmol.symmetry.SymmetryDesc
- retain_order - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- retrieveCount - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- returncmd - Static variable in class org.jmol.script.T
- returnToken() - Method in class org.jmol.script.ScriptTokenParser
- returnValue - Variable in class org.jmol.script.ScriptFunction
- reverse - Static variable in class org.jmol.script.T
- reverseAnimation() - Method in class org.jmol.viewer.AnimationManager
- reverseArray(int[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- reverseAtomSets() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- reverseChirality(String) - Method in interface org.jmol.api.SmilesMatcherInterface
- reverseChirality(String) - Method in class org.jmol.smiles.SmilesMatcher
-
Note, this may be incompatible with [$(select(..))] THIS IS NOT DEPENDABLE.
- reversecolor - Static variable in class org.jmol.script.T
- reversed - Variable in class org.jmol.modelsetbio.BioPolymer
- reversed - Variable in class org.jmol.renderbio.BioShapeRenderer
- reverseList(Lst<?>) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
- reverseModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- reverseObject(Object[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- reverseSets(AtomSetObject[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- rewind - Static variable in class org.jmol.script.T
- REWIND - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- rewindAnimation() - Method in class org.jmol.viewer.AnimationManager
- rfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- Rgb16 - Class in org.jmol.util
- Rgb16() - Constructor for class org.jmol.util.Rgb16
- rgb16sE - Variable in class org.jmol.g3d.TriangleRenderer
- rgb16sGouraud - Variable in class org.jmol.g3d.TriangleRenderer
- rgb16sW - Variable in class org.jmol.g3d.TriangleRenderer
- rgb16t1 - Variable in class org.jmol.g3d.TriangleRenderer
- rgb16t2 - Variable in class org.jmol.g3d.TriangleRenderer
- rgbColorModel - Static variable in class org.jmol.awt.Image
- rgbFractionalFromArgb(int) - Method in class org.jmol.export.___Exporter
- rgbFractionalFromColix(short) - Method in class org.jmol.export.___Exporter
- rho - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- rhoMin - Variable in class org.jmol.quantum.NciCalculation
- rhoMolecules - Variable in class org.jmol.quantum.NciCalculation
- rhoParam - Variable in class org.jmol.quantum.NciCalculation
- rhoPlot - Variable in class org.jmol.quantum.NciCalculation
- rhoStar - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- rhoStar - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- rhoStarField - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- rhoStarFieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- rhoStarLabel - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- rI - Variable in class org.jmol.util.ModulationSet
- ribbon - Static variable in class org.jmol.script.T
- ribbon_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_nucleic_acid_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_power_b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_sampling - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_side_chain_helper - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_throw - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_trace_atoms - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbon_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ribbonaspectratio - Static variable in class org.jmol.script.T
- ribbonAspectRatio - Variable in class org.jmol.viewer.GlobalSettings
- ribbonborder - Static variable in class org.jmol.script.T
- ribbonBorder - Variable in class org.jmol.renderbio.BioShapeRenderer
- ribbonBorder - Variable in class org.jmol.viewer.GlobalSettings
- ribbonBottomScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
- ribbonColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- Ribbons - Class in org.jmol.shapebio
- Ribbons() - Constructor for class org.jmol.shapebio.Ribbons
- RibbonsRenderer - Class in org.jmol.renderbio
- RibbonsRenderer() - Constructor for class org.jmol.renderbio.RibbonsRenderer
- ribbonTopScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
- ribbonTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- riboseOffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- right - Variable in class org.jmol.awtjs.swing.Insets
- right - Variable in class org.jmol.awtjs.swing.JSplitPane
- right - Static variable in class org.jmol.script.T
- right - Variable in class org.jmol.util.Modulation
- RIGHT - Static variable in class org.jmol.awtjs.swing.SwingConstants
- RIGHT - Static variable in class org.jmol.viewer.binding.Binding
- RIGHT_HELIX - Enum constant in enum org.jmol.modelsetbio.AlphaPolymer.Code
- RIGHT_TURN - Enum constant in enum org.jmol.modelsetbio.AlphaPolymer.Code
- rightAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- rightbrace - Static variable in class org.jmol.script.T
- rightOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- rightparen - Static variable in class org.jmol.script.T
- rightPlane - Variable in class org.openscience.jmol.app.surfacetool.Slice
- rightsquare - Static variable in class org.jmol.script.T
- ring5OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- ring6OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
- ringConnections - Variable in class org.jmol.smiles.SmilesSearch
- ringConnectivity - Variable in class org.jmol.smiles.SmilesAtom
- ringCount - Variable in class org.jmol.smiles.SmilesSearch
- ringCounts - Variable in class org.jmol.smiles.SmilesSearch
- ringData - Variable in class org.jmol.smiles.SmilesSearch
- ringDataMax - Variable in class org.jmol.smiles.SmilesSearch
- ringMembership - Variable in class org.jmol.smiles.SmilesAtom
- ringSets - Variable in class org.jmol.smiles.SmilesGenerator
- ringSets - Variable in class org.jmol.smiles.SmilesSearch
- ringSize - Variable in class org.jmol.smiles.SmilesAtom
- RL() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- rm - Variable in class org.jmol.viewer.Viewer
- rmaxx - Variable in class org.jmol.adapter.smarter.XtalSymmetry
-
range minima and maxima -- also usedf for cartesians comparisons
- rmaxy - Variable in class org.jmol.adapter.smarter.XtalSymmetry
-
range minima and maxima -- also usedf for cartesians comparisons
- rmaxz - Variable in class org.jmol.adapter.smarter.XtalSymmetry
-
range minima and maxima -- also usedf for cartesians comparisons
- rminx - Variable in class org.jmol.adapter.smarter.XtalSymmetry
-
range minima and maxima -- also usedf for cartesians comparisons
- rminy - Variable in class org.jmol.adapter.smarter.XtalSymmetry
-
range minima and maxima -- also usedf for cartesians comparisons
- rminz - Variable in class org.jmol.adapter.smarter.XtalSymmetry
-
range minima and maxima -- also usedf for cartesians comparisons
- rmsd - Static variable in class org.jmol.script.T
- rna - Static variable in class org.jmol.script.T
- RNA - Enum constant in enum org.jmol.c.STR
- RNA_MASK - Static variable in class org.jmol.viewer.JC
- rna3d - Static variable in class org.jmol.script.T
- rnl - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- robust_logs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- rock - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- rock - Static variable in class org.jmol.script.T
- rock_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- rocket - Static variable in class org.jmol.script.T
- rocketbarrels - Static variable in class org.jmol.script.T
- rocketBarrels - Variable in class org.jmol.viewer.GlobalSettings
- RocketRenderer - Class in org.jmol.renderbio
- RocketRenderer() - Constructor for class org.jmol.renderbio.RocketRenderer
- Rockets - Class in org.jmol.shapebio
- Rockets() - Constructor for class org.jmol.shapebio.Rockets
- RocketsRenderer - Class in org.jmol.renderbio
- RocketsRenderer() - Constructor for class org.jmol.renderbio.RocketsRenderer
- ROLES - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- root - Variable in class org.jmol.symmetry.CIPChirality
-
The atom for which we are determining the stereochemistry
- ROOT2 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
- ROOT3 - Static variable in class org.jmol.adapter.readers.quantum.JaguarReader
- ROOT3 - Static variable in class org.jmol.quantum.MOCalculation
- rootDistance - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Rule 1b measure: Distance from root of the corresponding nonduplicated atom (duplicate nodes only).
- rootPickingStyle - Variable in class org.jmol.viewer.ActionManager
- rootSubstituent - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
sphere-1 node in this atom's root branch
- rot - Variable in class org.jmol.render.SticksRenderer
- rotate - Static variable in class org.jmol.script.T
- rotate() - Method in class org.jmol.quantum.NMRNoeMatrix
- ROTATE_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- ROTATE_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- rotate3DBall(float, float, BS) - Method in class org.jmol.viewer.TransformManager
- rotate45 - Static variable in class org.jmol.script.T
- rotate4DBall(float, float, float) - Method in class org.jmol.viewer.TransformManager4D
- rotateAboutPointsInternal(JmolScriptEvaluator, P3, P3, float, float, boolean, BS, V3, Lst<P3>, float[], M4) - Method in class org.jmol.viewer.Viewer
- rotateAboutPointsInternal(JmolScriptEvaluator, T3, T3, float, float, boolean, boolean, BS, boolean, V3, Lst<P3>, float[], M4) - Method in class org.jmol.viewer.TransformManager
- RotateAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.RotateAction
- rotateAxes(int, V3[], P3, M3) - Method in interface org.jmol.api.SymmetryInterface
- rotateAxes(int, V3[], P3, M3) - Method in class org.jmol.symmetry.Symmetry
- rotateAxes(V3[], UnitCell, P3, M3) - Method in class org.jmol.symmetry.SymmetryOperation
- rotateAxisAngle(V3, float) - Method in class org.jmol.viewer.TransformManager
- rotateAxisAngle2(A4, BS) - Method in class org.jmol.viewer.TransformManager
- rotateAxisAngleAtCenter(JmolScriptEvaluator, P3, V3, float, float, boolean, BS) - Method in class org.jmol.viewer.TransformManager
- rotateAxisAngleAtCenter(JmolScriptEvaluator, P3, V3, float, float, boolean, BS) - Method in class org.jmol.viewer.Viewer
- rotateAxisAngleRadiansFixed(float, BS) - Method in class org.jmol.viewer.TransformManager
- rotateAxisAngleRadiansInternal(float, BS, M4) - Method in class org.jmol.viewer.TransformManager
- rotateFront() - Method in class org.jmol.api.JmolViewer
- rotateFront() - Method in class org.jmol.viewer.Viewer
- rotateHexCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- rotatePoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
- rotateSelected - Static variable in class org.jmol.script.T
- rotateSelected(float, float, BS) - Method in class org.jmol.viewer.Viewer
- rotateTranslate(Quat, T3, boolean) - Method in class org.jmol.shape.Mesh
- rotateXRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
- rotateXYBy(float, float) - Method in class org.jmol.viewer.Viewer
- rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager
- rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager4D
- rotateYRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
- rotateZBy(int, int, int) - Method in class org.jmol.viewer.TransformManager
- rotateZBy(int, int, int) - Method in class org.jmol.viewer.Viewer
- rotateZRadians(float) - Method in class org.jmol.viewer.TransformManager
- rotation - Static variable in class org.jmol.script.T
- rotation - Variable in class org.jmol.symmetry.HallRotationTerm
- rotationAxis - Variable in class org.jmol.shapesurface.LcaoCartoon
- rotationAxis - Variable in class org.jmol.viewer.TransformManager
- rotationCenterDefault - Variable in class org.jmol.viewer.TransformManager
- rotationDeg - Variable in class org.jmol.modelkit.ModelKit
- rotationMatrix - Variable in class org.jmol.modelset.Orientation
- rotationOrder - Variable in class org.jmol.symmetry.HallTranslation
- rotationradius - Static variable in class org.jmol.script.T
- rotationRadius - Variable in class org.jmol.modelset.Orientation
- rotationRadius - Variable in class org.jmol.thread.MoveToThread
- rotationRadiusDefault - Variable in class org.jmol.viewer.TransformManager
- rotationRate - Variable in class org.jmol.viewer.TransformManager
- rotationShift12ths - Variable in class org.jmol.symmetry.HallTranslation
- rotationTerms - Variable in class org.jmol.symmetry.HallInfo
- rotCode - Variable in class org.jmol.symmetry.HallRotation
- rotTransCart(SymmetryOperation, SymmetryInterface, P3, V3) - Static method in class org.jmol.symmetry.SymmetryDesc
- round() - Method in class org.openscience.jmol.app.janocchio.Measure
- round(double) - Static method in class org.jmol.export.___Exporter
- round(T3) - Static method in class org.jmol.export.___Exporter
- roundInt(int) - Static method in class org.jmol.util.GData
-
JavaScript won't really have an integer here after integer division.
- route - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- roving_byres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_cartoon - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_detail - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_isomesh - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_isosurface - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_labels - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_lines - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_map1_level - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_map1_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_map2_level - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_map2_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_map3_level - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_map3_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_nb_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_nonbonded - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_origin - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_origin_z - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_origin_z_cushion - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_polar_contacts - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_polar_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_ribbon - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- roving_sticks - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- row - Static variable in class org.jmol.script.T
- Row(int) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter.Row
- rowSelectionAllowed - Variable in class org.jmol.awtjs.swing.JTable
- rowspan - Variable in class org.jmol.awtjs.swing.Cell
- ROYGB - Static variable in class org.jmol.util.ColorEncoder
- rpower - Static variable in class org.jmol.quantum.NciCalculation
- rPt - Variable in class org.jmol.renderbio.NucleicRenderer
- rPt5 - Variable in class org.jmol.renderbio.NucleicRenderer
- rr - Variable in class org.jmol.renderbio.RocketRenderer
- rr - Variable in class org.jmol.renderbio.RocketsRenderer
- rs - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
atom radius + solvent radius
- rs2 - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
square of (atom radius + solvent radius)
- rScr - Variable in class org.jmol.renderbio.NucleicRenderer
- rScr5 - Variable in class org.jmol.renderbio.NucleicRenderer
- rsvs - Variable in class org.jmol.symmetry.SymmetryOperation
-
rsvs is the superspace group rotation-translation matrix.
- rsvs - Variable in class org.jmol.util.ModulationSet
-
the matrix representation for this atom's symmetry operation
- rubberband - Static variable in class org.jmol.script.T
- rubberbandSelectionMode - Variable in class org.jmol.viewer.ActionManager
- rule - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- RULE_1a - Static variable in class org.jmol.symmetry.CIPChirality
- RULE_1b - Static variable in class org.jmol.symmetry.CIPChirality
- RULE_2 - Static variable in class org.jmol.symmetry.CIPChirality
- RULE_2_nXX_EQ_XX - Static variable in class org.jmol.symmetry.CIPChirality
-
These elements have 100% natural abundance; we will use their isotope mass number instead of their actual average mass, since there is no difference
- RULE_2_REDUCE_ISOTOPE_MASS_NUMBER - Static variable in class org.jmol.symmetry.CIPChirality
-
These elements have an isotope number that is a bit higher than the average mass, even though their actual isotope mass is a bit lower.
- RULE_3 - Static variable in class org.jmol.symmetry.CIPChirality
- RULE_4a - Static variable in class org.jmol.symmetry.CIPChirality
- RULE_4b - Static variable in class org.jmol.symmetry.CIPChirality
- RULE_4c - Static variable in class org.jmol.symmetry.CIPChirality
- RULE_5 - Static variable in class org.jmol.symmetry.CIPChirality
- RULE_6 - Static variable in class org.jmol.symmetry.CIPChirality
- rule4Ref - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Rule 4b reference chirality (R or S, 1 or 2); root only
- rule4Type - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
the auxiiary chirality type: 0: ~, 1: R, 2: S; normalized to R/S even if M/P or C/T
- rule6refIndex - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
reference index for Rule 6 -- root atom only
- ruleNames - Static variable in class org.jmol.symmetry.CIPChirality
- ruleNames - Static variable in class org.jmol.viewer.JC
- run() - Method in class org.jmol.io.DOMReader
- run() - Method in class org.jmol.io.FileReader
- run() - Method in class org.jmol.io.FilesReader
- run() - Method in class org.jmol.script.CommandWatcherThread
- run() - Method in class org.jmol.script.ScriptProcessRunnable
- run() - Method in class org.jmol.thread.JmolThread
- run() - Method in class org.openscience.jmol.app.InputScannerThread
- run() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- run() - Method in class org.openscience.jmol.app.janocchio.NmrReaderThread
- run() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- run() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ExecuteCommandThread
- run() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
- run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioClientThread
- run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
- run1(int) - Method in class org.jmol.minimize.MinimizationThread
- run1(int) - Method in class org.jmol.navigate.Navigator
- run1(int) - Method in class org.jmol.script.CommandWatcherThread
- run1(int) - Method in class org.jmol.script.FileLoadThread
- run1(int) - Method in class org.jmol.script.ScriptDelayThread
- run1(int) - Method in class org.jmol.script.ScriptQueueThread
- run1(int) - Method in class org.jmol.thread.AnimationThread
- run1(int) - Method in class org.jmol.thread.HoverWatcherThread
- run1(int) - Method in class org.jmol.thread.JmolThread
- run1(int) - Method in class org.jmol.thread.MoveToThread
- run1(int) - Method in class org.jmol.thread.SpinThread
-
Java: run1(INIT) while(!interrupted()) { run1(MAIN) } run1(FINISH) JavaScript: run1(INIT) run1(MAIN) --> setTimeout to run1(CHECK) or run1(FINISH) and return run1(CHECK) --> setTimeout to run1(CHECK) or run1(MAIN) or run1(FINISH) and return
- run1(int) - Method in class org.jmol.thread.TimeoutThread
- run1(int) - Method in class org.jmol.thread.VibrationThread
- run1Move(int) - Method in class org.jmol.thread.MoveToThread
- run1MoveTo(int) - Method in class org.jmol.thread.MoveToThread
- runAllProcesses(Viewer) - Method in interface org.jmol.api.JmolParallelProcessor
- runAllProcesses(Viewer) - Method in class org.jmol.script.ScriptParallelProcessor
- runBufferedSafely(String, SB) - Method in class org.jmol.script.ScriptEval
- runButton - Variable in class org.jmol.console.GenericConsole
- runButton - Variable in class org.jmol.console.ScriptEditor
- runCheckBoxScript(SC, String, boolean) - Method in class org.jmol.popup.GenericPopup
- runFunctionAndRet(JmolScriptFunction, String, Lst<SV>, SV, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
- runNextScript() - Method in class org.jmol.script.ScriptQueueThread
- runPovCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- runProcess(ScriptProcess, ShapeManager) - Method in class org.jmol.script.ScriptParallelProcessor
- runScript(String) - Method in interface org.jmol.api.JmolScriptEvaluator
- runScript(String) - Method in class org.jmol.api.JmolViewer
-
starting with 14.8.2-beta-2017-02-06, uses script(xxxx) function; see runScriptCautiously for the older version
- runScript(String) - Method in interface org.jmol.api.JSVInterface
- runScript(String) - Method in class org.jmol.script.ScriptEval
- runScript(String) - Method in class org.jmol.viewer.ActionManager
- runScript(String) - Method in class org.jmol.viewer.Viewer
-
Run a script using the script function script("xxxxxx") using direct script tokens for script ( "xxxxxxx" )
- runScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
-
no queuing here -- called by MainFrame
- runScript(String, boolean, JmolViewer) - Method in class org.openscience.jmol.app.JmolApp
- runScriptBuffer(String, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
- runScriptBuffer(String, SB, boolean) - Method in class org.jmol.script.ScriptEval
-
runs a script immediately and sends selected output to a provided SB
- runScriptBuffered(String) - Method in class org.jmol.modelkit.ModelKit
- runScriptCautiously(String) - Method in class org.jmol.api.JmolViewer
-
Formerly runScript(script).
- runScriptCautiously(String) - Method in class org.jmol.viewer.Viewer
-
formerly runScript(), this method really can ONLY be called by the viewer being run from an already-running script.
- runScriptNow() - Method in class org.jmol.script.ScriptManager
- runScriptWithCallback(Thread, String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- runSleep(int, int) - Method in class org.jmol.thread.JmolThread
- runStatus - Static variable in class org.openscience.jmol.app.webexport.WebExport
- runUserAction(String, Object[], Viewer) - Static method in class org.jmol.script.ScriptEval
- RWB - Static variable in class org.jmol.util.ColorEncoder
S
- S - Static variable in class org.jmol.quantum.QS
- s0 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- s0f - Variable in class org.jmol.renderspecial.DrawRenderer
- s1 - Variable in class org.jmol.render.FontLineShapeRenderer
- s1 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- s10 - Static variable in class org.jmol.symmetry.PointGroup
- s12 - Static variable in class org.jmol.symmetry.PointGroup
- s1f - Variable in class org.jmol.renderspecial.DrawRenderer
- s2 - Variable in class org.jmol.render.FontLineShapeRenderer
- s2 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- s2f - Variable in class org.jmol.renderspecial.DrawRenderer
- s3 - Static variable in class org.jmol.symmetry.PointGroup
- s4 - Static variable in class org.jmol.symmetry.PointGroup
- s5 - Static variable in class org.jmol.symmetry.PointGroup
- s6 - Static variable in class org.jmol.symmetry.PointGroup
- s8 - Static variable in class org.jmol.symmetry.PointGroup
- sA - Variable in class org.jmol.g3d.Graphics3D
- safeJSON(String, Object) - Static method in class org.jmol.script.SV
-
Safely create a JSON key - object pair, allowing for already-named arrays
- sameAs(int, int) - Method in class org.jmol.modelset.Measurement
- sameAsIJ(int[], Point3fi[], int, int) - Method in class org.jmol.modelset.Measurement
- sameAsPoints(int[], Point3fi[]) - Method in class org.jmol.modelset.Measurement
- sampleModelBitMasks - Static variable in class org.jmol.awt.Image
- sasurface - Static variable in class org.jmol.script.T
- SAUSAGE - Static variable in class org.jmol.shapecgo.CGOMesh
- save - Static variable in class org.jmol.script.T
- save() - Method in class org.openscience.jmol.app.HistoryFile
-
Saves properties to the history file.
- save() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- save() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- SAVE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- save_pdb_ss - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- saveAmbient - Variable in class org.jmol.g3d.Graphics3D
- saveAs() - Method in class org.jmol.console.ImageDialog
- saveAsButton - Variable in class org.jmol.console.ScriptEditor
- saveBonds(String) - Method in class org.jmol.viewer.StateManager
- saveButton - Variable in class org.jmol.console.ScriptEditor
- saveButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- saveButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
- saveChooser - Static variable in class org.jmol.dialog.Dialog
- saveChooser - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- saveContext(String) - Method in class org.jmol.script.ScriptEval
- saveContext(String, Object) - Method in class org.jmol.viewer.StateManager
- saveCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
- saveCoordinates() - Method in class org.jmol.minimize.Minimizer
- saveCoordinates(String, BS) - Method in class org.jmol.viewer.StateManager
- saved - Static variable in class org.jmol.script.T
- saved - Variable in class org.jmol.viewer.StateManager
- saveDiffuse - Variable in class org.jmol.g3d.Graphics3D
- saveField - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- saveHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Just saves the path settings from this session.
- saveHistory() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- saveHistory() - Static method in class org.openscience.jmol.app.webexport.WebExport
- saveList - Static variable in class org.jmol.script.ScriptEval
- saveList() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
-
Saves the list to the history file.
- saveModelOrientation() - Method in class org.jmol.viewer.Viewer
- saveModelOrientation(int, Orientation) - Method in class org.jmol.modelset.ModelSet
- saveName - Variable in class org.jmol.modelset.Orientation
- saveName - Variable in class org.jmol.viewer.Connections
- saveName - Variable in class org.jmol.viewer.Scene
- saveNamfisChooser - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- saveNmrAction - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- SaveNmrAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.SaveNmrAction
- saveNmrChooser - Variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- saveOrientation(String, float[]) - Method in class org.jmol.viewer.StateManager
- savePathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- saveProperties(Properties) - Method in interface org.jmol.api.JSVInterface
- saveProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- saveproteinstructurestate - Static variable in class org.jmol.script.T
- saveProteinStructureState - Variable in class org.jmol.viewer.GlobalSettings
- saveRestorePriorities(boolean) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Reset priorities after each Rule 6 test.
- saveScene(String, Map<String, Object>) - Method in class org.jmol.viewer.StateManager
- saveSelection(String, BS) - Method in class org.jmol.viewer.StateManager
- saveState(String) - Method in class org.jmol.viewer.StateManager
- saveStructure(String) - Method in class org.jmol.viewer.StateManager
- saveTokens(T[][]) - Method in class org.jmol.script.ScriptContext
-
save pointers indicating state of if/then
- saveVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
- saveWindowSizes() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- saveWindowSizes() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- saveXYZCollection() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Saves the currently active collection as a multistep XYZ file.
- saveZip(boolean) - Method in class org.jmol.console.ScriptEditor
- say(String) - Method in class org.openscience.jmol.app.InputScannerThread
- say(String) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- say(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- sb - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- sB - Variable in class org.jmol.g3d.Graphics3D
- sbCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- sbConect - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- sbIgnored - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- sbKey - Variable in class org.jmol.minimize.MinAngle
- sbMap - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- sbmb - Variable in class org.jmol.minimize.forcefield.AtomType
-
MMFF special bond types 2, 3, 4, 9, 30, 37, 39, 54, 57, 58, 63, 64, 67, 75, 78, 80, 81 for which a=b-c=d bc bond should be considered single, not double
- sbOut - Variable in class org.jmol.jvxl.data.JvxlData
- sbOut - Variable in class org.jmol.jvxl.readers.Parameters
- sbSelected - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- sbTemp - Variable in class org.jmol.export._IdtfExporter
- sbTlsErrors - Variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
- sbTlsErrors - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- sbType - Variable in class org.jmol.minimize.MinAngle
- sc - Variable in class org.jmol.thread.JmolThread
- sC - Variable in class org.jmol.g3d.Graphics3D
- SC - Interface in org.jmol.api
-
SwingComponent interface common to javax.swing and org.jmol.awtjs.swing Can be augmented as needed, provided classes of org.jmol.awtjs.swing are also updated.
- scalarDictRef - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- scalarDictValue - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- scalarTitle - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- scale - Variable in class org.jmol.adapter.readers.simple.JSONReader
- scale - Variable in class org.jmol.jvxl.readers.Parameters
- scale - Variable in class org.jmol.modelset.TickInfo
- scale - Static variable in class org.jmol.script.T
- scale - Variable in class org.jmol.shape.Axes
- scale - Variable in class org.jmol.shapespecial.DrawMesh
- scale - Variable in class org.jmol.shapespecial.Ellipsoid
- scale - Variable in class org.jmol.shapespecial.Ellipsoids
- scale - Variable in class org.jmol.shapespecial.Polyhedron
- scale - Variable in class org.jmol.symmetry.PointGroup
- scale - Variable in class org.jmol.util.ModulationSet
-
an adjustable scaling factor, as for vibrations
- scale(int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- scale(Mesh, float) - Method in class org.jmol.shapecgo.CGO
- scale(Mesh, float) - Method in class org.jmol.shapespecial.Draw
- SCALE_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Maximum value for vector scale.
- SCALE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Precision of the vector scale slider
- SCALE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Initial value of vector scale.
- scale3d - Variable in class org.jmol.jvxl.data.JvxlData
- scale3d - Variable in class org.jmol.jvxl.readers.Parameters
- scale3d - Static variable in class org.jmol.script.T
- scale3d - Variable in class org.jmol.shape.Mesh
- scale3d - Variable in class org.jmol.shapesurface.Isosurface
- scale3D - Variable in class org.jmol.viewer.TransformManager
- scale3DAngstromsPerInch - Variable in class org.jmol.viewer.TransformManager
- scaleangstromsperinch - Static variable in class org.jmol.script.T
- scaleAxes(float[]) - Method in class org.jmol.shapespecial.Ellipsoid
- scaleBox(P3[], float) - Static method in class org.jmol.util.BoxInfo
- scaleDefaultPixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
- scaleFac - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- scaleFitToScreen(boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
- scaleFractionalVibs() - Method in class org.jmol.adapter.smarter.XtalSymmetry
-
magCIF files have moments expressed as Bohr magnetons along the cryrstallographic axes.
- scaleIsosurface(float) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- scaleObject - Variable in class org.jmol.shape.Echo
- scalePixelsPerAngstrom - Variable in class org.jmol.export.___Exporter
- scalePixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
- scalePixelsPerMicron - Variable in class org.jmol.modelset.Text
- scalePixelsPerMicron - Variable in class org.jmol.render.LabelsRenderer
- scalePixelsPerMicron - Variable in class org.jmol.render.MeshRenderer
- scalePixelsPerMicron - Variable in class org.jmol.shape.Labels
- scalePolyhedra(float) - Method in class org.jmol.shapespecial.Polyhedra
- scalePrimitiveData(int, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
- scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
Perform implementation-specific scaling.
- scaleSlaters - Variable in class org.jmol.adapter.readers.quantum.SlaterReader
- scaleSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- scaleText - Variable in class org.jmol.viewer.ShapeManager
- scaleToPerspective(int, float) - Method in class org.jmol.viewer.TransformManager
- scaleToScreen(int, int) - Method in class org.jmol.modelset.Group
- scaleToScreen(int, int) - Method in class org.jmol.viewer.TransformManager
- scaleVectorsToMax(float) - Method in class org.jmol.modelset.AtomCollection
-
Scales vibrations and associated vectors such that the maximum length is the given value
- scaleVibration(float) - Method in interface org.jmol.api.JmolModulationSet
- scaleVibration(float) - Method in class org.jmol.util.ModulationSet
- scaleX - Variable in class org.jmol.rendercgo.CGORenderer
-
UV mapping min/max x and y
- scaleXYZ - Variable in class org.jmol.shapespecial.Ellipsoid
- scaleY - Variable in class org.jmol.rendercgo.CGORenderer
-
UV mapping min/max x and y
- scaling - Variable in class org.jmol.shape.Frank
- scan() - Method in class org.openscience.jmol.app.InputScannerThread
- scanForOffsets(int, int[], byte[]) - Static method in class org.jmol.modelsetbio.Monomer
- scanInput - Variable in class org.openscience.jmol.app.JmolApp
- scanner - Variable in class org.openscience.jmol.app.InputScannerThread
- scanPoint - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
The scan point, where -1 denotes no scan information.
- scanTo(int, String) - Static method in class org.jmol.symmetry.SpaceGroupFinder
- scene - Static variable in class org.jmol.script.T
- scene - Variable in class org.jmol.viewer.Scene
- Scene - Class in org.jmol.viewer
- Scene(Map<String, Object>) - Constructor for class org.jmol.viewer.Scene
- scene_animation - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- scene_animation_duration - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- scene_buttons - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- scene_buttons_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- scene_current_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- scene_frame_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- scene_loop - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- scene_restart_movie_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SCENE_TAG - Static variable in class org.jmol.viewer.OutputManager
- sceneOrder - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- scenes_changed - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- schemes - Variable in class org.jmol.util.ColorEncoder
- scm - Variable in class org.jmol.viewer.Viewer
- score - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- score - Variable in class org.jmol.util.ContactPair
- scrBox - Variable in class org.jmol.renderbio.NucleicRenderer
- scrCoords - Variable in class org.jmol.renderspecial.DotsRenderer
- screen - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- screen - Variable in class org.jmol.render.LabelsRenderer
- SCREEN - Enum constant in enum org.jmol.atomdata.RadiusData.EnumType
- screenA - Variable in class org.jmol.renderbio.RocketRenderer
- screenArrowBot - Variable in class org.jmol.renderbio.BioShapeRenderer
- screenArrowBotPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
- screenArrowHead - Variable in class org.jmol.renderspecial.VectorsRenderer
- screenArrowTop - Variable in class org.jmol.renderbio.BioShapeRenderer
- screenArrowTopPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
- screenB - Variable in class org.jmol.renderbio.RocketRenderer
- screenC - Variable in class org.jmol.renderbio.RocketRenderer
- screenCorners - Variable in class org.jmol.renderbio.RocketRenderer
- screenDotCount - Variable in class org.jmol.renderspecial.DotsRenderer
- screenHeight - Variable in class org.jmol.export.___Exporter
- screenHeight - Variable in class org.jmol.viewer.TransformManager
- screenHeight - Variable in class org.jmol.viewer.Viewer
- screenLevel - Variable in class org.jmol.renderspecial.DotsRenderer
- screenPixelCount - Variable in class org.jmol.viewer.TransformManager
- screens - Variable in class org.jmol.render.MeshRenderer
- screens - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- screens3f - Variable in class org.jmol.renderspecial.DipolesRenderer
- screens3f - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- screenSize - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- screenVectorEnd - Variable in class org.jmol.renderspecial.VectorsRenderer
- screenVectorStart - Variable in class org.jmol.renderspecial.VectorsRenderer
- screenWidth - Variable in class org.jmol.export.___Exporter
- screenWidth - Variable in class org.jmol.viewer.TransformManager
- screenWidth - Variable in class org.jmol.viewer.Viewer
- screenx - Static variable in class org.jmol.script.T
- screenXY - Variable in class org.jmol.modelkit.ModelKit
- screenxyz - Static variable in class org.jmol.script.T
- screeny - Static variable in class org.jmol.script.T
- screenz - Static variable in class org.jmol.script.T
- screenZ - Variable in class org.jmol.rendercgo.CGORenderer
- script - Variable in class org.jmol.jvxl.readers.Parameters
- script - Variable in class org.jmol.modelset.Text
- script - Variable in class org.jmol.script.ScriptContext
- script - Variable in class org.jmol.script.ScriptEval
- script - Variable in class org.jmol.script.ScriptFunction
- script - Variable in class org.jmol.script.ScriptTokenParser
- script - Static variable in class org.jmol.script.T
- script - Variable in class org.jmol.shapesurface.Isosurface
- script - Variable in class org.jmol.thread.TimeoutThread
- script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
- script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
- script - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- script(String) - Method in interface org.jmol.api.JmolAppletInterface
- script(String) - Method in class org.jmol.api.JmolViewer
- script(String) - Method in class org.jmol.util.GenericApplet
- script(String) - Method in class org.jmol.viewer.Viewer
- script(String) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- SCRIPT - Enum constant in enum org.jmol.c.CBK
- SCRIPT_CHECK - Static variable in class org.jmol.util.GenericApplet
- SCRIPT_COMPLETED - Static variable in class org.jmol.viewer.JC
- SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JC
- SCRIPT_EXT - Static variable in class org.jmol.viewer.JC
- SCRIPT_GUI - Static variable in class org.jmol.viewer.JC
- SCRIPT_ISEDITOR - Static variable in class org.jmol.viewer.JC
- SCRIPT_NOENDCHECK - Static variable in class org.jmol.viewer.JC
- SCRIPT_NOWAIT - Static variable in class org.jmol.util.GenericApplet
- SCRIPT_ONLY - Static variable in interface org.jmol.api.JmolScriptManager
- SCRIPT_START - Static variable in class org.jmol.viewer.JC
- SCRIPT_STEP - Static variable in class org.jmol.viewer.JC
- SCRIPT_WAIT - Static variable in class org.jmol.util.GenericApplet
- SCRIPT_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- script1 - Variable in class org.jmol.modelset.StateScript
- script1 - Variable in class org.openscience.jmol.app.JmolApp
- script2 - Variable in class org.jmol.modelset.StateScript
- script2 - Variable in class org.openscience.jmol.app.JmolApp
- scriptAppendix - Variable in class org.jmol.shapesurface.Isosurface
- scriptButtonPercent - Static variable in class org.openscience.jmol.app.webexport.WebExport
- ScriptButtons - Class in org.openscience.jmol.app.webexport
- ScriptButtons(Viewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.ScriptButtons
- scriptCheck(String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptCheck(String) - Method in class org.jmol.api.JmolViewer
- scriptCheck(String) - Method in class org.jmol.util.GenericApplet
- scriptCheck(String) - Method in class org.jmol.viewer.Viewer
- scriptCheckRet(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
- scriptCheckRet(String, boolean) - Method in class org.jmol.script.ScriptManager
- scriptCheckRet(String, boolean) - Method in class org.jmol.viewer.Viewer
- scriptCommand - Static variable in class org.jmol.script.T
- scriptCommand - Variable in class org.jmol.shape.Mesh
- ScriptCompiler - Class in org.jmol.script
- ScriptCompiler(Viewer) - Constructor for class org.jmol.script.ScriptCompiler
- scriptCompleted(StatusManager, String, String) - Method in class org.jmol.viewer.ChimeMessenger
-
called when a script exits.
- scriptCompleted(StatusManager, String, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
- ScriptContext - Class in org.jmol.script
- ScriptContext() - Constructor for class org.jmol.script.ScriptContext
- scriptDelay - Variable in class org.jmol.viewer.GlobalSettings
- scriptDelayThread - Variable in class org.jmol.script.ScriptEval
- ScriptDelayThread - Class in org.jmol.script
- ScriptDelayThread(JmolScriptEvaluator, Viewer, int) - Constructor for class org.jmol.script.ScriptDelayThread
- scriptEcho(String) - Method in class org.jmol.viewer.Viewer
- scriptEditor - Variable in class org.jmol.console.JmolConsole
- scriptEditor - Variable in class org.jmol.viewer.Viewer
- ScriptEditor - Class in org.jmol.console
- ScriptEditor() - Constructor for class org.jmol.console.ScriptEditor
- ScriptEditor(Viewer, JFrame, JmolConsole) - Constructor for class org.jmol.console.ScriptEditor
- ScriptEditor.EditorDocument - Class in org.jmol.console
- ScriptEditor.EditorDocument.MyUndoableEditListener - Class in org.jmol.console
- ScriptEditor.EditorTextPane - Class in org.jmol.console
- ScriptEditorAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
- scriptEditorVisible - Variable in class org.jmol.viewer.Viewer
- ScriptError - Class in org.jmol.script
-
Error handling for ScriptEvaluator, ScriptProcess, and ScriptParams
- ScriptError() - Constructor for class org.jmol.script.ScriptError
- ScriptEval - Class in org.jmol.script
- ScriptEval() - Constructor for class org.jmol.script.ScriptEval
- ScriptException - Exception in org.jmol.script
- ScriptException(ScriptError, String, String, boolean) - Constructor for exception org.jmol.script.ScriptException
- ScriptExpr - Class in org.jmol.script
-
The ScriptExpr class holds the main functions for processing mathematical and atom selection expressions.
- ScriptExpr() - Constructor for class org.jmol.script.ScriptExpr
- ScriptExt - Class in org.jmol.scriptext
- ScriptExt() - Constructor for class org.jmol.scriptext.ScriptExt
- scriptExtensions - Variable in class org.jmol.script.ScriptCompiler
- scriptExtensions - Variable in class org.jmol.script.ScriptContext
- scriptExtensions - Variable in class org.jmol.script.ScriptEval
- scriptFilename - Variable in class org.openscience.jmol.app.JmolApp
- scriptFileName - Variable in class org.jmol.script.ScriptContext
- scriptFileName - Variable in class org.jmol.script.ScriptEval
- scriptFilePrefixes - Static variable in class org.jmol.viewer.FileManager
- ScriptFlowContext - Class in org.jmol.script
- ScriptFlowContext(ScriptCompiler, ContextToken, int, ScriptFlowContext, int, short) - Constructor for class org.jmol.script.ScriptFlowContext
- ScriptFunction - Class in org.jmol.script
- ScriptFunction() - Constructor for class org.jmol.script.ScriptFunction
- ScriptFunction(String, int) - Constructor for class org.jmol.script.ScriptFunction
- scriptIndex - Variable in class org.jmol.script.ScriptManager
- ScriptInterruption - Exception in org.jmol.script
- ScriptInterruption(ScriptEval, String, int) - Constructor for exception org.jmol.script.ScriptInterruption
- scriptLevel - Variable in class org.jmol.script.ScriptContext
- scriptLevel - Variable in class org.jmol.script.ScriptEval
- scriptManager - Variable in class org.jmol.script.CommandWatcherThread
- scriptManager - Variable in class org.jmol.script.ScriptQueueThread
- ScriptManager - Class in org.jmol.script
- ScriptManager() - Constructor for class org.jmol.script.ScriptManager
- ScriptMathProcessor - Class in org.jmol.script
-
Reverse Polish Notation Engine for IF, SET, and @{...} Just a (not so simple?) RPN processor that can handle boolean, int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f -- Bob Hanson 2/16/2007
- ScriptMathProcessor(ScriptExpr, boolean, boolean, boolean, boolean, boolean, String) - Constructor for class org.jmol.script.ScriptMathProcessor
- scriptNoWait(String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptNoWait(String) - Method in class org.jmol.util.GenericApplet
- ScriptParallelProcessor - Class in org.jmol.script
- ScriptParallelProcessor() - Constructor for class org.jmol.script.ScriptParallelProcessor
-
parallel operations
- ScriptParam - Class in org.jmol.script
-
The ScriptParam class holds methods used to parse parameters in Jmol scripts.
- ScriptParam() - Constructor for class org.jmol.script.ScriptParam
- ScriptProcess - Class in org.jmol.script
-
the idea here is that the process { ...
- ScriptProcess(String, ScriptContext) - Constructor for class org.jmol.script.ScriptProcess
- scriptProcessor(String, String, int) - Method in class org.jmol.util.GenericApplet
- ScriptProcessRunnable - Class in org.jmol.script
- ScriptProcessRunnable(ScriptParallelProcessor, ScriptProcess, Object, ShapeManager) - Constructor for class org.jmol.script.ScriptProcessRunnable
- scriptqueue - Static variable in class org.jmol.script.T
- scriptQueue - Variable in class org.jmol.script.ScriptManager
- scriptQueueRunning - Variable in class org.jmol.script.ScriptManager
- ScriptQueueThread - Class in org.jmol.script
- ScriptQueueThread(ScriptManager, Viewer, boolean, int) - Constructor for class org.jmol.script.ScriptQueueThread
- scriptreportinglevel - Static variable in class org.jmol.script.T
- scriptReportingLevel - Static variable in class org.jmol.script.ScriptEval
- scriptStatus(String) - Method in class org.jmol.viewer.Viewer
-
scriptCallback is the primary way to monitor script status.
- scriptStatusMsg(String, String) - Method in class org.jmol.viewer.Viewer
- ScriptTokenParser - Class in org.jmol.script
-
An abstract class subclassed by ScriptCompiler taking care of the second phase of syntax checking.
- ScriptTokenParser() - Constructor for class org.jmol.script.ScriptTokenParser
- scriptWait(String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptWait(String) - Method in class org.jmol.api.JmolViewer
- scriptWait(String) - Method in class org.jmol.util.GenericApplet
- scriptWait(String) - Method in class org.jmol.viewer.Viewer
- scriptWait(String, String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptWait(String, String) - Method in class org.jmol.util.GenericApplet
- scriptWaitOutput(String) - Method in interface org.jmol.api.JmolAppletInterface
- scriptWaitOutput(String) - Method in class org.jmol.util.GenericApplet
- scriptWaitStatus(String, String) - Method in class org.jmol.api.JmolViewer
- scriptWaitStatus(String, String) - Method in class org.jmol.viewer.Viewer
- ScriptWindowAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
- scrTemp - Variable in class org.jmol.renderspecial.DotsRenderer
- scrVib - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- sculpt_angl_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_auto_center - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_avd_excl - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_avd_gap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_avd_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_avd_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_bond_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_field_mask - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_hb_overlap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_hb_overlap_base - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_line_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_max_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_max_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_max_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_max_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_memory - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_min_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_min_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_min_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_min_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_nb_interval - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_plan_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_pyra_inv_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_pyra_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_tors_tolerance - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_tors_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_tri_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_tri_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_tri_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_tri_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_tri_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_vdw_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_vdw_scale14 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_vdw_vis_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_vdw_vis_mid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_vdw_vis_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_vdw_vis_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_vdw_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpt_vdw_weight14 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sculpting_cycles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sD - Variable in class org.jmol.util.Point3fi
-
screen diameter
- SDIM - Static variable in class org.jmol.util.Shader
- sdof_drag_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- search - Static variable in class org.jmol.script.T
- search - Variable in class org.jmol.smiles.SmilesMeasure
- search - Variable in class org.jmol.smiles.SmilesStereo
- search() - Method in class org.jmol.smiles.SmilesSearch
-
the start of the search.
- search2(boolean) - Method in class org.jmol.smiles.SmilesSearch
- searchForTurns(AlphaPolymer.Code[], float[], STR[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
- secondary_structure - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- secondAtomIndex - Variable in class org.jmol.modelkit.ModelKit
- secondCharOnly - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
- seconds - Variable in class org.jmol.script.ScriptDelayThread
- security - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seed - Variable in class org.jmol.util.Shader
- SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
- SEESAW - Static variable in class org.jmol.smiles.SmilesStereo
- SEGI - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- segments - Variable in class org.jmol.modelsetbio.ProteinStructure
- seitzMatrix - Variable in class org.jmol.symmetry.HallRotation
- seitzMatrix12ths - Variable in class org.jmol.symmetry.HallRotationTerm
- seitzMatrixInv - Variable in class org.jmol.symmetry.HallRotation
- sel_counter - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- select - Static variable in class org.jmol.script.T
- select - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- select(BS, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
- select(BS, int, boolean) - Method in class org.jmol.viewer.SelectionManager
- SELECT - Enum constant in enum org.jmol.c.CBK
- selectAll() - Method in class org.jmol.api.JmolViewer
- selectAll() - Method in class org.jmol.viewer.Viewer
- selectAll(boolean) - Method in class org.jmol.viewer.SelectionManager
- SelectallAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_DisplayPanel.SelectallAction
- selectAllAtoms(Lst<Object>, int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Collect all the atoms specified by an object state into a bit set.
- selectallmodels - Static variable in class org.jmol.script.T
- selectAllModels - Variable in class org.jmol.viewer.GlobalSettings
- selectAtoms(String) - Method in class org.jmol.viewer.ActionManager
- selectBonds(BS) - Method in class org.jmol.viewer.Viewer
- selectDisplayed(BS) - Method in class org.jmol.modelset.Trajectory
-
Remove trajectories that are not currently displayed from the visible frames bitset.
- selected - Variable in class org.jmol.awtjs.swing.AbstractButton
- selected - Static variable in class org.jmol.script.T
- selected - Variable in class org.jmol.smiles.SmilesAtom
- selectedAtomCount - Variable in class org.jmol.smiles.SmilesSearch
- selectedAtomIndex - Variable in class org.openscience.jmol.app.janocchio.LabelSetter
- selectedAtoms - Variable in class org.jmol.shapespecial.Ellipsoids
- selectedBonds - Variable in class org.jmol.shape.Sticks
- selectedCoupleRow - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- selectedFileName - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- selectedfloat - Static variable in class org.jmol.script.T
- selectedGroupCount - Variable in class org.jmol.modelset.Chain
-
Calculated just prior to coloring by group so that the range is appropriate for each chain.
- selectedIndex - Variable in class org.jmol.awtjs.swing.JComboBox
- selectedIndex - Variable in class org.jmol.modelset.Group
-
for coloring by group
- selectedMeasurementRow - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- selectedModel - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- selectedMolecules - Variable in class org.jmol.modelset.ModelSet
- selectedMonomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
- selectedNet - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- selectedNoeRow - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- selectedOctant - Variable in class org.jmol.g3d.SphereRenderer
- selectedOctant - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- selectedPoints - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- selectedPolyOnly - Variable in class org.jmol.render.MeshRenderer
- selectedPolyOnly - Variable in class org.jmol.shapesurface.PMeshWriter
- selectedTrajectory - Variable in class org.jmol.modelset.Model
- selectField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- selecthetero - Static variable in class org.jmol.script.T
- selecthydrogen - Static variable in class org.jmol.script.T
- selection - Static variable in class org.jmol.script.T
- selection_overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- selection_round_points - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- selection_visible_only - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- selection_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- selection_width_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- selection_width_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- selectionChanged(boolean) - Method in class org.jmol.viewer.SelectionManager
- selectionChanged(BS) - Method in interface org.jmol.api.JmolSelectionListener
-
Called when the selected atoms change
- selectionhalos - Static variable in class org.jmol.script.T
- selectionHalosEnabled - Variable in class org.jmol.viewer.Viewer
- selectionListener - Variable in class org.jmol.awtjs.swing.JTable
- SelectionManager - Class in org.jmol.viewer
- SelectionManager(Viewer) - Constructor for class org.jmol.viewer.SelectionManager
- selectionWorking - Variable in class org.jmol.viewer.ActionManager
- selectItemTok(T, int) - Static method in class org.jmol.script.SV
- selectItemVar(SV) - Static method in class org.jmol.script.SV
- selectNet() - Method in class org.jmol.adapter.readers.cif.TopoCifParser
- selectPocket(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- selectPocket(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
- selectRb(int) - Method in class org.jmol.viewer.ActionManager
- selectReaderAndGo(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
- selectSeqcodeRange(Group[], int, int, int, int, BS) - Static method in class org.jmol.modelset.ModelSet
- selectSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- selectStatus(BS, boolean, int, boolean, boolean) - Method in class org.jmol.viewer.Viewer
-
"SELECT" starting with comma triggers the SELECT callback from a SELECT command.
- semicolon - Static variable in class org.jmol.script.T
- sendBytes(byte[], NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- sendConsoleEcho(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
- sendConsoleEcho(String) - Method in class org.jmol.console.GenericConsole
- sendConsoleEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- sendConsoleMessage(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
- sendConsoleMessage(String) - Method in class org.jmol.console.GenericConsole
- sendConsoleMessage(String) - Method in class org.jmol.viewer.Viewer
- sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- sendJSpecView(String) - Method in class org.jmol.jsv.JSpecView
- sendKeyBuffer() - Method in class org.jmol.awt.Mouse
- sendKeyBuffer() - Method in class org.jmol.awtjs2d.Mouse
- sendMessage(Map<String, Object>, String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- sendNioSyncRequest(Object, int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- sendScript(String, String, boolean, boolean) - Method in class org.jmol.util.GenericApplet
- sendToJmol(int, String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
-
from JmolPanel and SYNC command
- sendToJmol(int, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
-
send the message - not for replies.
- sep - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- sep - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- SEP - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- seq_view - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_alignment - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_discrete_by_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_fill_char - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_fill_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_format - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_label_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_label_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_label_spacing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_label_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_location - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_unaligned_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seq_view_unaligned_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- seqAdv() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- seqcode - Variable in class org.jmol.modelset.Group
- seqcode - Static variable in class org.jmol.script.T
- seqcodes - Variable in class org.jmol.modelset.ModelLoader
- seqid - Static variable in class org.jmol.script.T
- seqMode - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- sequence - Static variable in class org.jmol.script.T
- SEQUENCE_NUMBER_FLAG - Static variable in class org.jmol.modelset.Group
- SEQUENCE_NUMBER_SHIFT - Static variable in class org.jmol.modelset.Group
- sequenceNumber - Variable in class org.jmol.adapter.smarter.Atom
- sequenceNumbers - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- serial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- SERIAL_NO - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- serialArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- serialID - Variable in class org.jmol.adapter.smarter.Structure
- serialID - Variable in class org.jmol.modelsetbio.ProteinStructure
- serialVersionUID - Static variable in class org.openscience.jmol.app.webexport.Test
- serMode - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- serverConnection - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- serverCycle() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- serverCycle() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
- serverService - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- serverSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- serverThread - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- SERVICE - Enum constant in enum org.jmol.c.CBK
- SERVICE_LOST - Static variable in class org.jmol.multitouch.ActionManagerMT
- session_cache_optimize - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- session_changed - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- session_compression - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- session_file - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- session_migration - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- session_version_check - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- set - Static variable in class org.jmol.script.T
- set - Variable in class org.jmol.smiles.SmilesRing
- set() - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
- set() - Method in class org.jmol.minimize.MinAtom
- set() - Method in class org.jmol.smiles.SmilesSearch
- set(float, float, float) - Method in interface org.jmol.util.Node
- set(int) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
- set(int, int) - Method in class org.jmol.awtjs.swing.Dimension
- set(int, int, char, int, int, char, int, int) - Method in class org.jmol.adapter.smarter.Structure
- set(int, int, int) - Method in class org.jmol.g3d.PixelatorShaded
- set(int, int, int, long) - Method in class org.jmol.viewer.MotionPoint
- set(int, String) - Method in class org.jmol.thread.TimeoutThread
- set(int, Map<String, Integer>, RadiusData, String, String, String, TickInfo, boolean, boolean, Boolean, boolean, int, short, Text, float) - Method in class org.jmol.modelset.MeasurementData
- set(int, BS, int[]) - Method in class org.jmol.minimize.MMConstraint
- set(long, int, int, int) - Method in class org.jmol.viewer.MouseState
- set(String) - Method in class org.jmol.viewer.binding.JmolBinding
- set(String, int) - Method in interface org.jmol.api.JmolParallelProcessor
- set(String, int) - Method in class org.jmol.modelset.LabelToken
- set(String, int) - Method in class org.jmol.script.ScriptFunction
- set(String, int, P3, P3[], int, int, int[][], int, int[][], int[][], V3[], BS, boolean, float, float) - Method in class org.jmol.shapespecial.Polyhedron
- set(Lst<Object>) - Method in class org.jmol.shapecgo.CGOMesh
- set(AtomSetCollectionReader) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
- set(AtomSetCollectionReader) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
- set(AtomSetCollectionReader) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- set(JmolJDXMOLReader, String, Map<String, Object>) - Method in interface org.jmol.api.JmolJDXMOLParser
- set(JmolJDXMOLReader, String, Map<String, Object>) - Method in class org.jmol.jsv.JDXMOLParser
- set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.CircleRenderer
- set(JmolRendererInterface, GData) - Method in interface org.jmol.g3d.G3DRenderer
- set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.HermiteRenderer
- set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.TriangleRenderer
- set(SymmetryInterface, Atom, Atom[], BS, float) - Method in class org.jmol.symmetry.UnitCellIterator
- set(AtomDataServer, int, short[]) - Method in interface org.jmol.api.JmolEnvCalc
- set(AtomDataServer, int, short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
- set(Bspt) - Method in class org.jmol.bspt.CubeIterator
- set(Calculations) - Method in class org.jmol.minimize.forcefield.Calculation
- set(ModelSet) - Method in class org.jmol.modelset.MeasurementPending
- set(ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
- set(ModelSet, int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelset.Model
- set(Monomer[]) - Method in class org.jmol.modelsetbio.BioPolymer
- set(RocketsRenderer) - Method in class org.jmol.renderbio.RocketRenderer
- set(Dipole) - Method in class org.jmol.shapespecial.Dipole
- set(SmilesBond) - Method in class org.jmol.smiles.SmilesBond
- set(PointGroup, T3[]) - Method in class org.jmol.symmetry.PointGroup
- set(Font, short, int, float) - Method in class org.jmol.modelset.Text
- set(MeshSlicer) - Method in class org.jmol.util.MeshCapper
- set(MeshSurface) - Method in class org.jmol.util.MeshSlicer
- set(FileManager) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
- set(FileManager, Viewer, Object, Map<String, Object>) - Method in class org.jmol.io.DOMReader
- set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
- set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in class org.jmol.io.FilesReader
- set(TransformManager, Viewer) - Method in interface org.jmol.api.JmolNavigatorInterface
- set(TransformManager, Viewer) - Method in class org.jmol.navigate.Navigator
- set(Viewer) - Method in class org.jmol.adapter.readers.quantum.NBOParser
- set(Viewer) - Method in interface org.jmol.api.JmolDataManager
- set(Viewer) - Method in class org.jmol.quantum.MepCalculation
- set(Viewer) - Method in class org.jmol.viewer.ChimeMessenger
- set(Viewer) - Method in class org.jmol.viewer.DataManager
- set(Viewer) - Method in interface org.jmol.viewer.JmolChimeMessenger
- set(Viewer, BS) - Method in class org.jmol.symmetry.CIPData
-
Actual constructor.
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CIFWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.CMLWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.PDBWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.PWMATWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.QCJSONWriter
- set(Viewer, OC, Object[]) - Method in class org.jmol.adapter.writers.XSFWriter
- set(Viewer, OC, Object[]) - Method in interface org.jmol.api.JmolWriter
- set(Viewer, ModelSet) - Method in class org.jmol.modelsetbio.BioExt
- set(Viewer, ModelSet) - Method in class org.jmol.modelsetbio.BioModelSet
- set(Viewer, ModelSet, Lst<P3[]>) - Method in class org.jmol.modelset.Trajectory
- set(Viewer, ShapeManager) - Method in interface org.jmol.api.JmolRepaintManager
- set(Viewer, ShapeManager) - Method in class org.jmol.render.RepaintManager
- SET_OPTIONS - Static variable in class org.jmol.modelkit.ModelKit
- set2(int, boolean) - Method in class org.jmol.smiles.SmilesBond
- set2(P3, P3) - Method in class org.jmol.shapespecial.Dipole
- set2(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.Monomer
- set2a(SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
- set2AtomValue(Atom, Atom, float) - Method in class org.jmol.shapespecial.Dipole
- set2D() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- set2DLengths(int, int) - Method in class org.jmol.modelset.ModelLoader
- set2dZ(int, int, V3) - Method in class org.jmol.modelset.ModelLoader
- set2Value(P3, P3, float) - Method in class org.jmol.shapespecial.Dipole
- set3dContourVector(Lst<Object>, int[][], T3[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
-
Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position.
- set4(int, int, int, int) - Method in class org.jmol.awtjs.swing.Color
- set4(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
- setAaTokenCompiled() - Method in class org.jmol.script.ScriptCompiler
- setABC(int) - Method in class org.jmol.util.MeshSurface
- setABC(V3, V3, V3) - Method in class org.jmol.util.SimpleUnitCell
- setAbstractButtonLabels(Map<String, Object>, Map<String, String>) - Static method in class org.jmol.console.GenericConsole
- setACDAssignments(String, String, int, Lst<String[]>, String) - Method in interface org.jmol.api.JmolJDXMOLParser
- setACDAssignments(String, String, int, Lst<String[]>, String) - Method in class org.jmol.jsv.JDXMOLParser
- setAction(int, long) - Method in class org.jmol.viewer.Gesture
- setActionCommand(String) - Method in interface org.jmol.api.SC
- setActionCommand(String) - Method in class org.jmol.awt.AwtSwingComponent
- setActionCommand(String) - Method in class org.jmol.awtjs.swing.JComponent
- setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
-
Changes the activation state for a logging level.
- setActiveMenu(String) - Method in class org.jmol.modelkit.ModelKitPopup
-
Set the active menu and request a repaint.
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.JmolDataReader
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.P2nReader
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PdbReader
-
adaptable via subclassing
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PqrReader
- setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- setAlignment(int) - Method in class org.jmol.modelset.Text
- setAlignmentLCR(String) - Method in class org.jmol.modelset.Text
- setAll(int) - Static method in class org.jmol.util.BSUtil
- setAll(P3, M3, P3, float, float, float, float, float, float, float, float, float, float, float) - Method in class org.jmol.viewer.TransformManager
- setAllButton - Variable in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- setAllButton - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- setAllButton - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- setAllButtonActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- setAllButtonActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- setAllButtonActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- setAllConformation(BS) - Method in class org.jmol.modelsetbio.BioModelSet
- setAllDefaultStructure(BS) - Method in class org.jmol.modelsetbio.BioModelSet
- setAllowJSThreads(boolean) - Method in class org.jmol.script.ScriptEval
- setAllProteinType(BS, STR) - Method in class org.jmol.modelsetbio.BioModelSet
-
called from state STRUCTURE command
- setAllStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.BioModelSet
- setAmbientOcclusion(int) - Method in class org.jmol.util.GData
- setAmbientPercent(int) - Method in class org.jmol.util.GData
-
fractional distance from black for ambient color
- setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.util.Rgb16
- setAngleType(MinAngle) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
-
Get the angle type: 0 The angle i-j-k is a "normal" bond angle 1 Either bond i-j or bond j-k has a bond type of 1 2 Bonds i-j and j-k each have bond types of 1; the sum is 2.
- setAngleUnits(int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setAngleVariables(Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
- setAnimation(int) - Method in class org.jmol.viewer.Viewer
- setAnimationDirection(int) - Method in class org.jmol.viewer.AnimationManager
- setAnimationFps(int) - Method in class org.jmol.api.JmolViewer
- setAnimationFps(int) - Method in class org.jmol.viewer.AnimationManager
- setAnimationFps(int) - Method in class org.jmol.viewer.Viewer
- setAnimationLast() - Method in class org.jmol.viewer.AnimationManager
- setAnimationMode(String) - Method in class org.jmol.viewer.Viewer
- setAnimationNext() - Method in class org.jmol.viewer.AnimationManager
- setAnimationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
- setAnimationOn(boolean) - Method in class org.jmol.viewer.Viewer
- setAnimationPrevious() - Method in class org.jmol.viewer.AnimationManager
- setAnimationRange(int, int) - Method in class org.jmol.viewer.AnimationManager
- setAnimationRange(int, int) - Method in class org.jmol.viewer.Viewer
- setAnimationRelative(int) - Method in class org.jmol.viewer.AnimationManager
- setAnimationReplayMode(int, float, float) - Method in class org.jmol.viewer.AnimationManager
- setAnimDisplay(BS) - Method in class org.jmol.viewer.Viewer
- setAnisoBorU(Atom, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAnisotropy(P3) - Method in class org.jmol.jvxl.readers.Parameters
- setAnnotationAtoms(Viewer, Map<String, SV>, int) - Method in class org.jmol.dssx.AnnotationParser
- setAntialias(boolean) - Method in class org.jmol.viewer.TransformManager
- setAntialias(int, boolean) - Method in class org.jmol.viewer.Viewer
- setAPa(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.AtomCollection
- setAPm(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
- setAppletContext(String) - Method in class org.jmol.viewer.FileManager
- setAppletPath(String, boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
- setAppletProxy(String) - Method in class org.jmol.viewer.FileManager
- setApplySymmetryToBonds(boolean) - Method in class org.jmol.viewer.Viewer
- setArc(T3, T3, T3, float, float, float, float) - Method in class org.jmol.renderspecial.DrawRenderer
- setAromatic(int, Node[], BS, Lst<Object>, BS, int, boolean, boolean, boolean, VTemp, Lst<BS>, Lst<SmilesRing>, int[], boolean) - Static method in class org.jmol.smiles.SmilesAromatic
-
Main entry point.
- setArrays(Atom[], BS, Bond[], int, boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- setAsBallRotation(M4, float, float, float, float) - Method in class org.jmol.viewer.TransformManager4D
-
4D ball rotation from nominal dx, dy, dz motion.
- setAtom(int[], String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- setAtom(int, int, P3, float, BS, int, short, int, boolean) - Method in class org.jmol.modelset.Atom
- setAtom(String) - Method in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- setAtom(Atom, int, int, int, float, float, float) - Method in class org.jmol.adapter.readers.simple.InputReader
- setAtom(Atom, int, String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
- setAtom2(SmilesAtom, SmilesSearch) - Method in class org.jmol.smiles.SmilesBond
-
from parse ring
- setAtom2dZ(Atom, Atom, V3, V3, V3, int) - Static method in class org.jmol.modelset.ModelLoader
-
set the z based on a cos relationship to the y axis.
- setAtomBits(BS) - Method in class org.jmol.modelset.Chain
- setAtomBits(BS) - Method in class org.jmol.modelset.Group
-
note that we may pick up additional bits here that were added later
- setAtomBits(BS) - Method in interface org.jmol.modelset.Structure
- setAtomBits(BS) - Method in class org.jmol.modelsetbio.BioPolymer
- setAtomBits(BS) - Method in class org.jmol.modelsetbio.ProteinStructure
- setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Chain
- setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelset.Group
-
Setting and clearing
- setAtomBitsAndClear(BS, BS) - Method in interface org.jmol.modelset.Structure
- setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
- setAtomBitsAndClear(BS, BS) - Method in class org.jmol.modelsetbio.ProteinStructure
- setAtomChooser() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setAtomChooser() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setAtomClickability() - Method in class org.jmol.shape.AtomShape
- setAtomClickability() - Method in class org.jmol.shape.Balls
- setAtomClickability() - Method in class org.jmol.shape.Labels
- setAtomClickability() - Method in class org.jmol.shape.Shape
- setAtomClickability() - Method in class org.jmol.shape.Sticks
- setAtomClickability() - Method in class org.jmol.shapebio.Backbone
- setAtomClickability() - Method in class org.jmol.shapebio.BioShape
- setAtomClickability() - Method in class org.jmol.shapebio.BioShapeCollection
- setAtomClickability() - Method in class org.jmol.shapespecial.Dots
- setAtomClickability() - Method in class org.jmol.shapespecial.Ellipsoids
- setAtomColor(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setAtomCoord(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
- setAtomCoord(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setAtomCoord2(BS, int, Object) - Method in class org.jmol.modelset.AtomCollection
- setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
- setAtomCoords(BS, int, Object) - Method in class org.jmol.modelset.ModelSet
- setAtomCoords(BS, int, Object) - Method in class org.jmol.viewer.Viewer
- setAtomCoordScaled(Atom, String[], int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setAtomCoordsRelative(T3, BS) - Method in class org.jmol.modelset.ModelSet
- setAtomCoordsRelative(T3, BS) - Method in class org.jmol.viewer.Viewer
- setAtomCoordTokens(Atom, String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setAtomData(int, String, String, boolean) - Method in class org.jmol.modelset.AtomCollection
- setAtomData(int, String, String, boolean) - Method in class org.jmol.viewer.Viewer
- setAtomDefs() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setAtomI(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
- setAtomicAndIsotopeNumber(int) - Method in class org.jmol.modelset.Atom
- setAtomicMass(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the atomic mass of the atom.
- setAtomicOrbital(float[]) - Method in class org.jmol.jvxl.readers.Parameters
- setAtomIndexes(int, int) - Method in class org.jmol.util.Tensor
- setAtomInfo(int[], int[], int[], boolean[], float[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setAtomLabel(String, int) - Method in class org.jmol.viewer.ShapeManager
- setAtomMap(int[], int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setAtomMapAnyCase() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomName(int, String, boolean) - Method in class org.jmol.modelset.AtomCollection
- setAtomName(String) - Method in class org.jmol.smiles.SmilesAtom
- setAtomName(Atom, String, String) - Method in class org.jmol.adapter.readers.more.GromacsReader
- setAtomNames() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
- setAtomNamesAndNumbers(int, int, AtomCollection, boolean) - Method in class org.jmol.modelset.ModelSet
- setAtomNumber(int, int, boolean) - Method in class org.jmol.modelset.AtomCollection
- setAtomPositions() - Method in class org.jmol.minimize.Minimizer
- setAtomPositions(int, int, P3[], P3[], float, V3[], boolean) - Method in class org.jmol.modelset.Trajectory
-
A generic way to set atom positions, possibly from trajectories but also possibly from an array.
- setAtomProp(String, Object, BS) - Method in class org.jmol.script.ScriptEval
- setAtomProperties() - Method in class org.jmol.modelset.ModelLoader
- setAtomProperties(String, Object, int, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
- setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.viewer.Viewer
- setAtomResno(int, int) - Method in class org.jmol.modelset.AtomCollection
- setAtomsCoordRelative(BS, float, float, float) - Method in class org.jmol.modelset.AtomCollection
- setAtomSeqID(int, int) - Method in class org.jmol.modelset.AtomCollection
- setAtomSetCollectionPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the partial atomic charges based on asc auxiliary info
- setAtomSetEnergy(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomSetFrequency(int, String, String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomSetInfo() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- setAtomSetInfoMd() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- setAtomSetModelProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and molecular energies
- setAtomSetModelPropertyForSet(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the a property for the an AtomSet
- setAtomSetName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the name for the current AtomSet
- setAtomSetNumber(int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setAtomSetPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the partial atomic charges based on atomSet auxiliary info
- setAtomSetSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setAtomsForSmiles(Viewer, String) - Method in class org.jmol.symmetry.CIPDataSmiles
- setAtomsPicked(BS, String) - Method in class org.jmol.viewer.ActionManager
- setAtomTensors(int, Lst<Object>) - Method in class org.jmol.modelset.AtomCollection
- setAtomType(int, String) - Method in class org.jmol.modelset.AtomCollection
- setAtomTypes(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
- setAtomTypes(Atom[], BS, SmilesMatcherInterface, Lst<BS>[], boolean) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
-
The file MMFF94-smarts.txt is derived from MMFF94-smarts.xlsx.
- setAtomVibrationVector(int, T3) - Method in class org.jmol.modelset.AtomCollection
- setAtropicity - Variable in class org.jmol.smiles.SmilesSearch
- setAtropisomerOptions() - Method in class org.jmol.modelset.Bond
- setAtropType(int) - Method in class org.jmol.smiles.SmilesBond
- setAttr(String, float) - Method in class org.jmol.export._MayaExporter
- setAttr(String, int) - Method in class org.jmol.export._MayaExporter
- setAttr(String, T3) - Method in class org.jmol.export._MayaExporter
- setAttributes() - Method in class org.jmol.console.ScriptEditor
- setAutoBond(boolean) - Method in class org.jmol.api.JmolViewer
- setAutoBond(boolean) - Method in class org.jmol.viewer.Viewer
- setAutoscrolls(boolean) - Method in interface org.jmol.api.SC
- setAutoscrolls(boolean) - Method in class org.jmol.awt.AwtSwingComponent
- setAutoscrolls(boolean) - Method in class org.jmol.awtjs.swing.JComponent
- setAxes(int) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- setAxes(DrawMesh) - Static method in class org.jmol.shapespecial.Draw
- setAxesMode(int) - Method in class org.jmol.viewer.Viewer
- setAxesOrientationRasmol(boolean) - Method in class org.jmol.api.JmolViewer
- setAxesOrientationRasmol(boolean) - Method in class org.jmol.viewer.Viewer
- setAxesScale(int, float) - Method in class org.jmol.viewer.Viewer
- setB(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
- setBackground(GenericColor) - Method in class org.jmol.awtjs.swing.Component
- setBackgroundArgb(int) - Method in class org.jmol.util.GData
-
sets background color to the specified argb value
- setBackgroundColor(int) - Method in class org.jmol.g3d.Platform3D
- setBackgroundImage(Object) - Method in class org.jmol.util.GData
- setBackgroundImage(String, Object) - Method in class org.jmol.viewer.Viewer
- setBackgroundModelIndex(int) - Method in class org.jmol.viewer.AnimationManager
- setBackgroundModelIndex(int) - Method in class org.jmol.viewer.Viewer
- setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
- setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Platform3D
- setBackgroundTransparent(boolean) - Method in class org.jmol.util.GData
- setBaseModels(BS) - Method in class org.jmol.modelset.Trajectory
-
set bits for all base models only
- setBbcage(float) - Method in class org.jmol.util.BoxInfo
- setBBox(T3, float) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setBBoxAll() - Method in class org.jmol.jvxl.readers.SurfaceReader
- setBf(int) - Method in class org.jmol.modelset.AtomCollection
- setBFactor(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
- setBgcolix(int, short) - Method in class org.jmol.shape.Labels
- setBinding(Binding) - Method in class org.jmol.multitouch.ActionManagerMT
- setBinding(Binding) - Method in class org.jmol.viewer.ActionManager
- setBioAtom(char) - Method in class org.jmol.smiles.SmilesAtom
- setBioColix(short) - Method in class org.jmol.renderbio.BioShapeRenderer
- setBiomolecule(Map<String, Object>, BS) - Method in class org.jmol.adapter.readers.cif.MMCifReader
- setBiomoleculeAtomCounts() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- setBiomolecules() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- setBioPolymer(BioPolymer, int) - Method in class org.jmol.modelsetbio.Monomer
- setBioPolymers(BioModel, boolean) - Method in class org.jmol.dssx.DSSR1
- setBitSet(BS, BS, int) - Static method in class org.jmol.viewer.SelectionManager
- setBitsetProperty(BS, int, int, float, T) - Method in class org.jmol.script.ScriptExpr
- setBond(int, Bond) - Method in class org.jmol.modelset.BondCollection
- setBond(Bond, String[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
- setBondArray() - Method in class org.jmol.smiles.SmilesAtom
- setBondAtom(SmilesBond, SmilesAtom, SmilesAtom, SmilesSearch) - Method in class org.jmol.smiles.SmilesParser
-
set the bond and look for a=a, setting AROMATIC_DOUBLE automatically if found
- setBondChirality(SimpleNode, SimpleNode, SimpleNode, SimpleNode, boolean) - Method in class org.jmol.symmetry.CIPChirality
-
Determine the axial or E/Z chirality for the a-b bond.
- setBondDirections() - Method in class org.jmol.smiles.SmilesGenerator
-
Creates global BitSets bsBondsUp and bsBondsDown.
- setBondIndex(int, boolean) - Method in class org.jmol.modelkit.ModelKit
-
Set the bond for rotation -- called by Sticks.checkObjectHovered via Viewer.highlightBond.
- setBonding(AtomSetCollection, int) - Method in class org.jmol.adapter.readers.more.JcampdxReader
-
add bonding to a set of ModelData based on a MOL file only if the this set has no bonding already
- setBondingAndMolecules() - Method in class org.jmol.adapter.readers.cif.CifReader
-
(1) If GEOM_BOND records are present, we (a) use them to generate bonds (b) add H atoms to bonds if necessary (c) turn off autoBonding ("hasBonds") (2) If MOLECULAR, then we (a) use {1 1 1} if lattice is not defined (b) use asc.bonds[] to construct a preliminary molecule and connect as we go (c) check symmetry for connections to molecule in any one of the 27 3x3 adjacent cells (d) move those atoms and their connected branch set (e) iterate as necessary to get all atoms desired (f) delete unselected atoms (g) set all coordinates as Cartesians (h) remove all unit cell information
- setBondingRadius(int, float) - Method in class org.jmol.modelset.AtomCollection
- setBondMeasure(int, MeasurementPending) - Method in class org.jmol.modelkit.ModelKit
- setBondParameters(Bond, int, float, float, int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
used in PyMOL reader to set unique bond settings and for valence
- setBonds() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
Note that setting bonds from _struct_conn is only done if we have updated CIF files, which include _chem_comp_bond.
- setBonds(SmilesBond[]) - Method in class org.jmol.smiles.SmilesAtom
- setBondTolerance(float) - Method in class org.jmol.api.JmolViewer
- setBondTolerance(float) - Method in class org.jmol.viewer.Viewer
- setBondTypes(Bond[], int, BS) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- setBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
- setBooleanProperty(String, boolean) - Method in class org.jmol.script.ScriptParam
- setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
- setBooleanPropertyTok(String, int, boolean) - Method in class org.jmol.viewer.Viewer
- setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.modelset.ModelSet
- setBoundBox(T3, T3, boolean, float) - Method in class org.jmol.util.BoxInfo
- setBoundBoxFromOABC(T3[]) - Method in class org.jmol.util.BoxInfo
- setBoundingBox(P3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setBoundingBox(P3[]) - Method in class org.jmol.util.MeshSurface
- setBox(float, float, P3) - Method in class org.jmol.renderbio.RocketRenderer
- setBox(float, float, P3, V3, V3, P3, float) - Method in class org.jmol.modelsetbio.Sheet
- setBox(P3, P3) - Method in class org.jmol.util.MeshSurface
- setBoxOffsetsInWindow(float, float, float) - Method in class org.jmol.modelset.Text
- setBoxXY(float, float, float, float, float[], boolean) - Static method in class org.jmol.modelset.Text
- setBraceCount - Variable in class org.jmol.script.ScriptCompiler
- setBranch2dZ(Atom, BS, BS, V3, V3, V3, int) - Static method in class org.jmol.modelset.ModelLoader
- setBs(Atom[], int, BS[], BS) - Method in class org.jmol.adapter.readers.cif.CifReader
-
iteratively run through connected atoms, adding them to the set
- setBsHidden(BS) - Method in class org.jmol.modelset.AtomCollection
- setBsVdw() - Method in class org.jmol.shapesurface.Isosurface
- setBuf() - Method in class org.jmol.g3d.Pixelator
- setButton(String) - Method in class org.jmol.console.GenericConsole
- setButton(String) - Method in class org.jmol.console.JmolConsole
- setButton(String) - Method in class org.jmol.console.ScriptEditor
- setButton(String) - Method in class org.jmol.consolejs.AppletConsole
- setButton(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- setC(short) - Method in interface org.jmol.api.JmolRendererInterface
-
sets current color from colix color index
- setC(short) - Method in class org.jmol.export.Export3D
-
sets current color from colix color index
- setC(short) - Method in class org.jmol.g3d.Graphics3D
-
sets current color from colix color index
- setC(short) - Method in class org.jmol.util.GData
- setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.ModulationSet
-
get updated value for offset vector and for occupancy
- setCalcPoint(T3, T3, float, float) - Method in class org.jmol.util.Vibration
- setCalculationType() - Method in class org.jmol.adapter.readers.quantum.GamessReader
- setCallback(String, Object) - Method in interface org.jmol.api.JmolAppletInterface
- setCallback(String, Object) - Method in class org.jmol.util.GenericApplet
-
set a callback either as a function or a function name from JavaScript
- setCallbackFunction(String, Object) - Method in class org.jmol.viewer.StatusManager
-
Set a JmolScript or JavaScript or Java callback.
- setCallbackFunction(String, String) - Method in interface org.jmol.api.JmolCallbackListener
- setCallbackFunction(String, String) - Method in class org.jmol.console.GenericConsole
- setCallbackFunction(String, String) - Method in class org.jmol.util.GenericApplet
-
From StatusManager
- setCallbackFunction(String, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- setCamera(float, float) - Method in class org.jmol.viewer.TransformManager
- setCameraDepthPercent(float, boolean) - Method in class org.jmol.viewer.TransformManager
-
either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model
- setCapacity(int) - Method in class org.jmol.modelset.AtomCollection
- setCapOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setCaretPosition(int) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- setCartesianOffset(T3) - Method in class org.jmol.symmetry.UnitCell
- setCarveSets(Map<String, Lst<Object>>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setCE(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
- setCel(boolean) - Method in class org.jmol.util.GData
- setCel(boolean, int, int) - Method in class org.jmol.util.Shader
- setCell(String) - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- setCellParams() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- setCellParams() - Method in class org.jmol.util.SimpleUnitCell
- setCellSelectionEnabled(boolean) - Method in class org.jmol.awtjs.swing.JTable
- setCelPower(int) - Method in class org.jmol.util.GData
- setCenter() - Method in class org.jmol.viewer.TransformManager
- setCenter(int) - Method in class org.jmol.shapespecial.DrawMesh
- setCenter(P3) - Method in class org.jmol.shapespecial.Ellipsoid
- setCenter(T3, float) - Method in interface org.jmol.api.AtomIndexIterator
- setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
- setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
- setCenter(T3, float) - Method in class org.jmol.symmetry.UnitCellIterator
- setCenter2(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
- setCenterAt(int, P3) - Method in class org.jmol.viewer.TransformManager
- setCenterBitSet(BS, boolean) - Method in class org.jmol.viewer.Viewer
- setCenters() - Method in class org.jmol.shapespecial.DrawMesh
- setCenterSelected() - Method in class org.jmol.api.JmolViewer
- setCenterSelected() - Method in class org.jmol.viewer.Viewer
- setCentroid() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- setCentroid(BS, int[]) - Method in class org.jmol.modelset.ModelSet
-
deletes molecules based on: CENTROID -- molecular centroid is not in unit cell CENTROID PACKED -- all molecule atoms are not in unit cell
- setCGO(Lst<Object>) - Method in class org.jmol.shapecgo.CGO
- setCGO(Lst<Object>) - Method in class org.jmol.viewer.Viewer
- setChainID(int, String) - Method in class org.jmol.modelset.AtomCollection
- setChainID(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setCharge(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the charge of the atom.
- setCharges() - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- setChemicalShiftReference(String, float) - Method in interface org.jmol.api.JmolNMRInterface
- setChemicalShiftReference(String, float) - Method in class org.jmol.quantum.NMRCalculation
- setCHequation(String) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setCHequation(String) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- setChiralClass(SmilesAtom) - Method in class org.jmol.smiles.SmilesStereo
- setCIPChirality(int) - Method in class org.jmol.modelset.Atom
- setCIPChirality(int) - Method in class org.jmol.modelset.Bond
-
Not implemented.
- setCIPChirality(int) - Method in class org.jmol.smiles.SmilesAtom
- setCIPChirality(int) - Method in class org.jmol.util.Edge
- setCIPChirality(int) - Method in interface org.jmol.util.Node
- setCIPChirality(int) - Method in interface org.jmol.util.SimpleNode
- setCIPInfo(String, int, String) - Method in class org.jmol.symmetry.CIPDataTracker
- setCIR(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
- setClickable(int) - Method in class org.jmol.modelset.Atom
- setClipboard(Object) - Static method in class org.jmol.awt.AwtClipboard
-
Transfers text or image into the clipboard.
- setCoeffs(int, boolean) - Method in class org.jmol.quantum.MOCalculation
- setColix(short) - Method in class org.jmol.render.MeshRenderer
- setColix(short) - Method in class org.jmol.renderbio.BioShapeRenderer
- setColix(short) - Method in class org.jmol.util.MeshSurface
- setColixAndPalette(short, byte, int) - Method in class org.jmol.shape.AtomShape
- setColixBack(short) - Method in class org.jmol.util.MeshSurface
- setColixBack(short, BS) - Method in class org.jmol.shapebio.BioShape
- setColixBackgroundContrast(int) - Method in class org.jmol.viewer.ColorManager
- setColixBS(short, byte, BS) - Method in class org.jmol.shapebio.BioShape
- setColixDipole(short, int, BS) - Method in class org.jmol.shapespecial.Dipoles
- setColixes(short[], BS) - Method in class org.jmol.shapebio.BioShape
- setCollectionName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setColor(int) - Method in class org.jmol.util.GData
- setColor(short) - Method in class org.jmol.shape.Measures
- setColorBackground(String) - Method in class org.jmol.api.JmolViewer
- setColorBackground(String) - Method in class org.jmol.viewer.Viewer
- setColorByScore(float, int) - Method in class org.jmol.shapesurface.Contact
- setColorCommand() - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
just sets the color command for this isosurface.
- setColorNoisy(int) - Method in class org.jmol.g3d.Graphics3D
- setColorOptions(SB, int, int, int) - Method in class org.jmol.scriptext.IsoExt
- setColorPhase(IsosurfaceMesh, short, short) - Method in class org.jmol.shapesurface.Isosurface
- setColors(short[], float) - Method in class org.jmol.adapter.readers.pymol.JmolObject
- setColorScheme(String, boolean) - Method in class org.jmol.util.ColorEncoder
- setColorsFromJvxlData(int) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
from Isosurface.notifySurfaceGenerationCompleted() starting with Jmol 12.1.50, JVXL files contain color, translucency, color scheme information, and vertex color mappings (as from COLOR ISOSURFACE {hydrophobic} WHITE), returning these settings when the JVXL file is opened.
- setColumnComparator(Class, Comparator) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setCommand(T) - Method in class org.jmol.script.ScriptCompiler
- setCommandHooks() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setCommonDefaults() - Method in class org.jmol.viewer.StateManager
- setCompiler() - Method in interface org.jmol.api.JmolScriptEvaluator
- setCompiler() - Method in class org.jmol.script.ScriptEval
- setConformation(BS) - Method in class org.jmol.modelset.ModelSet
- setConformation(BS) - Method in class org.jmol.modelsetbio.BioPolymer
- setConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
- setConsole(JmolAppConsoleInterface) - Method in class org.jmol.api.JmolViewer
-
sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(vwr, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java
- setConsoleFontScale(int) - Method in class org.jmol.viewer.Viewer
- setConsoleTextPane(AppConsole.ConsoleTextPane) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- setConstraints(Lst<MMConstraint>) - Method in class org.jmol.minimize.forcefield.Calculations
- setConstraints(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
- setContactBitSets(BS, BS, boolean, float, RadiusData, boolean) - Method in class org.jmol.scriptext.MathExt
- setContacts(Object[], boolean) - Method in class org.jmol.shapesurface.Contact
- setContext(ScriptContext) - Method in class org.jmol.console.ScriptEditor
- setContourData(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- setContourVector(Lst<Object>, int, BS, float, short, int, SB) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
- setCoord(SimpleNode, CIPChirality.CIPAtom[]) - Method in class org.jmol.symmetry.CIPData
-
set the coordinate -- SMILES only
- setCoord(SimpleNode, CIPChirality.CIPAtom[]) - Method in class org.jmol.symmetry.CIPDataSmiles
- setCoordinatesAreFractional(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setCoords(Calculation, int) - Method in class org.jmol.minimize.forcefield.Calculations
- setCorrelationTime(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
set the correlation time to be used in the NOE calculation
- setCorrelationTimeTauPS(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
set the correlation time to be used in the NOE calculation
- setCorrelationTimeTauPS(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- setCount(int) - Method in class org.jmol.modelset.Measurement
- setCount(int) - Method in class org.jmol.modelset.MeasurementPending
- setCountM(int) - Method in class org.jmol.modelset.Measurement
- setCouples() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- setCouples() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- setCoupleWeight(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- setCrystallographicDefaults() - Method in class org.jmol.modelset.ModelSet
- setCrystallographicDefaults() - Method in class org.jmol.viewer.StateManager
- setCurrent(long, int, int, int) - Method in class org.jmol.viewer.ActionManager
- setCurrent(MouseState, int) - Method in class org.jmol.viewer.MouseState
- setCurrentAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets the number for the current AtomSet
- setCurrentCage(String) - Method in class org.jmol.viewer.Viewer
- setCurrentColorRange(String) - Method in class org.jmol.viewer.Viewer
- setCurrentDirectoryAll(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setCurrentModelID(String) - Method in class org.jmol.viewer.Viewer
- setCurrentModelIndex(int) - Method in class org.jmol.viewer.Viewer
- setCurrentModelIndexClear(int, boolean) - Method in class org.jmol.viewer.Viewer
- setCurrentModelInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets auxiliary information for the AtomSet
- setCursor(int) - Method in class org.jmol.viewer.Viewer
- setCursor(int, Object) - Method in interface org.jmol.api.GenericPlatform
- setCursor(int, Object) - Static method in class org.jmol.awt.Display
- setCursor(int, Object) - Method in class org.jmol.awt.Platform
- setCursor(int, Object) - Method in class org.jmol.awtjs2d.Platform
- setCursor(JSmolAppletObject, int) - Method in interface org.jmol.api.js.JmolToJSmolInterface
- setCursorWait(boolean) - Method in class org.jmol.script.ScriptError
- setCutoff(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
sets the cutoff distance beyond which atom interactions are not considered
- setCutoffAng(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
sets the cutoff distance beyond which atom interactions are not considered
- setCutoffAng(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
sets the cutoff distance beyond which atom interactions are not considered
- setCutoffAutomatic() - Method in class org.jmol.jvxl.readers.MapFileReader
- setCutoffAutomatic() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
- setData(String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
-
A general-purpose data storage method.
- setData(String, Object[], int, int, int, int, int, int) - Method in interface org.jmol.api.JmolDataManager
- setData(String, Object[], int, int, int, int, int, int) - Method in class org.jmol.viewer.DataManager
-
This method needs to be redone using a class instead of Object[]
- setData(String, String, Object, Object) - Method in class org.jmol.script.FileLoadThread
-
Called by Jmol._loadFileAsyncDone(this.vwr.html5Applet).
- setData(Lst<Object[]>, int) - Method in class org.jmol.minimize.forcefield.MMFFOOPCalc
- setData(Lst<Object[]>, int[]) - Method in class org.jmol.minimize.forcefield.UFFAngleCalc
- setData(Lst<Object[]>, int[]) - Method in class org.jmol.minimize.forcefield.UFFTorsionCalc
- setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.Calculation
- setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.MMFFESCalc
- setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.MMFFVDWCalc
- setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.UFFDistanceCalc
- setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.UFFOOPCalc
- setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.UFFVDWCalc
- setData(Lst<Object[]>, MinAngle) - Method in class org.jmol.minimize.forcefield.MMFFAngleCalc
- setData(Lst<Object[]>, MinAngle) - Method in class org.jmol.minimize.forcefield.MMFFSBCalc
- setData(Lst<Object[]>, MinBond) - Method in class org.jmol.minimize.forcefield.MMFFDistanceCalc
- setData(Lst<Object[]>, MinTorsion) - Method in class org.jmol.minimize.forcefield.MMFFTorsionCalc
- setDataDistanceToPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
- setDebugging() - Method in interface org.jmol.api.JmolScriptEvaluator
- setDebugging() - Method in class org.jmol.script.ScriptEval
- setDebugScript(boolean) - Method in class org.jmol.api.JmolViewer
- setDebugScript(boolean) - Method in class org.jmol.viewer.Viewer
- setDefaultColors(boolean) - Method in class org.jmol.viewer.ColorManager
- setDefaultColors(boolean) - Method in class org.jmol.viewer.Viewer
- setDefaultLattice(P3) - Method in class org.jmol.viewer.Viewer
- setDefaultPerspective() - Method in class org.jmol.viewer.TransformManager
- setDefaultRendering(int) - Method in class org.jmol.modelset.ModelLoader
- setDefaults - Variable in class org.jmol.shape.Labels
-
defaults are set after giving SELECT NONE;
- setDefaultState(int) - Method in class org.jmol.modelkit.ModelKit
- setDefaultsType(String) - Method in class org.jmol.viewer.Viewer
- setDefinedFaces(P3[], int[][]) - Method in class org.jmol.shapespecial.Polyhedra
- setDegree(int) - Method in class org.jmol.smiles.SmilesAtom
- setDepth(int) - Method in class org.jmol.util.GData
-
clipping from the front and the back
- setDesiredQpt(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
- setDFCoord(Map<String, Object>) - Method in class org.jmol.adapter.writers.QCJSONWriter
- setDialog() - Method in class org.jmol.awtjs.swing.JDialog
-
Set it into DOM, but don't show it yet.
- setDialog(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
The HTML for this dialog has been generated.
- setDialogLocation(Point) - Method in class org.jmol.dialog.FileChooser
- setDialogSize(Dimension) - Method in class org.jmol.dialog.FileChooser
- setDiffusePercent(int) - Method in class org.jmol.util.GData
-
df in I = df * (N dot L) + sf * (R dot V)^p
- setDihedrals(float[], BS[], float) - Method in class org.jmol.modelset.ModelSet
- setDihedrals(float[], BS[], float) - Method in class org.jmol.viewer.Viewer
- setDipole() - Method in class org.jmol.shapespecial.Dipoles
- setDipole(String[]) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- setDipoleAtoms(Atom, Atom, float, float) - Method in class org.jmol.shapespecial.Dipoles
- setDiscreteColixes(float[], short[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setDisplay(Object) - Method in class org.jmol.util.GenericApplet
- setDisplay(Object) - Method in class org.jmol.viewer.Viewer
- setDisplay(BS) - Method in class org.jmol.viewer.AnimationManager
- setDivisor(String) - Static method in class org.jmol.symmetry.SymmetryOperation
-
Sets the divisor to 0 for n/9 or n/mm
- setDoTranslate(boolean) - Static method in class org.jmol.i18n.GT
- setDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
- setDragAtomIndex(int) - Method in class org.jmol.viewer.ActionManager
- setDrawing(int[]) - Method in class org.jmol.shapespecial.Draw
- setE(double[], double) - Method in class org.jmol.quantum.MOCalculation
- setEccentricity(P4) - Method in class org.jmol.jvxl.readers.Parameters
- setEchoStateActive(boolean) - Method in class org.jmol.modelset.ModelSet
- setEditorTextPane(ScriptEditor.EditorTextPane) - Method in class org.jmol.console.ScriptEditor.EditorDocument
- setElement(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
- setElementAndIsotope(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
-
allow 13C, 15N, 2H, etc.
- setElementArgb(int, int) - Method in class org.jmol.viewer.ColorManager
- setElementArgb(int, int) - Method in class org.jmol.viewer.Viewer
- setElementColor(String, int) - Method in class org.jmol.script.ScriptEval
- setElementSymbol(Atom, String) - Static method in class org.jmol.adapter.readers.cif.TopoCifParser
- setEllipsoidAF(float[]) - Method in class org.jmol.jvxl.readers.Parameters
- setEllipsoidP4(P4) - Method in class org.jmol.jvxl.readers.Parameters
- setEnabled(boolean) - Method in interface org.jmol.api.JmolAbstractButton
- setEnabled(boolean) - Method in interface org.jmol.api.SC
- setEnabled(boolean) - Method in class org.jmol.awt.AwtSwingComponent
- setEnabled(boolean) - Method in class org.jmol.awtjs.swing.Component
- setEnabled(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- setEnabled(JmolAbstractButton, boolean) - Static method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- setEnables() - Method in class org.jmol.console.ScriptEditor
- setEne() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Set all ene-related fields upon finding the second atom.
- setEnergies(String, String, int) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- setEnergy() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
-
Interpret the Energy= line for non SCF type energy output
- setEnergy() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- setEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
- setEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
- setEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
- setEnergy(float) - Method in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- setEnergy(String, String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- setEnergyUnits() - Method in class org.jmol.minimize.Minimizer
- setEqualPt - Variable in class org.jmol.script.ScriptCompiler
- setError(boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- setError(Throwable) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setErrorMessage(String) - Method in class org.jmol.script.ScriptError
- setErrorMessage(String, String) - Method in class org.jmol.viewer.Viewer
- setEval(JmolScriptEvaluator) - Method in class org.jmol.thread.JmolThread
-
JavaScript only -- -- scriptDelay, moveTo, spin -- save context for restoration later -- move program counter forward one command
- setException(ScriptException, String, String) - Method in class org.jmol.script.ScriptEval
- setExpCouple(String, int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setExpDist(String, int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setExplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the number of explicit hydrogen atoms bonded with this atom.
- setExpNoe(String, int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setF(String, float) - Method in class org.jmol.viewer.GlobalSettings
- setFancyArrowHead(int) - Method in class org.jmol.renderbio.BioMeshRenderer
- setFancyConic(int, int) - Method in class org.jmol.renderbio.BioMeshRenderer
- setFancyRibbon(int) - Method in class org.jmol.renderbio.BioMeshRenderer
- setFieldText() - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- setFile() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- setFileData(Viewer, Object) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setFileInfo(String[]) - Method in class org.jmol.viewer.FileManager
-
Set fullPathName, fileName, and nameAsGiven
- setFileLoadStatus(String, String, String, String, int, boolean, Boolean) - Method in class org.jmol.viewer.StatusManager
- setFileLoadStatus(FIL, String, String, String, String, Boolean) - Method in class org.jmol.viewer.Viewer
- setFilename(String) - Method in class org.jmol.console.ScriptEditor
- setFileType(String) - Method in class org.jmol.viewer.FileManager
- setFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setFilterAtomTypeStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setFinalOperations() - Method in class org.jmol.symmetry.SpaceGroup
- setFinalOperations(int, String, P3[], int, int, boolean, String) - Method in interface org.jmol.api.SymmetryInterface
- setFinalOperations(int, String, P3[], int, int, boolean, String) - Method in class org.jmol.symmetry.Symmetry
- setFinalOperationsForAtoms(int, P3[], int, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- setFixedRotationCenter(T3) - Method in class org.jmol.viewer.TransformManager
- setFlags(int) - Method in class org.jmol.smiles.SmilesSearch
- setFlags(AtomType) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- setFloatProperty(String, float) - Method in class org.jmol.api.JmolViewer
- setFloatProperty(String, float) - Method in class org.jmol.script.ScriptParam
- setFloatProperty(String, float) - Method in class org.jmol.viewer.Viewer
- setFloatPropertyTok(String, int, float) - Method in class org.jmol.viewer.Viewer
- setFlowEnd(int, String) - Method in class org.jmol.script.ScriptCompiler
-
generate a new end token with pointer to the start or to default as the intValue and set it as the command token
- setFocus() - Method in class org.jmol.viewer.Viewer
- setFont(int, int) - Method in class org.jmol.shape.Labels
- setFont(short, String, Font) - Method in class org.jmol.export._VrmlExporter
- setFont(Object, Font) - Method in interface org.jmol.api.GenericGraphics
- setFont(Object, Font) - Method in class org.jmol.awt.AwtG2D
- setFont(Object, Font) - Method in class org.jmol.awtjs2d.JsG2D
- setFont(Font) - Method in class org.jmol.g3d.Graphics3D
- setFont(Font) - Method in class org.jmol.util.GData
- setFont(Font, boolean) - Method in class org.jmol.modelset.Text
- setFontBold(String, float) - Method in class org.jmol.util.GData
- setFontFromFid(int) - Method in class org.jmol.modelset.Text
- setFontScale(float) - Method in class org.jmol.modelset.Text
- setFontScale(int) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- setForcesUsingNumericalDerivative(MinAtom, int) - Method in class org.jmol.minimize.forcefield.ForceField
- setFormalCharge(int) - Method in class org.jmol.modelset.Atom
- setFormalCharges(BS, int) - Method in class org.jmol.modelset.AtomCollection
- setFormats(String) - Method in class org.jmol.shape.Measures
- setForVdwClash(boolean) - Method in class org.jmol.util.ContactPair
- setFractional(SymmetryInterface, T3, P3, P3) - Static method in class org.jmol.symmetry.SymmetryDesc
-
Set pt01 to pt00, possibly adding offset into unit cell
- setFractionalCoord(int, float, boolean) - Method in class org.jmol.modelset.Atom
- setFractionalCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setFractionalCoordPt(P3, P3, boolean) - Method in class org.jmol.modelset.Atom
- setFractionalCoordTo(P3, boolean) - Method in class org.jmol.modelset.Atom
- setFrame(int) - Method in class org.jmol.viewer.AnimationManager
- setFrameCount(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- setFrameDelayMs(long) - Method in class org.jmol.viewer.Viewer
- setFrameDelayMs(long, BS) - Method in class org.jmol.modelset.ModelSet
- setFrameDeltaCouple(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- setFrameDeltaDisplay(FrameDeltaDisplay) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setFrameDeltaNoe(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- setFrameLocation(Point, JmolPanel) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setFrameLocation(Point, JmolPanel) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setFrameModelInfo(String, Object) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- setFrameNumberChangeViewer(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- setFrameNumberFromViewer(int) - Method in class org.openscience.jmol.app.janocchio.FrameCounter
- setFrameNumberFromViewer(int) - Method in class org.openscience.jmol.app.janocchio.PopulationDisplay
- setFrameObject(int, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setFrameOffset(int) - Method in class org.jmol.viewer.TransformManager
- setFrameOffsets(BS, boolean) - Method in class org.jmol.viewer.Viewer
- setFrameRangeVisible() - Method in class org.jmol.viewer.AnimationManager
- setFrameSet(int) - Method in class org.jmol.script.ScriptEval
- setFrameTitle(int, String) - Method in class org.jmol.viewer.Viewer
- setFrameTitle(BS, Object) - Method in class org.jmol.modelset.ModelSet
- setFrameTitleObj(Object) - Method in class org.jmol.viewer.Viewer
- setFrameVariables() - Method in class org.jmol.viewer.Viewer
- setFrankMenu(String) - Method in class org.jmol.popup.JmolPopup
- setFrankOn(boolean) - Method in class org.jmol.api.JmolViewer
- setFrankOn(boolean) - Method in class org.jmol.viewer.Viewer
- setFreqValue(float, String[]) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- setFromAsymmetricTensor(double[][], String, String) - Method in class org.jmol.util.Tensor
-
Standard constructor for QM tensors
- setFromAxes(V3[]) - Method in class org.jmol.util.Tensor
-
Standard constructor for ellipsoids based on axes
- setFromBits(int, BS) - Method in class org.jmol.geodesic.EnvelopeCalculation
- setFromEigenVectors(T3[], float[], String, String, Tensor) - Method in class org.jmol.util.Tensor
-
Standard constructor for charge and iso.
- setFromMatrix(float[], boolean) - Method in class org.jmol.symmetry.SymmetryOperation
- setFromMD(MeasurementData, boolean) - Method in class org.jmol.modelset.Measurement
- setFromThermalEquation(double[], String) - Method in class org.jmol.util.Tensor
-
standard constructor for thermal ellipsoids convention beta (see http://www.iucr.org/iucr-top/comm/cnom/adp/finrepone/finrepone.html)
- setFullPath(Map<String, Object>, String) - Method in class org.jmol.viewer.OutputManager
- setFunction(ScriptFunction) - Method in class org.jmol.script.ScriptFlowContext
- setFunction(ScriptFunction, String, int, int, short[], int[][], Lst<T[]>) - Static method in class org.jmol.script.ScriptFunction
- setFunctionXY(Lst<Object>) - Method in class org.jmol.jvxl.readers.Parameters
- setFunctionXYZ(Lst<Object>) - Method in class org.jmol.jvxl.readers.Parameters
- setGamma(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
- setGap(P3, int) - Method in class org.jmol.shapespecial.Polyhedra
- setGeneralBindings() - Method in class org.jmol.viewer.binding.JmolBinding
- setGestureSwipeFactor(float) - Method in class org.jmol.viewer.ActionManager
- setGhostOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setGlobals() - Method in class org.jmol.renderbio.BioShapeRenderer
- setGlobals() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- setGlobals() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
- setGouraud(int, int, int) - Method in class org.jmol.g3d.TriangleRenderer
- setGraphicsColor(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
- setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
- setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
- setGreyscaleMode(boolean) - Method in class org.jmol.util.GData
-
controls greyscale rendering
- setGridLimitsForAtom(P3, float, P3i, P3i) - Method in class org.jmol.jvxl.readers.AtomDataReader
- setGroup(Chain, String, int, int, int) - Method in class org.jmol.modelset.Group
- setGroup1(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
- setGroup1(ModelSet, int) - Method in interface org.jmol.api.JmolAnnotationParser
- setGroup1(ModelSet, int) - Method in class org.jmol.dssx.AnnotationParser
- setGroup1(ModelSet, int) - Method in class org.jmol.dssx.DSSR1
- setGroupID(String) - Method in class org.jmol.modelset.Group
- setGroupID(String) - Method in class org.jmol.modelsetbio.Monomer
- setGroupLists(int) - Method in class org.jmol.modelsetbio.BioResolver
- setGroupParameter(int, float) - Method in class org.jmol.modelsetbio.Monomer
- setGroupVisibilities() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setGroupVisible(PyMOLGroup, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Iterate through groups, setting visibility flags.
- setHasUnitCell() - Method in class org.jmol.modelkit.ModelKit
- setHaveHsAlready(boolean) - Method in class org.jmol.modelsetbio.BioResolver
- setHeader() - Method in class org.jmol.jvxl.readers.NffReader
- setHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
- setHeader() - Method in class org.jmol.jvxl.readers.Ras3DReader
- setHeader(String) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- setHeader(String, String) - Method in class org.jmol.jvxl.readers.AtomDataReader
- setHetero() - Method in class org.jmol.adapter.readers.cif.MMCifReader
- setHideNotSelected(boolean) - Method in class org.jmol.viewer.SelectionManager
- setHistory(String) - Method in class org.jmol.viewer.Viewer
- setHMSymbol(String) - Method in class org.jmol.symmetry.SpaceGroup
- setHorizAlignment(int, int) - Method in class org.jmol.shape.Labels
- setHorizAlignment(int, int) - Static method in class org.jmol.viewer.JC
- setHoverEnabled(boolean) - Method in class org.jmol.viewer.Viewer
- setHoverLabel(String) - Method in class org.jmol.viewer.Viewer
- setHoverLabel(String, String) - Method in class org.jmol.modelkit.ModelKit
- setHydrogen(int, int, String, P3) - Method in class org.jmol.modelsetbio.BioResolver
- setHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
-
Finalizes the hydrogen count hydrogens in a
SmilesMolecule
. - setHydrogens(BS) - Method in class org.jmol.viewer.Viewer
- setHydrophobicity(int, float) - Method in class org.jmol.modelset.AtomCollection
- setI(String, int) - Method in class org.jmol.viewer.GlobalSettings
- setIcon(Object) - Method in interface org.jmol.api.SC
- setIcon(Object) - Method in class org.jmol.awt.AwtSwingComponent
- setIcon(Object) - Method in class org.jmol.awtjs.swing.AbstractButton
- setImage(Object) - Method in interface org.jmol.api.GenericImageDialog
- setImage(Object) - Method in class org.jmol.console.ImageDialog
- setImage(Object) - Method in class org.jmol.modelset.Text
- setImageDimensions(int, int) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Sets the output image dimensions.
- setImageInfo(int, int, String) - Method in interface org.jmol.api.JmolDialogInterface
- setImageInfo(int, int, String) - Method in class org.jmol.dialog.Dialog
- setImplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the number of implicit hydrogen atoms bonded with this atom.
- setIndex(int) - Method in class org.jmol.smiles.SmilesAtom
-
Constructs a
SmilesAtom
. - setIndexes(DefaultMutableTreeNode) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Sets the indexes to the atomSetIndex values of each leaf of the node.
- setIndices() - Method in class org.jmol.shape.Measures
- setInfo(int, Object, Object) - Method in class org.jmol.modelset.ModelSet
- setInfo(String) - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- setInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setInfo(Viewer, Map<String, Object>, Atom[]) - Method in class org.jmol.shapespecial.Polyhedron
- setInMotion(boolean) - Method in class org.jmol.api.JmolViewer
- setInMotion(boolean) - Method in class org.jmol.viewer.Viewer
- setInsertedCommand(String) - Method in class org.jmol.viewer.Viewer
- setInt(int) - Method in class org.jmol.util.Rgb16
- setIntoFrame() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setIntoFrame() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setIntProperty(String, int) - Method in class org.jmol.api.JmolViewer
- setIntProperty(String, int) - Method in class org.jmol.script.ScriptParam
- setIntProperty(String, int) - Method in class org.jmol.viewer.Viewer
- setIntPropertyTok(String, int, int) - Method in class org.jmol.viewer.Viewer
- setInverseNormixes() - Static method in class org.jmol.util.Normix
- setInvoker(Object) - Method in class org.jmol.awtjs.swing.JPopupMenu
- setIsoMeshColor(IsosurfaceMesh, String) - Method in class org.jmol.shapesurface.Isosurface
- setIsPDB() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- SETITEM - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- SETITEMS - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- setIteratorForAtom(AtomIndexIterator, int, float) - Method in interface org.jmol.atomdata.AtomDataServer
- setIteratorForAtom(AtomIndexIterator, int, float) - Method in class org.jmol.viewer.Viewer
- setIteratorForAtom(AtomIndexIterator, int, int, float, RadiusData) - Method in class org.jmol.modelset.ModelSet
- setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in interface org.jmol.atomdata.AtomDataServer
- setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.modelset.ModelSet
- setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.viewer.Viewer
- setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.api.JmolViewer
- setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.Viewer
- setJmolDataFrame(String, int, int) - Method in class org.jmol.modelset.ModelSet
- setJmolDefaults() - Method in class org.jmol.api.JmolViewer
- setJmolDefaults() - Method in class org.jmol.viewer.StateManager
- setJmolDefaults() - Method in class org.jmol.viewer.Viewer
- setJmolLewisStructure(Map<String, Object>, int, int) - Method in class org.jmol.adapter.readers.quantum.NBOParser
-
Starting with a structure map, do what needs to be done to change the current Jmol structure to that in terms of bonding and formal charge.
- setJmolSize(Dimension) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.api.JmolViewer
- setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.Viewer
- setJSOptions(Map<String, Object>) - Method in class org.jmol.util.GenericApplet
- setJSpecView(String, boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- setJvxlColorMap(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
set up the jvxlData fields needed for either just the header (isAll = false) or the full file (isAll = true)
- setJvxlData(JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setJvxlDataRendering() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setJvxlInfo() - Method in class org.jmol.shapesurface.Isosurface
- setKeepChars(boolean) - Method in class org.jmol.adapter.readers.xml.XmlReader
- setLabel(int, String) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- setLabel(Object, BS) - Method in class org.jmol.viewer.ShapeManager
- setLabel(String) - Method in class org.openscience.jmol.app.jsonkiosk.BannerFrame
- setLabel(String, String) - Method in class org.jmol.modelkit.ModelKitPopup
- setLabel(LabelToken[][], String, int, boolean) - Method in class org.jmol.shape.Labels
- setLabelArray(String[]) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setLabelArray(String[]) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setLabelColix(int, short, byte) - Method in class org.jmol.shape.Labels
- setLabelPosition(P3, float[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setLabels() - Method in class org.jmol.console.GenericConsole
- setLabels() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- setLabels() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- setLabels(Map<String, String[]>, String, String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- setLabelString(int, String) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- setLastColix(int, boolean) - Method in class org.jmol.util.Shader
- setLastGrey(int) - Static method in class org.jmol.util.C
- setLattice(char, boolean) - Method in class org.jmol.symmetry.SpaceGroup
- setLattice(int) - Method in interface org.jmol.api.SymmetryInterface
-
set symmetry lattice type using Hall rotations
- setLattice(int) - Method in class org.jmol.symmetry.Symmetry
- setLatticeCells() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setLatticeParam(int) - Method in class org.jmol.symmetry.SpaceGroup
- setLatticeParameter(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setLatticeVectors() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- setLcao() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setLcao(String, int) - Method in class org.jmol.jvxl.readers.Parameters
- setLcaoOn(boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
- setLcaoOn(int, boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
- setLeadAtomIndex() - Method in class org.jmol.modelsetbio.Monomer
- setLeftComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
- setLengths() - Method in class org.jmol.shapespecial.Ellipsoid
- setLigandModel(String, String) - Method in class org.jmol.viewer.Viewer
- setLighting(int) - Method in class org.jmol.shape.Mesh
- setLightSource(float, float, float) - Method in class org.jmol.util.Shader
- setLine() - Method in class org.jmol.script.ScriptFlowContext
- setLine(String) - Method in interface org.jmol.api.JmolJDXMOLParser
- setLine(String) - Method in class org.jmol.jsv.JDXMOLParser
- setLinearOffsets() - Method in class org.jmol.jvxl.calc.MarchingCubes
- setLineBits(float, float) - Method in class org.jmol.g3d.LineRenderer
- setLink(int[], int[], String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- setLoader(ModelLoader) - Method in class org.jmol.modelsetbio.BioResolver
- setLoadFormat(String, char, boolean) - Method in class org.jmol.viewer.Viewer
-
Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first.
- setLoadNote() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setLoadParameters(Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
- setLoadState(Map<String, Object>) - Method in class org.jmol.viewer.FileManager
- setLobe(P4) - Method in class org.jmol.jvxl.readers.Parameters
- setLocalPath(Viewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
-
called by getImageFileNameFromDialog called by getOpenFileNameFromDialog called by getSaveFileNameFromDialog called by classifyName for any full file load called from the CD command currentLocalPath is set in all cases and is used specifically for dialogs as a first try defaultDirectoryLocal is set only when not from a dialog and is used only in getLocalPathForWritingFile or from an open/save dialog.
- setLocation(int[]) - Method in class org.jmol.awtjs.swing.JDialog
- setLogFile(String) - Method in class org.jmol.viewer.OutputManager
- setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
-
Replaces the current logger implementation by a new one.
- setLoggingEnabled(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- setLogic() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- setLogLevel(int) - Static method in class org.jmol.util.Logger
-
Activates all logging levels up through a given level.
- setLp(P4) - Method in class org.jmol.jvxl.readers.Parameters
- setlrefSingle(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setM(ModelSet, Measurement, float, short, String, int) - Method in class org.jmol.modelset.Measurement
- setMad(short) - Method in class org.jmol.modelset.Bond
- setMad(short, BS, float[]) - Method in class org.jmol.shapebio.BioShape
- setMadAtom(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
- setMads(int, boolean) - Method in class org.jmol.renderbio.BioShapeRenderer
-
set diameters for a bioshape
- setMads(short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
- setManager(Object, Viewer, Object) - Method in class org.jmol.minimize.MinimizationThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.script.CommandWatcherThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.AnimationThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.JmolThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.MoveToThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.SpinThread
- setManager(Object, Viewer, Object) - Method in class org.jmol.thread.VibrationThread
- setManagerMove(Object[]) - Method in class org.jmol.thread.MoveToThread
-
MOVE is a much simpler command.
- setManagerMoveTo(Object[]) - Method in class org.jmol.thread.MoveToThread
-
MOVETO is a more complex command.
- setMap(Map<String, String[]>, String, int, boolean) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
- setMapBitSet(Map<String, BS>, int, int, String) - Static method in class org.jmol.util.BSUtil
- setMappingPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
- setMapRanges(SurfaceReader, boolean) - Method in class org.jmol.jvxl.readers.Parameters
- setMarBond(short) - Method in class org.jmol.api.JmolViewer
- setMarBond(short) - Method in class org.jmol.viewer.Viewer
- setMargin(float) - Method in class org.jmol.util.BoxInfo
- SETMASK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- setMatchingAtom(Node, int) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the number of a matching atom in a molecule.
- setMatrices() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- setMatrix() - Method in class org.jmol.jvxl.data.VolumeData
- setMatrix(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
- setMatrixFromXYZ(String, int, boolean) - Method in class org.jmol.symmetry.SymmetryOperation
- setMaximumSize(int) - Method in class org.jmol.viewer.Viewer
- setMaxSize(int) - Method in class org.jmol.util.CommandHistory
-
Resets maximum size of command queue.
- setMenu(String, boolean) - Method in class org.jmol.api.JmolViewer
- setMenu(String, boolean) - Method in class org.jmol.viewer.Viewer
- setMenu(ModelKitPopup) - Method in class org.jmol.modelkit.ModelKit
- setMenuKeys(String, String) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setMenuKeys(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
-
opportunity to adjust menus for a custom application
- setMenuNBO(JMenu) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setMenuState() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setMep(float[], boolean) - Method in class org.jmol.jvxl.readers.Parameters
- setMerged(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setMesh(String) - Method in class org.jmol.shape.MeshCollection
- setMeshCreator(Object) - Method in class org.jmol.viewer.Viewer
-
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
- setMeshDisplayProperty(int, int, int) - Method in class org.jmol.script.ScriptEval
- setMeshI() - Method in class org.jmol.shapesurface.Isosurface
- setMeshTokenProperty(Mesh, int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
- setMinBondDistance(float) - Method in class org.jmol.api.JmolViewer
- setMinBondDistance(float) - Method in class org.jmol.viewer.Viewer
- setMinimizationOn(boolean) - Method in class org.jmol.minimize.Minimizer
- setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
- setMinimumSize(Dimension) - Method in class org.jmol.awtjs.swing.JScrollPane
- setMinMax(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
- setMinMax(int) - Method in class org.jmol.quantum.QuantumCalculation
- setMinMax(int, int, int, int, int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setMinMax0(P3, P3) - Method in class org.jmol.adapter.readers.cif.MSRdr
- setMinMax0(P3, P3) - Method in interface org.jmol.adapter.smarter.MSInterface
- setMinMaxLatticeParameters(int, P3i, P3i, int) - Static method in class org.jmol.util.SimpleUnitCell
- setMixingTime(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
sets the mixing time for the NOE experiment
- setMixingTimeSec(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
sets the mixing time for the NOE experiment
- setMixingTimeSec(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
sets the mixing time for the NOE experiment
- setMKState(int) - Method in class org.jmol.modelkit.ModelKit
- setMMTFSymmetry() - Method in class org.jmol.adapter.readers.cif.MMTFReader
- setMnemonic(char) - Method in interface org.jmol.api.JmolAbstractButton
- setMnemonic(char) - Method in class org.jmol.console.JmolLabel
- setMO(int, float[]) - Method in class org.jmol.jvxl.readers.Parameters
- setMO(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- setMod(String, P3, P3, int, Lst<Modulation>, M3, Matrix[], SymmetryInterface, int, int, Vibration, boolean) - Method in class org.jmol.util.ModulationSet
-
A collection of modulations for a specific atom.
- setMoData(Lst<Object[]>, int, float[], int, boolean, int, String, String, boolean) - Method in class org.jmol.scriptext.IsoExt
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MOReader
- setModDim(int) - Method in class org.jmol.adapter.readers.cif.MSRdr
- setModDim(int) - Method in class org.jmol.symmetry.SymmetryOperation
- setModel(int) - Method in interface org.jmol.api.JmolJSpecView
- setModel(int) - Method in class org.jmol.jsv.JSpecView
- setModel(int) - Method in class org.jmol.modelset.Trajectory
-
The user has used the MODEL command to switch to a new set of atom coordinates Or has specified a trajectory in a select, display, or hide command.
- setModel(int, boolean) - Method in class org.jmol.viewer.AnimationManager
- setModel(BS) - Method in class org.jmol.minimize.Minimizer
- setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceField
- setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
- setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in interface org.jmol.api.AtomIndexIterator
- setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.modelset.AtomIteratorWithinModel
- setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.symmetry.UnitCellIterator
- setModelCage(int, SymmetryInterface) - Method in class org.jmol.modelset.ModelSet
- setModelCagePts(int, T3[], String) - Method in class org.jmol.script.ScriptEval
- setModelFields() - Method in class org.jmol.minimize.forcefield.ForceField
- setModelIndex() - Method in class org.jmol.shapespecial.Dipoles
- setModelIndex(int) - Method in class org.jmol.modelset.StateScript
- setModelIndex(short) - Method in class org.jmol.modelset.Measurement
- setModelInfoForSet(String, Object, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
-
Sets auxiliary information for an AtomSet
- setModelkitMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- setModelKitMode(boolean) - Method in class org.jmol.viewer.Viewer
- setModelkitProperty(String, Object) - Method in class org.jmol.viewer.Viewer
- setModelKitRotateBondIndex(int) - Method in class org.jmol.viewer.Viewer
- setModelNameNumberProperties(int, int, String, int, Properties, Map<String, Object>, String) - Method in class org.jmol.modelset.ModelLoader
- setModelParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
- setModelPDB(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setModelSet(ModelSet) - Method in class org.jmol.modelset.MeasurementData
- setModelSet(ModelSet) - Method in class org.jmol.shape.Shape
- setModelSet(ModelSet) - Method in class org.jmol.viewer.ShapeManager
- setModelSet(ModelSet) - Method in class org.jmol.viewer.Viewer
- setModelVisibility() - Method in class org.jmol.viewer.ShapeManager
-
Sets shape visibility flags, including ATOM_VIS_INFRAME and ATOM_VIS_NOTHIDDEN.
- setModelVisibility() - Method in class org.jmol.viewer.Viewer
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Bbcage
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Halos
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.MeshCollection
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Shape
- setModelVisibilityFlags(BS) - Method in class org.jmol.shape.TextShape
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapebio.BioShapeCollection
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapecgo.CGO
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Dipoles
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Draw
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Ellipsoids
- setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Polyhedra
- setModeMouse(int) - Method in class org.jmol.viewer.ActionManager
-
only NONE (-1) is implemented; it just stops the hoverWatcher thread so that the vwr references are all removed
- setModifyKeys(Map<String, String>) - Method in class org.jmol.util.JSONWriter
- setModTQ(T3, boolean, T3, boolean, float) - Method in interface org.jmol.api.JmolModulationSet
- setModTQ(T3, boolean, T3, boolean, float) - Method in class org.jmol.util.ModulationSet
-
Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.
- setModulation(boolean, SymmetryInterface) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Both the Jana reader and the CIF reader will call this to set the modulation for a given model.
- setModulation(boolean, SymmetryInterface) - Method in interface org.jmol.adapter.smarter.MSInterface
- setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.modelset.ModelSet
-
Sets the modulation for all atoms in bs.
- setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.viewer.Viewer
- setModulationForStructure(int, boolean) - Method in class org.jmol.adapter.readers.cif.MSRdr
-
Called when structure creation is complete and all modulation data has been collected.
- setmolCDKuptodate(boolean) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setmolCDKuptodate(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setMolecularModulation(String, float, float) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
Add the modulation after applying rigid-body phase correction
- setMoment() - Method in interface org.jmol.api.JmolModulationSet
- setMoment() - Method in class org.jmol.util.ModulationSet
- setMore() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- setMore() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- setMorphCount(int) - Method in class org.jmol.viewer.AnimationManager
- setMOs(String) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
- setMotion(int, boolean) - Method in class org.jmol.viewer.ActionManager
- setMotionFixed(BS) - Method in class org.jmol.viewer.Viewer
- setMotionFixedAtoms(BS) - Method in class org.jmol.viewer.SelectionManager
- setMotionFixedAtoms(BS) - Method in class org.jmol.viewer.Viewer
- setMouseActions(int, int, boolean) - Method in class org.jmol.viewer.ActionManager
- setMouseDragFactor(float) - Method in class org.jmol.viewer.ActionManager
- setMouseMode() - Method in class org.jmol.viewer.ActionManager
- setMouseWheelFactor(float) - Method in class org.jmol.viewer.ActionManager
- setMovableBitSet(BS, boolean) - Method in class org.jmol.viewer.Viewer
- setMovableX(int) - Method in class org.jmol.modelset.Text
- setMovableXPercent(int) - Method in class org.jmol.modelset.Text
- setMovableY(int) - Method in class org.jmol.modelset.Text
- setMovableYPercent(int) - Method in class org.jmol.modelset.Text
- setMovableZPercent(int) - Method in class org.jmol.modelset.Text
- setMovie(Map<String, Object>) - Method in class org.jmol.viewer.AnimationManager
-
support for PyMOL movies and anim FRAMES [....] currently no support for scripted movies
- setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
- setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
- setMustResume() - Method in class org.jmol.script.ScriptContext
- setMyError(String) - Method in class org.jmol.adapter.readers.xml.XmlReader
- setName(String) - Method in interface org.jmol.api.SC
- setName(String) - Method in class org.jmol.awt.AwtSwingComponent
- setName(String) - Method in class org.jmol.awtjs.swing.Component
- setName(String) - Method in class org.jmol.script.SV
- setName(String) - Method in class org.jmol.symmetry.SpaceGroup
- setNames(String, BS, int) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- setNames(String, BS, int) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- setNavFps(int) - Method in class org.jmol.viewer.TransformManager
- setNavigatePt(P3) - Method in class org.jmol.viewer.TransformManager
-
scripted entry point for navigation
- setNavigationDepthPercent(float) - Method in interface org.jmol.api.JmolNavigatorInterface
- setNavigationDepthPercent(float) - Method in class org.jmol.navigate.Navigator
- setNavigationDepthPercent(float) - Method in class org.jmol.viewer.TransformManager
-
sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be <0 or >100)
- setNavigationDepthPercent(float) - Method in class org.jmol.viewer.Viewer
- setNavigationMode(boolean) - Method in class org.jmol.viewer.TransformManager
- setNavigationMode(boolean) - Method in class org.jmol.viewer.Viewer
- setNavigationOffsetRelative() - Method in interface org.jmol.api.JmolNavigatorInterface
- setNavigationOffsetRelative() - Method in class org.jmol.navigate.Navigator
- setNavigationOffsetRelative() - Method in class org.jmol.viewer.TransformManager
- setNavigationSlabOffsetPercent(float) - Method in class org.jmol.viewer.TransformManager
- setNavOn(boolean) - Method in class org.jmol.viewer.TransformManager
- setNavPercent(P3) - Method in class org.jmol.navigate.Navigator
- setNavXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
- setNboLabels(String[], int, Lst<Map<String, Object>>, int, String) - Static method in class org.jmol.adapter.readers.quantum.GenNBOReader
- setNBOType(Map<String, Object>, String) - Method in class org.jmol.scriptext.IsoExt
- setNci(boolean) - Method in class org.jmol.jvxl.readers.Parameters
- setNeighbors(int) - Method in class org.jmol.renderbio.BioShapeRenderer
- setNested(int, Object) - Method in class org.jmol.smiles.SmilesSearch
- setNewRotationCenter(P3) - Method in class org.jmol.viewer.Viewer
- setNewRotationCenter(P3, boolean) - Method in class org.jmol.viewer.TransformManager
- setNewSetCommand(boolean, String) - Method in class org.jmol.script.ScriptCompiler
- setNewWindowParametersForExport() - Method in class org.jmol.util.GData
- setNext(String, String, int[], int) - Static method in class org.jmol.jvxl.readers.XmlReader
-
shift pointer to a new tag or field contents
- setNMRfreq(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
-
set the NMR frequency for the NOE simulation
- setNMRfreqMHz(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
set the NMR frequency for the NOE simulation
- setNMRfreqMHz(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
-
set the NMR frequency for the NOE simulation
- setNoAutoBond() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setNode() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Set the atom to have substituents.
- setNode(int[], String) - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- setNoeExprefValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setNoeNPrefIndices(int[]) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setNOEs() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThread
- setNOEs() - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- setNoesy(boolean) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
sets the experiemnt type to NOESY or ROESY
- setNoesy(boolean) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- setNoesy(boolean) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setNoeWeight(double) - Method in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- setNonhydrogenDegree(int) - Method in class org.jmol.smiles.SmilesAtom
- setNoPrompt() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- setNormalization(Object) - Method in class org.jmol.quantum.MOCalculation
- setNormixes(V3[]) - Method in class org.jmol.shape.Mesh
- setO(String, Object) - Method in class org.jmol.viewer.GlobalSettings
- setOabc(String, float[], T3[]) - Static method in class org.jmol.util.SimpleUnitCell
-
set cell vectors by string
- setObjectArgb(String, int) - Method in class org.jmol.script.ScriptEval
- setObjectArgb(String, int) - Method in class org.jmol.viewer.Viewer
- setObjectColor(String, String) - Method in class org.jmol.viewer.Viewer
- setObjectMad10(int, String, int) - Method in class org.jmol.script.ScriptEval
- setObjectMad10(int, String, int) - Method in class org.jmol.viewer.Viewer
-
input here is a JC.SHAPE_xxxx identifier
- setObjectProp(String, int) - Method in class org.jmol.viewer.Viewer
- setObjectProp(String, int, int) - Method in class org.jmol.script.ScriptEval
- setObjectProperty() - Method in class org.jmol.script.ScriptEval
- setObjectPropSafe(String, int) - Method in interface org.jmol.api.JmolScriptEvaluator
- setObjectPropSafe(String, int) - Method in class org.jmol.script.ScriptEval
-
called by Viewer in setting up a PyMOL scene.
- setObjectVisibility(String, boolean) - Method in class org.jmol.viewer.Viewer
- setOccupancy(double[], double, double) - Method in class org.jmol.util.ModulationSet
-
get the occupancy, first from the reader, then from renderer
- setOccupancy(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
- setOffset(int) - Method in interface org.jmol.api.SymmetryInterface
- setOffset(int) - Method in class org.jmol.modelset.Text
- setOffset(int) - Method in class org.jmol.symmetry.Symmetry
- setOffset(P3) - Method in class org.jmol.shapespecial.Polyhedron
- setOffset(T3) - Method in class org.jmol.symmetry.UnitCell
- setOffsetPositions() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- setOffsetPt(P3) - Method in class org.jmol.shapespecial.Dipole
- setOffsetPt(T3) - Method in interface org.jmol.api.SymmetryInterface
- setOffsetPt(T3) - Method in class org.jmol.symmetry.Symmetry
- setOffsets(int, int) - Method in class org.jmol.shape.Labels
- setOopVariables(Calculation, boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- setOpacity255(int) - Method in class org.jmol.awt.AwtColor
- setOpacity255(int) - Method in class org.jmol.awtjs.swing.Color
- setOptions(String) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- setOptions(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
- setOrbital(int, float[]) - Method in class org.jmol.shapesurface.MolecularOrbital
- setOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
- setOrder(int) - Method in class org.jmol.modelset.Bond
- setOutputChannel(GenericBinaryDocument, OC) - Method in interface org.jmol.jvxl.api.MeshDataServer
- setOutputChannel(GenericBinaryDocument, OC) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setOutputChannel(GenericBinaryDocument, OC) - Method in class org.jmol.shapesurface.Isosurface
- setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setOxidationStates() - Method in class org.jmol.adapter.readers.cif.CifReader
- setPairVariables(Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
- setPanel(JPanel) - Method in class org.openscience.jmol.app.jsonkiosk.KioskFrame
- setParallel() - Method in class org.jmol.viewer.ShapeManager
- setParallel(boolean) - Method in class org.jmol.viewer.Viewer
- setparam - Static variable in class org.jmol.script.T
- setParameter(String, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
- setParameters(VolumeData, Parameters) - Method in class org.jmol.jvxl.calc.MarchingCubes
- setParams(Object[], int[], BS) - Method in class org.jmol.shapebio.BioShape
- setParamsFromMatrix() - Method in class org.jmol.util.SimpleUnitCell
- setParent(Object) - Method in class org.jmol.awtjs.swing.Component
- setPartialCharge(int, float, boolean) - Method in class org.jmol.modelset.AtomCollection
- setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
- setPass2(boolean) - Method in class org.jmol.util.GData
- setPathForAllFiles(String) - Method in class org.jmol.viewer.FileManager
- setPdbConectBonding(int, int, BS) - Method in class org.jmol.modelset.ModelSet
- setPeakData(Lst<Object[]>, int) - Method in class org.jmol.jsv.JDXMOLParser
- setPendingMeasurement(MeasurementPending) - Method in class org.jmol.viewer.Viewer
- setPercentVdwAtom(int) - Method in class org.jmol.api.JmolViewer
- setPercentVdwAtom(int) - Method in class org.jmol.viewer.Viewer
- setPerspectiveDepth(boolean) - Method in class org.jmol.api.JmolViewer
- setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.TransformManager
- setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.Viewer
- setPhongExponent(int) - Method in class org.jmol.util.GData
-
p in I = df * (N dot L) + sf * (R dot V)^p
- setPhononVector(float[], Atom, V3, V3, V3) - Method in class org.jmol.adapter.readers.xtal.CastepReader
-
transform complex vibration vector to a real vector by applying the appropriate translation, storing the results in v
- setPicked(int, boolean) - Method in class org.jmol.viewer.Viewer
- setPickingMode(int) - Method in class org.jmol.viewer.ActionManager
- setPickingMode(String, int) - Method in class org.jmol.viewer.Viewer
- setPickingStyle(int) - Method in class org.jmol.viewer.ActionManager
- setPickingStyle(String, int) - Method in class org.jmol.viewer.Viewer
- setPlanarKey(int, int, int, int, Boolean) - Method in class org.jmol.inchi.InChIJNI
- setPlane(int, float[]) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- setPlane(P4) - Method in class org.jmol.jvxl.readers.Parameters
- setPlaneParameters(P4) - Method in class org.jmol.jvxl.data.VolumeData
- setPlanes(float[][]) - Method in class org.jmol.quantum.NciCalculation
-
Raw file data planes are passed to us here from VolumeFileReader
- setPlanes(float[][]) - Method in class org.jmol.quantum.QuantumPlaneCalculation
-
Planes to use for holding raw file data.
- setPluginOption(String, String, String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setPlugins() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setPoint(float[], int, int, int) - Static method in class org.jmol.util.MeshSlicer
- setPointer(int, int) - Method in class org.jmol.shape.Labels
- setPointer(int, int) - Static method in class org.jmol.viewer.JC
- setPointGroup(SymmetryInterface, T3, T3[], BS, boolean, float, float, int, boolean) - Method in interface org.jmol.api.SymmetryInterface
- setPointGroup(SymmetryInterface, T3, T3[], BS, boolean, float, float, int, boolean) - Method in class org.jmol.symmetry.Symmetry
- setPoints(int) - Method in class org.jmol.shape.Axes
- setPoints(int, int) - Method in class org.jmol.shapespecial.Draw
- setPoints(ModelSet, int[], Point3fi[], TickInfo) - Method in class org.jmol.modelset.Measurement
- setPointsFromBitset() - Method in class org.jmol.shapespecial.Polyhedra
- setPolygon(int) - Method in class org.jmol.shapespecial.Draw
- setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
- setPopInDim(int, int) - Static method in class org.openscience.jmol.app.webexport.WebExport
- setPopulationDisplay(PopulationDisplay) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- setPos(float) - Method in class org.jmol.modelset.Text
- setPosition(float, float, boolean, float[]) - Method in class org.jmol.modelset.Text
- setPositions() - Method in class org.jmol.adapter.readers.simple.AmpacReader
- setPreferredScrollableViewportSize(Dimension) - Method in class org.jmol.awtjs.swing.JTable
- setPreferredSize(Dimension) - Method in class org.jmol.awtjs.swing.Component
- setPreferredWidth(int) - Method in interface org.jmol.awtjs.swing.TableColumn
- setPreliminary(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- setPreserveState(boolean) - Method in class org.jmol.modelset.AtomCollection
- setPreviewOptions(boolean) - Method in class org.jmol.dialog.FilePreview
- setPrimitive(int) - Method in class org.jmol.smiles.SmilesBond
- setPrincipalAxis(int, int) - Method in class org.jmol.symmetry.PointGroup
- setPrincipalPlane(int, int) - Method in class org.jmol.symmetry.PointGroup
- setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
- setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
- setProp(String, Object, BS) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setProp(Ellipsoid, int, Object) - Method in class org.jmol.shapespecial.Ellipsoids
- setPropAS(String, Object, BS) - Method in class org.jmol.shape.AtomShape
- setPropBSC(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
- setProperties(String, float[], int) - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- setProperties(Properties) - Method in interface org.jmol.api.JSVInterface
- setProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- setProperties(Lst<Object>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
-
Set property_xxx for atoms from list of name, data, modelIndex series.
- setProperty(String, Object) - Method in class org.jmol.minimize.Minimizer
- setProperty(String, Object) - Method in class org.jmol.modelkit.ModelKit
-
Modify the state by setting a property.
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Axes
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Balls
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Bbcage
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Echo
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Frank
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Halos
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Hover
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Labels
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Measures
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Shape
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Stars
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Sticks
- setProperty(String, Object, BS) - Method in class org.jmol.shape.Uccage
- setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Backbone
- setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShape
- setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
- setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Trace
- setProperty(String, Object, BS) - Method in class org.jmol.shapecgo.CGO
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dipoles
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dots
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Draw
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Ellipsoids
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Polyhedra
- setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Vectors
- setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Contact
- setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
- setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.LcaoCartoon
- setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.MolecularOrbital
- setPropertyColorRange(float, float) - Method in class org.jmol.viewer.ColorManager
- setPropertyColorRangeData(float[], BS) - Method in class org.jmol.viewer.ColorManager
- setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.ColorManager
- setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- setPropertyFor(int, Dipole, int, float) - Method in class org.jmol.shapespecial.Dipoles
- setPropertySuper(String, Object, BS) - Method in class org.jmol.shapecgo.CGO
- setPropertySuper(String, Object, BS) - Method in class org.jmol.shapespecial.Draw
- setPropertySuper(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
- setPropertyTok(int, boolean, int, float) - Method in class org.jmol.shapespecial.Dipoles
- setPropFLS(String, Object) - Method in class org.jmol.shape.FontLineShape
- setPropI(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
- setPropMC(String, Object, BS) - Method in class org.jmol.shape.MeshCollection
- setProps(String, String, int) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
- setProps(String, String, int) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
- setPropS(String, Object, BS) - Method in class org.jmol.shape.Shape
- setPropTS(String, Object, BS) - Method in class org.jmol.shape.TextShape
- setProteinStructureType(STR, int) - Method in class org.jmol.modelset.Group
- setProteinStructureType(STR, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
- setProteinType(BS, STR) - Method in class org.jmol.modelset.ModelSet
- setProteinType(STR, BS) - Method in class org.jmol.viewer.Viewer
- setPt0(int, boolean) - Method in class org.jmol.script.ScriptFlowContext
- setPtVector(P3, V3) - Method in class org.jmol.shapespecial.Dipole
- setPutty(float[], BS) - Method in class org.jmol.shapebio.Trace
-
PyMOL-based "putty"
- setPyMOLDefaults() - Method in class org.jmol.viewer.StateManager
- setPymolLabel(int, Text, String) - Method in class org.jmol.shape.Labels
- setPymolLabels(Map<Integer, Text>, BS) - Method in class org.jmol.shape.Labels
- setPymolOffset(int, float[]) - Method in class org.jmol.shape.Labels
-
Sets offset using PyMOL standard array; only operates in cases where label is already defined
- setRadical(P4) - Method in class org.jmol.jvxl.readers.Parameters
- setRadii() - Method in class org.jmol.jvxl.readers.AtomDataReader
- setRadius(float) - Method in class org.jmol.modelset.Atom
- setRange(float, float, boolean) - Method in class org.jmol.util.ColorEncoder
- setRanges(float, int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
- setRasmolDefaults() - Method in class org.jmol.api.JmolViewer
- setRasmolDefaults() - Method in class org.jmol.viewer.Viewer
- setRasMolDefaults() - Method in class org.jmol.viewer.StateManager
- setRastAB(int, int, int, int) - Method in class org.jmol.g3d.PrecisionRenderer
- setRastABFloat(float, float, float, float) - Method in class org.jmol.g3d.PrecisionRenderer
- setReader() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setReader(CifReader) - Method in interface org.jmol.adapter.readers.cif.CifReader.Parser
- setReader(CifReader) - Method in class org.jmol.adapter.readers.cif.TopoCifParser
-
filter "TOPOS_TYPES=hb" will only load hydrogen bonds; options include v, vw, and hb
- setReaderObjectInfo(String, int, String, boolean, Lst<Object>, Lst<Object>, String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setReaderObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setRedLevel(double) - Method in class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- setRedValue(double) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setRedValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setRef(V3) - Method in class org.jmol.smiles.PolyhedronStereoSorter
- setRefreshing(boolean) - Method in class org.jmol.viewer.Viewer
- setRequiredFile(String, String) - Method in interface org.jmol.jvxl.api.MeshDataServer
- setRequiredFile(String, String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
- setRequiredFile(String, String) - Method in class org.jmol.shapesurface.Isosurface
- setRes(Atom) - Method in class org.jmol.dssx.DSSR1
- setResno(int) - Method in class org.jmol.modelset.Group
- setRgb(Rgb16) - Method in class org.jmol.util.Rgb16
- setRhoStar(double) - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- setRhoStar(double) - Method in class org.openscience.jmol.app.janocchio.NmrMolecule
- setRhoStar(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setRightComponent(JComponent) - Method in class org.jmol.awtjs.swing.JSplitPane
- setRigidBodyPhase(String, double[]) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
Adjust phases to match the difference between the atom's position and the rigid molecular fragment's reference point.
- setRigidBodyRotations(String, float[][]) - Method in class org.jmol.adapter.readers.xtal.JanaReader
-
Transform unphased Fourier x,y,z cos/sin coefficients in a rigid body system based on distance from center.
- setRingConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
- setRingData(BS, Lst<BS>[], boolean) - Method in class org.jmol.smiles.SmilesSearch
-
Sets up all aromatic and ring data.
- setRingMembership(int) - Method in class org.jmol.smiles.SmilesAtom
- setRingsClickable() - Method in class org.jmol.modelsetbio.NucleicMonomer
- setRingSize(int) - Method in class org.jmol.smiles.SmilesAtom
- setRingsVisible(boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
- setRotateMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- setRotation(M3) - Method in class org.jmol.viewer.TransformManager
- setRotationCenterAndRadiusXYZ(T3, boolean) - Method in class org.jmol.viewer.TransformManager
- setRotationMatrix(M3) - Method in class org.jmol.g3d.Graphics3D
- setRotationPointXY(P3) - Method in class org.jmol.viewer.TransformManager
- setRotationRadius(float, boolean) - Method in class org.jmol.viewer.TransformManager
- setRotationRadius(float, boolean) - Method in class org.jmol.viewer.Viewer
- setRotationRadius(int, float) - Method in class org.jmol.modelset.ModelSet
- setRowSelectionAllowed(boolean) - Method in class org.jmol.awtjs.swing.JTable
- setRowSelectionInterval(int, int) - Method in class org.jmol.awtjs.swing.JTable
- setRubberbandArgb(int) - Method in class org.jmol.viewer.ColorManager
- setRule6Full(boolean) - Method in class org.jmol.symmetry.CIPData
- setSaveEnabled(String) - Method in class org.jmol.console.ScriptEditor
- setScale() - Method in class org.jmol.viewer.ShapeManager
- setScale(float) - Method in class org.jmol.modelset.Text
- setScale(float) - Method in class org.jmol.shape.Axes
- setScale(float, boolean) - Method in class org.jmol.shapespecial.Ellipsoid
- setScaleAngstromsPerInch(float) - Method in class org.jmol.viewer.TransformManager
- setScalePixelsPerMicron(float) - Method in class org.jmol.modelset.Text
- setScaling() - Method in class org.jmol.shape.Labels
- setSceneObject(String, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Set scene object/state-specific global fields and settings based on the name and state or stored values from when the file was loaded.
- setScreenDimension(int, int) - Method in class org.jmol.api.JmolViewer
- setScreenDimension(int, int) - Method in class org.jmol.util.GenericApplet
- setScreenDimension(int, int) - Method in class org.jmol.viewer.Viewer
- setScreened(boolean) - Method in class org.jmol.g3d.Graphics3D
- setScreeni(P3, P3i) - Method in class org.jmol.g3d.Graphics3D
- setScreenParameters(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
- setScreenParameters0(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
- setScript(String) - Method in class org.jmol.modelset.Text
- setScript(String) - Method in class org.jmol.script.ScriptFunction
- setScriptButtonPercent(int) - Static method in class org.openscience.jmol.app.webexport.WebExport
- setScriptEcho(String, boolean) - Method in class org.jmol.viewer.StatusManager
- setScriptExtensions() - Method in class org.jmol.script.ScriptEval
- setScriptFileReferences(String, String, String, String) - Static method in class org.jmol.viewer.FileManager
- setScriptFileRefs(String, String, boolean) - Static method in class org.jmol.viewer.FileManager
-
Sets all local file references in a script file to point to files within dataPath.
- setScriptInfo(String) - Method in class org.jmol.shapesurface.Isosurface
- setScriptQueue(boolean) - Method in class org.jmol.viewer.Viewer
- setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.StatusManager
- setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.Viewer
- setSecStrucMenu(SC, Map<String, Object>) - Method in class org.jmol.popup.JmolPopup
- setSelectAllSubset(boolean) - Method in class org.jmol.viewer.AnimationManager
- setSelectBindings() - Method in class org.jmol.viewer.binding.DragBinding
- setSelectBindings() - Method in class org.jmol.viewer.binding.JmolBinding
- setSelectBindings() - Method in class org.jmol.viewer.binding.PfaatBinding
- setSelectBindings() - Method in class org.jmol.viewer.binding.RasmolBinding
- setSelected(boolean) - Method in interface org.jmol.api.SC
- setSelected(boolean) - Method in class org.jmol.awt.AwtSwingComponent
- setSelected(boolean) - Method in class org.jmol.awtjs.swing.AbstractButton
- setSelected(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- setSelected(BS) - Method in class org.jmol.smiles.SmilesSearch
- setSelected(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
Convey to the HTML object that this check box's selection has been changed.
- setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.SelectionManager
- setSelectedAtomIndex(int) - Method in class org.openscience.jmol.app.janocchio.LabelSetter
- setSelectedFloats(float, BS, float[]) - Static method in class org.jmol.viewer.DataManager
- setSelectedIndex(int) - Method in class org.jmol.awtjs.swing.JComboBox
- setSelectedIndex(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
Convey to the HTML object that this combo box's selected item has been changed.
- setSelectedOctant() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
- setSelectedTranslation(BS, char, float, float) - Method in class org.jmol.viewer.TransformManager
- setSelectedValue(int, int, SV) - Method in class org.jmol.script.SV
- setSelectionHalos(boolean) - Method in class org.openscience.jmol.app.janocchio.NMR_Viewer
- setSelectionHalosEnabled(boolean) - Method in class org.jmol.viewer.Viewer
- setSelectionSet(BS) - Method in class org.jmol.api.JmolViewer
- setSelectionSet(BS) - Method in class org.jmol.viewer.Viewer
- setSelectionSet(BS, int) - Method in class org.jmol.viewer.SelectionManager
- setSelectionSubset(BS) - Method in class org.jmol.viewer.SelectionManager
- setShapeErrorState(int, String) - Method in class org.jmol.viewer.Viewer
- setShapeId(int, int, boolean) - Method in class org.jmol.scriptext.ScriptExt
- setShapeNameParameter(int) - Method in class org.jmol.script.ScriptEval
- setShapeProperty(int, String, Object) - Method in class org.jmol.script.ScriptEval
- setShapeProperty(int, String, Object) - Method in class org.jmol.scriptext.ScriptExt
- setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Viewer
- setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.script.ScriptEval
- setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.viewer.ShapeManager
- setShapeSize(int, int, BS) - Method in class org.jmol.viewer.Viewer
- setShapeSize(int, RadiusData) - Method in class org.jmol.script.ScriptEval
- setShapeSizeBs(int, int, BS) - Method in class org.jmol.script.ScriptEval
- setShapeSizeBs(int, int, RadiusData, BS) - Method in class org.jmol.viewer.ShapeManager
- setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shape.Shape
- setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.Backbone
- setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.BioShapeCollection
- setShapeTranslucency(int, String, String, float, BS) - Method in class org.jmol.script.ScriptEval
- setShapeVis() - Method in class org.jmol.viewer.ShapeManager
- setShapeVisibility(boolean) - Method in class org.jmol.modelset.Bond
- setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Atom
- setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Group
- setShowAxes(boolean) - Method in class org.jmol.viewer.Viewer
- setShowBbcage(boolean) - Method in class org.jmol.viewer.Viewer
- setShowHydrogens(boolean) - Method in class org.jmol.api.JmolViewer
- setShowHydrogens(boolean) - Method in class org.jmol.viewer.Viewer
- setShowMeasurements(boolean) - Method in class org.jmol.api.JmolViewer
- setShowMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
- setShowUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
- setShowWithin(Lst<P3>, float, boolean) - Method in class org.jmol.shape.Mesh
- setSigma(String, Matrix) - Method in class org.jmol.symmetry.SymmetryOperation
- setSilent(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
- setSimpleCage(SymmetryInterface) - Method in class org.jmol.modelset.Model
- setSingleItem(Lst<Object>) - Method in class org.jmol.shape.Measures
- setSite(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
- setSize(float) - Method in class org.jmol.adapter.readers.pymol.JmolObject
- setSize(int, float) - Method in class org.jmol.script.ScriptEval
- setSize(int, BS) - Method in class org.jmol.shape.AtomShape
- setSize(int, BS) - Method in class org.jmol.shape.Balls
- setSize(int, BS) - Method in class org.jmol.shape.Measures
- setSize(int, BS) - Method in class org.jmol.shape.Shape
- setSize(int, BS) - Method in class org.jmol.shape.Sticks
-
sets the size of a bond, or sets the selectedBonds set
- setSize(int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
- setSize2(int, BS) - Method in class org.jmol.shape.AtomShape
- setSizeBio(int) - Method in class org.jmol.script.ScriptEval
- setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.AtomShape
- setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Balls
- setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Shape
- setSizeRD(RadiusData, BS) - Method in class org.jmol.shapespecial.Dots
- setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shape.AtomShape
- setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shapespecial.Vectors
- setSlab(int) - Method in interface org.jmol.api.JmolGraphicsInterface
- setSlab(int) - Method in class org.jmol.export.Export3D
- setSlab(int) - Method in class org.jmol.util.GData
-
clipping from the front and the back
- setSlabAndZShade(int, int, int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
- setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.export.Export3D
- setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.util.GData
- setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.TransformManager
-
set internal slab or depth from screen-based slab or depth
- setSlabEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
- setSlabRange(float) - Method in class org.jmol.viewer.TransformManager
- setSlaters(boolean) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
after the vectors intinfo and floatinfo are completed, we
- setSlice(float, float, float, float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
-
Defines a slice within which isosurfaces (and in future? atoms) are displayed.
- setSlice(float, float, float, float, P3, V3, boolean) - Method in class org.openscience.jmol.app.surfacetool.Slice
-
Sets the right plane and left plane bounding a slice.
- setSliceAnglefromZ(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setSliceAngleXY(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setSlicePosition(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setSliceThickness(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setSmilesString(String) - Method in class org.jmol.viewer.Viewer
- setSolvent(String, float) - Method in class org.jmol.jvxl.readers.Parameters
- setSortingStatus(int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setSpaceGroup(boolean) - Method in interface org.jmol.api.SymmetryInterface
- setSpaceGroup(boolean) - Method in class org.jmol.symmetry.Symmetry
- setSpaceGroup(int, SymmetryInterface, BS) - Method in class org.jmol.modelset.ModelSet
- setSpaceGroupFrom(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setSpaceGroupName(String) - Method in interface org.jmol.api.SymmetryInterface
- setSpaceGroupName(String) - Method in class org.jmol.symmetry.Symmetry
- setSpaceGroupTo(Object) - Method in interface org.jmol.api.SymmetryInterface
- setSpaceGroupTo(Object) - Method in class org.jmol.symmetry.Symmetry
- setSpectraMenu(SC, Lst<String>) - Method in class org.jmol.popup.JmolPopup
- setSpectrumPeaks(int, String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
- setSpectrumPeaks(int, String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
- setSpecular(boolean) - Method in class org.jmol.util.GData
- setSpecularExponent(int) - Method in class org.jmol.util.GData
-
log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of shades
- setSpecularPercent(int) - Method in class org.jmol.util.GData
-
sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything, really
- setSpecularPower(int) - Method in class org.jmol.util.GData
-
fractional distance to white for specular dot
- setSphere(float, boolean) - Method in class org.jmol.jvxl.readers.Parameters
- setSphereMatrix(T3, float, float, float, A4, M4) - Method in class org.jmol.export.__CartesianExporter
- setSpin(String, int) - Method in class org.jmol.viewer.Viewer
- setSpin(JmolScriptEvaluator, boolean, float, Lst<P3>, float[], BS, boolean) - Method in class org.jmol.viewer.TransformManager
- setSpinFps(int) - Method in class org.jmol.viewer.TransformManager
- setSpinOff() - Method in class org.jmol.viewer.TransformManager
- setSpinOn() - Method in class org.jmol.viewer.TransformManager
- setSpinVectors() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setSpinXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
- setsSuccessful - Variable in class org.jmol.jvxl.data.MeshData
- setStartupBooleans() - Method in class org.jmol.viewer.Viewer
- setState() - Method in class org.jmol.console.ScriptEditor
- setStateCount(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setStatement(T[], int) - Method in class org.jmol.script.ScriptExpr
-
provides support for @x and @{....} in statements.
- setStateScriptVersion(Viewer, String) - Static method in class org.jmol.script.ScriptManager
- setStatic(int, int) - Method in interface org.jmol.api.JmolScriptEvaluator
- setStatic(int, int) - Method in class org.jmol.script.ScriptEval
-
set a static variable, with checking for range
- setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusBar
- SetStatusAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
- setStatusAppletReady(String, boolean) - Method in class org.jmol.viewer.StatusManager
- setStatusAtomHovered(int, String) - Method in class org.jmol.viewer.StatusManager
- setStatusAtomMoved(boolean, BS) - Method in class org.jmol.viewer.Viewer
- setStatusAtomMoved(BS) - Method in class org.jmol.viewer.StatusManager
- setStatusAtomPicked(int, String, Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
- setStatusAtomPicked(int, String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
- setStatusChanged(String, int, Object, boolean) - Method in class org.jmol.viewer.StatusManager
- setStatusClicked(int, int, int, int, int) - Method in class org.jmol.viewer.StatusManager
- setStatusDragDropped(int, int, int, String, String[]) - Method in class org.jmol.util.GenericApplet
- setStatusDragDropped(int, int, int, String, String[]) - Method in class org.jmol.viewer.StatusManager
- setStatusDragDropped(int, int, int, String, String[]) - Method in class org.jmol.viewer.Viewer
-
Allows a handler to set Jmol variable doDrop=false to cancel and also set the file type directly (Java) via the Jmol variable dropFileType (Java or JavaScript) if desired.
- setStatusFrameChanged(boolean, boolean) - Method in class org.jmol.viewer.Viewer
- setStatusFrameChanged(int, int, int, int, int, float, String) - Method in class org.jmol.viewer.StatusManager
- setStatusListener(JmolStatusListener) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.StatusManager
- setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.Viewer
- setStatusModelKit(int) - Method in class org.jmol.viewer.StatusManager
- setStatusObjectHovered(String, String, T3) - Method in class org.jmol.viewer.StatusManager
- setStatusPicked(int, T3, Map<String, Object>) - Method in class org.jmol.shape.MeshCollection
- setStatusResized(int, int) - Method in class org.jmol.viewer.StatusManager
- setStatusResized(int, int) - Method in class org.jmol.viewer.Viewer
-
resizeCallback is called whenever the applet gets a resize notification from the browser jmolSetCallback("resizeCallback", "myResizeCallback") function myResizeCallback(width, height) {}
- setStatusSelect(BS) - Method in class org.jmol.viewer.StatusManager
-
Callback for selection change.
- setStatusSelect(BS) - Method in class org.jmol.viewer.Viewer
-
Make the SelectCallback call and reset the hasSelected value to false.
- setStatusStructureModified(int, int, int, String, int, BS) - Method in class org.jmol.viewer.StatusManager
- setStereo(boolean, Object) - Method in class org.jmol.viewer.Viewer
- setStereoDegrees(float) - Method in class org.jmol.viewer.TransformManager
- setStereoFromSmiles(BS, int, SimpleNode[]) - Method in class org.jmol.symmetry.CIPChirality
- setStereoGraphics(boolean) - Method in interface org.jmol.api.JmolAppletInterface
- setStereoGraphics(boolean) - Method in class org.jmol.util.GenericApplet
- setStereoMode(int[], STER, float) - Method in class org.jmol.viewer.Viewer
- setStereoMode(STER) - Method in class org.jmol.viewer.TransformManager
- setStereoMode2(int[]) - Method in class org.jmol.viewer.TransformManager
- setStereoTemp(SimpleNode[], SimpleNode, float) - Method in class org.jmol.smiles.SmilesGenerator
- setStrandCount() - Method in class org.jmol.renderbio.StrandsRenderer
- setStrandCount(int, int) - Method in class org.jmol.viewer.Viewer
- setStream(OutputStream) - Method in class org.jmol.util.JSONWriter
- setStream(String, boolean) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- setStringProperty(String, String) - Method in class org.jmol.api.JmolViewer
- setStringProperty(String, String) - Method in class org.jmol.script.ScriptParam
- setStringProperty(String, String) - Method in class org.jmol.util.GenericApplet
- setStringProperty(String, String) - Method in class org.jmol.viewer.Viewer
- setStringPropertyTok(String, int, String) - Method in class org.jmol.viewer.Viewer
- setStrokeBold(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
- setStrokeBold(Object, boolean) - Method in class org.jmol.awt.AwtG2D
- setStrokeBold(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
- setStrucNo(int) - Method in class org.jmol.modelset.Group
- setStrucNo(int) - Method in class org.jmol.modelsetbio.AlphaMonomer
- setStrucNo(int) - Method in class org.jmol.modelsetbio.Monomer
- setStructure - Variable in class org.jmol.dssx.DSSP
- setStructure(String, Translator) - Method in class org.jmol.popup.PopupResource
- setStructure(JmolAdapterStructureIterator) - Method in class org.jmol.modelsetbio.BioResolver
-
note that istart and iend will be adjusted.
- setStructure(ProteinStructure) - Method in class org.jmol.modelsetbio.AlphaMonomer
- setStructureBS(int, int, STR, BS, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
-
bits in the bitset determines the type
- setStructureIndexes() - Method in class org.jmol.modelset.ModelSet
- setStructureList(float[], STR) - Method in class org.jmol.viewer.GlobalSettings
- setStructureList(float[], STR) - Method in class org.jmol.viewer.Viewer
- setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelset.ModelSet
- setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.AminoPolymer
- setStructureTypes() - Method in class org.jmol.renderbio.BioShapeRenderer
- setStrut(int, int, int, Lst<Atom>, BS, BS, Lst<Atom[]>, BS, BS, BS, int) - Static method in class org.jmol.modelsetbio.BioExt
- setSubsystem(String, Subsystem) - Method in class org.jmol.adapter.readers.cif.MSRdr
- setSubsystemOptions() - Method in class org.jmol.adapter.readers.cif.MSRdr
- setSurfaceInfo(P4, P3, int, String) - Method in class org.jmol.jvxl.data.JvxlData
- setSurfaceInfoFromBitSet(BS, P4) - Method in class org.jmol.jvxl.data.JvxlData
- setSurfaceInfoFromBitSetPts(BS, P4, P3) - Method in class org.jmol.jvxl.data.JvxlData
- setSurfaceToolParam() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setSymbol(String) - Method in class org.jmol.smiles.SmilesAtom
-
Sets the symbol of the atm.
- setSymEdit(int) - Method in class org.jmol.modelkit.ModelKit
- setSymmetry() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- setSymmetry() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
- setSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.Subsystem
- setSymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setSymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setSymmetryInfo(int, Map<String, Object>, float[]) - Method in interface org.jmol.api.SymmetryInterface
- setSymmetryInfo(int, Map<String, Object>, float[]) - Method in class org.jmol.symmetry.Symmetry
-
Set space group and unit cell from the auxiliary info generated by the model adapter.
- setSymmetryInfo(Map<String, Object>, float[], SpaceGroup) - Method in class org.jmol.symmetry.SymmetryInfo
- setSymmetryMinMax(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setSymmetryOperator(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setSymmetryOps() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setSymmetryRange(float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setSymop(int, boolean) - Method in class org.jmol.modelset.Atom
- setSymViewState(int) - Method in class org.jmol.modelkit.ModelKit
- setSync() - Method in class org.jmol.viewer.Viewer
- setSync(String) - Method in class org.jmol.viewer.StatusManager
- setSyncDriver(int) - Method in class org.jmol.viewer.StatusManager
- setSyncDriver(int) - Method in class org.jmol.viewer.Viewer
- setSyncStarting() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setSyncTarget(int, boolean) - Method in class org.jmol.viewer.Viewer
- settable - Static variable in class org.jmol.script.T
- setTableHeader(JTableHeader) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setTableModel(TableModel) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setTag(char[], BS, char) - Method in class org.jmol.dssx.DSSP
- setTainted(boolean) - Method in class org.jmol.viewer.Viewer
- setTaintedAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
- setTAtom(Atom, Atom) - Static method in class org.jmol.adapter.readers.cif.TopoCifParser
- setTempPoints(P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
- setTempVertex(T3, T3, T3) - Static method in class org.jmol.export.___Exporter
- setTensor(Tensor) - Method in class org.jmol.shapespecial.Ellipsoid
- setTensors() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setTensors() - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setText(String) - Method in interface org.jmol.api.JmolAbstractButton
- setText(String) - Method in interface org.jmol.api.js.GenericConsoleTextArea
- setText(String) - Method in interface org.jmol.api.SC
- setText(String) - Method in class org.jmol.awt.AwtSwingComponent
- setText(String) - Method in class org.jmol.awtjs.swing.Component
- setText(String) - Method in interface org.jmol.awtjs.swing.SwingController
-
Convey to the HTML object that this component's text has been changed.
- setText(String) - Method in interface org.jmol.console.GenericTextArea
- setText(String) - Method in class org.jmol.modelset.Text
- setText(String, String) - Method in class org.jmol.popup.GenericPopup
- setText(String, Font, int, int, int, int, int) - Method in class org.jmol.g3d.TextString
- setTextPosition(int) - Method in class org.jmol.util.GData
- setThisScheme(String, int[]) - Method in class org.jmol.util.ColorEncoder
- setTimeout(String, int, String) - Method in class org.jmol.viewer.Viewer
- setTimeout(Viewer, Map<String, Object>, String, int, String) - Static method in class org.jmol.thread.TimeoutThread
- setTimeReversal(int) - Method in class org.jmol.symmetry.SymmetryOperation
-
set the time reversal, and indicate internally in xyz as appended ",m" or ",-m"
- setTimeReversal(int, int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setTimeReversal(int, int) - Method in interface org.jmol.api.SymmetryInterface
- setTimeReversal(int, int) - Method in class org.jmol.symmetry.Symmetry
- settings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- setTitle() - Method in class org.jmol.console.GenericConsole
- setTitle() - Method in class org.jmol.console.JmolConsole
- setTitle() - Method in class org.jmol.consolejs.AppletConsole
- setTitle(Object) - Method in class org.jmol.shape.MeshCollection
- setTitle(String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
- setTitle(String) - Method in interface org.jmol.api.js.JSConsole
- setTitle(String) - Method in class org.jmol.awtjs.swing.JDialog
- setTitle(String) - Method in interface org.jmol.consolejs.JSConsole
- setTlsGroups(int, int, SymmetryInterface) - Method in class org.jmol.adapter.readers.pdb.PdbReader
-
Sets the atom property property_tlsGroup based on TLS group ranges and adds "TLS" key to model's auxiliaryInfo.
- setTlsTensor(Atom, Map<String, Object>, SymmetryInterface) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- setToken(Viewer, String, LabelToken, int, int, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
-
sets a label token based on a label string
- setTokenProperty(int, boolean) - Method in class org.jmol.shape.Mesh
- setTokenProperty(int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
- setToolTipText(String) - Method in interface org.jmol.api.JmolAbstractButton
- setTop(SmilesSearch) - Method in class org.jmol.smiles.SmilesSearch
- setTopoAtom(int, int, String, int, int) - Method in class org.jmol.smiles.SmilesAtom
- setTopoCoordinates(SmilesAtom, SmilesAtom, SmilesAtom, SmilesAtom, int) - Static method in class org.jmol.smiles.SmilesSearch
- setTopoCoordinates(SmilesAtom, SmilesAtom, SmilesAtom, Node[], boolean) - Method in class org.jmol.smiles.SmilesStereo
- setTorsionData(T3, T3, T3, T3, VTemp, boolean) - Static method in class org.jmol.smiles.SmilesMeasure
-
calculate temporary points
- setTorsionType(MinTorsion) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
-
Get the torsion type for [a,b,c,d], also called "FF class".
- setTorsionVariables(Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
- setTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setTrajectory(int) - Method in class org.jmol.modelset.ModelSet
- setTrajectoryBs(BS) - Method in class org.jmol.modelset.ModelSet
- setTrajectoryName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setTransform(float, float, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setTranslationFractions() - Method in class org.jmol.viewer.TransformManager
- setTranslations() - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
-
allows for web page material to be internationalized, inserting language-specific code, as for WebExport, or by inserting boiler-plate information, as for About_xx.html
- setTranslucency(String, Font, Graphics3D) - Method in class org.jmol.g3d.TextRenderer
-
retrieve grey-scale pixel map from the platform, then round it off
- setTranslucent(boolean, float) - Method in class org.jmol.modelset.Atom
- setTranslucent(boolean, float) - Method in class org.jmol.modelset.Bond
- setTranslucent(boolean, float) - Method in class org.jmol.shape.Mesh
- setTranslucent(boolean, float) - Method in class org.jmol.shapespecial.Dipole
- setTranslucent(boolean, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setTranslucent(boolean, BS, float) - Method in class org.jmol.shapebio.BioShape
- setTranslucent(float, boolean) - Method in class org.jmol.modelset.Text
- setTranslucentVertices(BS) - Method in class org.jmol.util.MeshSurface
-
Must create bsTransPolygons, polygonTranslucencies, and new triangle set for partially translucent polygons
- setTransparentCursor(Object) - Method in interface org.jmol.api.GenericPlatform
- setTransparentCursor(Object) - Static method in class org.jmol.awt.Display
- setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
- setTransparentCursor(Object) - Method in class org.jmol.awtjs2d.Platform
- setTriangleTranslucency(short, short, short) - Method in class org.jmol.g3d.Graphics3D
- setType(int) - Method in class org.jmol.util.Vibration
- setType(String) - Method in class org.jmol.util.Tensor
-
Note that type may be null here to skip type initialization and allow later setting of type; this should be used with care.
- setU(Atom, int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
- setUndoMax(int) - Method in class org.jmol.viewer.StateManager
- setUniqueBond(int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setUniqueBonds(BS, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setUniqueObjects(int, BS, int, int, int, float, int, float, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- setUniqueSettings(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
-
Create uniqueSettings from the "unique_settings" map item.
- setUnitCell() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
- setUnitCell(float[], boolean) - Method in interface org.jmol.api.SymmetryInterface
- setUnitCell(float[], boolean) - Method in class org.jmol.symmetry.Symmetry
- setUnitCell(float[], M3, P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- setUnitCell(float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setUnitCell(int) - Method in class org.jmol.modelkit.ModelKit
- setUnitCell(int) - Method in class org.jmol.modelset.Trajectory
- setUnitCell(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
- setUnitCell(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
- setUnitCellAtomIndex(int) - Method in class org.jmol.viewer.AnimationManager
- setUnitCellItem(int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setUnitCellOffset(SymmetryInterface, T3, int) - Static method in class org.jmol.modelset.ModelSet
- setUnitCellOrientation() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
- setUnits(boolean) - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
catalog units
- setUnits(String) - Method in class org.jmol.viewer.GlobalSettings
- setUnits(String, boolean) - Method in class org.jmol.viewer.Viewer
- setUnits(String, int) - Method in class org.jmol.script.ScriptEval
- setUnitVectors() - Method in class org.jmol.jvxl.data.VolumeData
- setup(boolean) - Method in class org.jmol.jvxl.readers.AtomDataReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMepReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoPlaneReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- setup(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
- setup(boolean) - Method in class org.jmol.shapesurface.PMeshWriter
- setup(int, float[], P3[], BS) - Method in class org.jmol.quantum.MepCalculation
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.cif.MMTFReader
-
standard set up
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.more.MdCrdReader
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
- setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setup(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
- setup(Viewer, Container, String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- setup2() - Method in class org.jmol.jvxl.readers.AtomDataReader
- setupAC() - Method in class org.jmol.modelset.AtomCollection
- setupASCR(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
- setupBC() - Method in class org.jmol.modelset.BondCollection
- setupCalculation() - Method in class org.jmol.jvxl.readers.IsoMOReader
- setupCalculation(Map<String, Object>, boolean, VolumeData, BS, T3[], Atom[], int, int[][], float[], float[], boolean, float[][], T3[]) - Method in class org.jmol.quantum.MOCalculation
- setupCalculation(VolumeData, BS, BS, BS[], T3[], int, boolean, T3[], float[], int) - Method in class org.jmol.quantum.NciCalculation
- setupCalculations() - Method in class org.jmol.minimize.forcefield.Calculations
- setupCalculations() - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
- setupCalculations() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
- setupConsole() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setupConsole() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setupCoordinates(float[], float[], BS, T3[], Atom[], T3[], boolean) - Method in class org.jmol.quantum.QuantumCalculation
- setupDisplay() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setupDisplay() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setupDnD() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setupDnD() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setupLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- setupLabels(Map<String, String>) - Method in class org.jmol.console.GenericConsole
- setupLabels0(Map<String, String>) - Method in class org.jmol.console.GenericConsole
- setupLabels0(Map<String, String>) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- setupMinimization() - Method in class org.jmol.minimize.Minimizer
- setupModelAdapterAndViewer() - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- setupModelAdapterAndViewer() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- setupNav(float, P3[][], P3[], int, int) - Method in class org.jmol.navigate.Navigator
- setupNavTo() - Method in class org.jmol.navigate.Navigator
- setupPS(AlphaPolymer, STR, int, int) - Method in class org.jmol.modelsetbio.ProteinStructure
- setupRR(BioShape, boolean) - Method in class org.jmol.renderbio.RocketsRenderer
- setupType(String) - Method in class org.jmol.jvxl.readers.IsoFxyReader
- setupUI(boolean) - Method in interface org.jmol.api.JmolDialogInterface
- setupUI(boolean) - Method in class org.jmol.dialog.Dialog
- setupUIManager() - Static method in class org.jmol.dialog.Dialog
-
Setup the UIManager (for i18n)
- setUseMolecular(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- setUserAtomTypes() - Method in class org.jmol.adapter.readers.more.ForceFieldReader
- setUserScale(int[]) - Method in class org.jmol.util.ColorEncoder
- setUserVariable(String, SV) - Method in class org.jmol.viewer.GlobalSettings
- setUserVdw(VDW) - Method in class org.jmol.viewer.Viewer
- setv(SV) - Method in class org.jmol.script.SV
-
Creates a NEW version of the variable.
- setValence(int) - Method in class org.jmol.modelset.Atom
- setValence(int) - Method in class org.jmol.smiles.SmilesAtom
- setValue(float) - Method in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
- setValue(float) - Method in class org.jmol.shapespecial.Dipole
- setValueAt(Object, int, int) - Method in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleTableModel
- setValueAt(Object, int, int) - Method in class org.openscience.jmol.app.janocchio.NoeTable.NoeTableModel
- setValueAt(Object, int, int) - Method in class org.openscience.jmol.app.janocchio.TableSorter
- setValueMinMax() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
- setValues(M3, P3, P3) - Method in class org.jmol.thread.MoveToThread
- setValues(LabelToken[], Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
- setVariable(int, int, String, boolean) - Method in class org.jmol.script.ScriptExpr
- setVariables() - Method in class org.jmol.render.MeshRenderer
- setVariables(Map<String, SV>, Lst<SV>) - Method in class org.jmol.script.ScriptFunction
- setVdwStr(String) - Method in class org.jmol.viewer.Viewer
- setVectorAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVectors(String, float[], float[], float[], int) - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- setVectorScale(float) - Method in class org.jmol.api.JmolViewer
- setVectorScale(float) - Method in class org.jmol.viewer.Viewer
- setVersionSettings() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
-
Attempt to adjust for PyMOL versions.
- setVertexAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVertexColixesForAtoms(Viewer, short[], int[], BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setVertexColorMap() - Method in class org.jmol.shapesurface.IsosurfaceMesh
- setVertexSets(boolean) - Method in class org.jmol.jvxl.data.MeshData
- setVertexSource() - Method in class org.jmol.jvxl.readers.AtomDataReader
- setVib(boolean, float) - Method in class org.jmol.util.ModulationSet
- setVibrationOn(boolean) - Method in class org.jmol.viewer.TransformManager
- setVibrationPeriod(float) - Method in class org.jmol.api.JmolViewer
- setVibrationPeriod(float) - Method in class org.jmol.viewer.TransformManager
-
sets the period of vibration -- period > 0: sets the period and turns vibration on -- period < 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Float.NaN: uses current setting (frame change)
- setVibrationPeriod(float) - Method in class org.jmol.viewer.Viewer
- setVibrationScale(float) - Method in class org.jmol.api.JmolViewer
- setVibrationScale(float) - Method in class org.jmol.viewer.TransformManager
- setVibrationScale(float) - Method in class org.jmol.viewer.Viewer
- setVibrationsFromProperties() - Method in class org.jmol.adapter.readers.spartan.SpartanArchive
- setVibrationT(float) - Method in class org.jmol.viewer.TransformManager
- setVibrationVector() - Method in class org.jmol.modelset.Atom
- setVibrationVector(int, T3) - Method in class org.jmol.modelset.AtomCollection
- setVibrationVector2(int, int, float) - Method in class org.jmol.modelset.AtomCollection
- setViewer(boolean) - Method in class org.jmol.viewer.AnimationManager
- setViewer(PlatformViewer, Object) - Method in interface org.jmol.api.GenericPlatform
- setViewer(PlatformViewer, Object) - Method in class org.jmol.awt.Platform
- setViewer(PlatformViewer, Object) - Method in class org.jmol.awtjs2d.Platform
- setViewer(Viewer) - Method in class org.jmol.adapter.writers.MOLWriter
- setViewer(Viewer) - Method in interface org.jmol.api.JmolJSpecView
- setViewer(Viewer) - Method in interface org.jmol.api.JmolNMRInterface
- setViewer(Viewer) - Method in interface org.jmol.api.JmolPropertyManager
- setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptEvaluator
- setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptManager
- setViewer(Viewer) - Method in class org.jmol.console.GenericConsole
- setViewer(Viewer) - Method in class org.jmol.jsv.JSpecView
- setViewer(Viewer) - Method in class org.jmol.modelsetbio.BioResolver
- setViewer(Viewer) - Method in class org.jmol.quantum.NMRCalculation
- setViewer(Viewer) - Method in class org.jmol.script.ScriptEval
- setViewer(Viewer) - Method in class org.jmol.script.ScriptManager
- setViewer(Viewer) - Method in class org.jmol.util.BZone
- setViewer(Viewer) - Method in class org.jmol.viewer.JmolStateCreator
- setViewer(Viewer) - Method in class org.jmol.viewer.PropertyManager
- setViewer(Viewer) - Method in class org.jmol.viewer.StateCreator
- setViewer(Viewer) - Method in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- setViewer(Viewer, double) - Method in class org.jmol.viewer.OutputManager
- setViewer(Viewer, String) - Method in class org.jmol.multitouch.ActionManagerMT
- setViewer(Viewer, String) - Method in class org.jmol.thread.JmolThread
- setViewer(Viewer, String) - Method in class org.jmol.viewer.ActionManager
- setViewerG3dShapeID(Viewer, int) - Method in class org.jmol.render.ShapeRenderer
- setVis(Map<?, Ellipsoid>, BS) - Method in class org.jmol.shapespecial.Ellipsoids
- setVisibilityFlags(int) - Method in class org.jmol.shape.Mesh
- setVisibilityInfo() - Method in class org.jmol.shape.Measures
- setVisible(boolean) - Method in interface org.jmol.api.JmolAppConsoleInterface
- setVisible(boolean) - Method in interface org.jmol.api.JmolScriptEditorInterface
- setVisible(boolean) - Method in interface org.jmol.api.js.JSConsole
- setVisible(boolean) - Method in class org.jmol.awtjs.swing.Component
- setVisible(boolean) - Method in class org.jmol.awtjs.swing.JDialog
- setVisible(boolean) - Method in class org.jmol.console.AppletConsole
- setVisible(boolean) - Method in class org.jmol.console.GenericConsole
- setVisible(boolean) - Method in class org.jmol.console.JmolConsole
- setVisible(boolean) - Method in class org.jmol.console.ScriptEditor
- setVisible(boolean) - Method in class org.jmol.consolejs.AppletConsole
- setVisible(boolean) - Method in interface org.jmol.consolejs.JSConsole
- setVisible(boolean) - Method in class org.jmol.shapespecial.Polyhedra
- setVisible(boolean) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- setVisible(boolean) - Method in interface org.openscience.jmol.app.JmolPlugin
- setVisible(Component) - Method in interface org.jmol.awtjs.swing.SwingController
-
Convey to the HTML object that this component's text has been changed.
- setVolumeData() - Method in class org.jmol.jvxl.readers.AtomDataReader
- setVolumeData() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
- setVolumeData() - Method in class org.jmol.jvxl.readers.IsoFxyReader
- setVolumeData() - Method in class org.jmol.jvxl.readers.IsoShapeReader
- setVolumeData() - Method in class org.jmol.jvxl.readers.VolumeDataReader
- setVolumeData(int, VolumeData, ContactPair, float, int) - Method in class org.jmol.shapesurface.Contact
- setVolumeDataADR() - Method in class org.jmol.jvxl.readers.AtomDataReader
- setVolumeDataParams() - Method in class org.jmol.jvxl.readers.VolumeDataReader
- setVolumeDataV(VolumeData) - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVolumeForPlane() - Method in class org.jmol.jvxl.readers.AtomDataReader
- setVolumetricAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVolumetricOrigin(float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
- setVolumetricOriginAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
- setVolumetricVector(int, float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
- setVolumetricXml() - Method in class org.jmol.jvxl.data.VolumeData
- setVoxel(int, int, int, int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
- setVoxelCounts(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
- setVoxelData(int, float) - Method in class org.jmol.jvxl.data.VolumeData
- setVoxelDataAsArray(float[][][]) - Method in class org.jmol.jvxl.data.VolumeData
- setVoxelMap() - Method in class org.jmol.jvxl.data.VolumeData
- setVoxelMapValue(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
-
for sparse data mapping, as for a plane
- setVoxelRange(int, float, float, float, int, float) - Method in class org.jmol.jvxl.readers.VolumeDataReader
- setVoxels() - Method in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- setVoxels() - Method in class org.jmol.jvxl.readers.IsoIntersectReader
- setWebPageAuthor(String) - Static method in class org.openscience.jmol.app.webexport.WebExport
- setWhiteSpace(boolean) - Method in class org.jmol.util.JSONWriter
- setWidthHeight(boolean) - Method in class org.jmol.util.GData
- setWidthHeightVar() - Method in class org.jmol.viewer.Viewer
- setWindow(int, int, float) - Method in class org.jmol.modelset.Text
- setWindowCentered(boolean) - Method in class org.jmol.viewer.TransformManager
- setWindowDimensions(float[]) - Method in class org.jmol.viewer.Viewer
- setWindowParameters(int, int) - Method in interface org.jmol.api.GenericGraphics
- setWindowParameters(int, int) - Method in class org.jmol.awt.AwtG2D
- setWindowParameters(int, int) - Method in class org.jmol.awtjs2d.JsG2D
- setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
- setWindowParameters(int, int, boolean) - Method in class org.jmol.util.GData
- setWinParams(int, int, boolean) - Method in class org.jmol.util.GData
- setWriteNullAsString(boolean) - Method in class org.jmol.util.JSONWriter
-
Set option to write a null as the string "null" or just null itself.
- setXYA(float[], int) - Method in class org.jmol.modelset.Text
- setXYZ(P3, boolean) - Method in class org.jmol.modelset.Text
- setXYZ(T3) - Method in class org.jmol.util.ModulationSet
- setXYZ(T3) - Method in class org.jmol.util.Vibration
- setXYZ(QuantumCalculation, boolean) - Method in class org.jmol.quantum.QMAtom
- setXYZBohr(T3[]) - Method in class org.jmol.quantum.QuantumCalculation
- setXYZBohrI(float[], int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
- setXYZs(int, int, int, int) - Method in class org.jmol.modelset.Text
- setYellowLevel(double) - Method in class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- setYellowValue(double) - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- setYellowValue(double) - Method in class org.openscience.jmol.app.janocchio.NoeTable
- setZIndex(int) - Method in class org.jmol.awtjs.swing.JDialog
- setZMargin(int) - Method in class org.jmol.g3d.Graphics3D
- setZoomEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
- setZoomHeight(boolean, boolean) - Method in class org.jmol.viewer.TransformManager
- setZPos(int, int, boolean) - Method in class org.jmol.shape.Labels
- setZPosition(int, int) - Static method in class org.jmol.viewer.JC
- setZs(int, int) - Method in class org.jmol.modelset.Text
- setZShadeEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
- sextuple - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- sfacElementSymbols - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
- sg - Variable in class org.jmol.jvxl.readers.SurfaceReader
- sg - Variable in class org.jmol.shapesurface.Isosurface
- SG - Static variable in class org.jmol.symmetry.SpaceGroup
- SG_ALIASES - Static variable in class org.jmol.adapter.readers.xtal.CgdReader
- SGAtom(int, int, String, int) - Constructor for class org.jmol.symmetry.SpaceGroupFinder.SGAtom
- sgIndex - Static variable in class org.jmol.symmetry.SpaceGroup
- sgName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- sgName - Variable in class org.jmol.symmetry.SymmetryInfo
- SHADE_INDEX_LAST - Static variable in class org.jmol.util.Shader
- SHADE_INDEX_MAX - Static variable in class org.jmol.util.Shader
- SHADE_INDEX_NOISY_LIMIT - Static variable in class org.jmol.util.Shader
- SHADE_INDEX_NORMAL - Static variable in class org.jmol.util.Shader
- SHADE_SLAB_CLIPPED - Static variable in class org.jmol.g3d.SphereRenderer
- shadeIndexes - Variable in class org.jmol.g3d.Graphics3D
- shadeIndexes2Sided - Variable in class org.jmol.g3d.Graphics3D
- shader - Variable in class org.jmol.g3d.CylinderRenderer
- shader - Variable in class org.jmol.g3d.LineRenderer
- shader - Variable in class org.jmol.g3d.SphereRenderer
- shader - Variable in class org.jmol.util.GData
- Shader - Class in org.jmol.util
-
All functions.
- Shader() - Constructor for class org.jmol.util.Shader
- shader_path - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- shadesA - Variable in class org.jmol.g3d.CylinderRenderer
- shadesB - Variable in class org.jmol.g3d.CylinderRenderer
- shadesCurrent - Variable in class org.jmol.g3d.Graphics3D
- shape - Variable in class org.jmol.render.ShapeRenderer
- shape - Static variable in class org.jmol.script.T
- shape - Variable in class org.jmol.shapebio.BioShape
- Shape - Class in org.jmol.shape
-
Shape now encompasses: AtomShape (abstract) | Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors | GeoSurface BioShapeCollection (abstract) | Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace Dipoles FontLineShape (abstract) | Axes, Bbcage, Frank, Uccage Measures MeshCollection (abstract) | | Draw Isosurface | LcaoCartoon, MolecularOrbital, Pmesh Sticks | Hsticks, Sssticks TextShape (abstract) | Echo, Hover
- Shape() - Constructor for class org.jmol.shape.Shape
- SHAPE_AXES - Static variable in class org.jmol.viewer.JC
- SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JC
- SHAPE_BALLS - Static variable in class org.jmol.viewer.JC
- SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JC
- SHAPE_CARTOON - Static variable in class org.jmol.viewer.JC
- SHAPE_CGO - Static variable in class org.jmol.viewer.JC
- SHAPE_CONTACT - Static variable in class org.jmol.viewer.JC
- SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JC
- SHAPE_DOTS - Static variable in class org.jmol.viewer.JC
- SHAPE_DRAW - Static variable in class org.jmol.viewer.JC
- SHAPE_ECHO - Static variable in class org.jmol.viewer.JC
- SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JC
- SHAPE_FRANK - Static variable in class org.jmol.viewer.JC
- SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JC
- SHAPE_HALOS - Static variable in class org.jmol.viewer.JC
- SHAPE_HOVER - Static variable in class org.jmol.viewer.JC
- SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JC
- SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JC
- SHAPE_LABELS - Static variable in class org.jmol.viewer.JC
- SHAPE_LAST_ATOM_VIS_FLAG - Static variable in class org.jmol.viewer.JC
- SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JC
- SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JC
- SHAPE_MEASURES - Static variable in class org.jmol.viewer.JC
- SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JC
- SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JC
- SHAPE_MO - Static variable in class org.jmol.viewer.JC
- SHAPE_NBO - Static variable in class org.jmol.viewer.JC
- SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JC
- SHAPE_PMESH - Static variable in class org.jmol.viewer.JC
- SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JC
- SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JC
- SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JC
- SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JC
- SHAPE_STARS - Static variable in class org.jmol.viewer.JC
- SHAPE_STICKS - Static variable in class org.jmol.viewer.JC
- SHAPE_STRANDS - Static variable in class org.jmol.viewer.JC
- SHAPE_STRUTS - Static variable in class org.jmol.viewer.JC
- SHAPE_TRACE - Static variable in class org.jmol.viewer.JC
- SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JC
- SHAPE_VECTORS - Static variable in class org.jmol.viewer.JC
- shapeClassBases - Static variable in class org.jmol.viewer.JC
- shapeCommand - Static variable in class org.jmol.script.T
- shapeID - Variable in class org.jmol.render.ShapeRenderer
- shapeID - Variable in class org.jmol.shape.Shape
- shapely - Static variable in class org.jmol.script.T
- SHAPELY - Enum constant in enum org.jmol.c.PAL
- SHAPELY - Static variable in class org.jmol.util.ColorEncoder
- shapeManager - Variable in class org.jmol.render.RepaintManager
- shapeManager - Variable in class org.jmol.script.ScriptProcessRunnable
- ShapeManager - Class in org.jmol.viewer
- ShapeManager(Viewer) - Constructor for class org.jmol.viewer.ShapeManager
- ShapeRenderer - Class in org.jmol.render
- ShapeRenderer() - Constructor for class org.jmol.render.ShapeRenderer
- shapes - Variable in class org.jmol.viewer.ShapeManager
- shapeTokenIndex(int) - Static method in class org.jmol.viewer.JC
- shapeVisibilityFlags - Variable in class org.jmol.modelset.Atom
- shapeVisibilityFlags - Variable in class org.jmol.modelset.Bond
- shapeVisibilityFlags - Variable in class org.jmol.modelset.Group
- shapeVisibilityFlags - Variable in class org.jmol.viewer.Connection
- sheet - Static variable in class org.jmol.script.T
- Sheet - Class in org.jmol.modelsetbio
- Sheet(AlphaPolymer, int, int, STR) - Constructor for class org.jmol.modelsetbio.Sheet
- SHEET - Enum constant in enum org.jmol.c.STR
- SHEET_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- sheetOffsets - Variable in class org.jmol.dssx.DSSP
- sheetsmoothing - Static variable in class org.jmol.script.T
- sheetSmoothing - Variable in class org.jmol.modelsetbio.BioPolymer
- sheetSmoothing - Variable in class org.jmol.renderbio.BioShapeRenderer
- sheetSmoothing - Variable in class org.jmol.viewer.GlobalSettings
- SHELL - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- shellCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
- shellCount - Variable in class org.jmol.adapter.readers.spartan.SpartanArchive
- shellOrder - Static variable in class org.jmol.quantum.MOCalculation
- shells - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- shells - Variable in class org.jmol.adapter.writers.QCJSONWriter
- shells - Variable in class org.jmol.quantum.MOCalculation
- shellsByUniqueAtom - Variable in class org.jmol.adapter.readers.quantum.PsiReader
- shelxLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- ShelxReader - Class in org.jmol.adapter.readers.xtal
-
A reader for SHELX output (RES) files.
- ShelxReader() - Constructor for class org.jmol.adapter.readers.xtal.ShelxReader
- SHIFT - Static variable in class org.jmol.viewer.binding.Binding
- SHIFT_MASK - Static variable in class org.jmol.awtjs.Event
- shiftBits(BS, BS) - Static method in class org.jmol.adapter.readers.cif.TopoCifParser
-
Shift bits to the left to account for missing atoms in the final atom list.
- shiftBits(BS, BS, boolean, int) - Static method in class org.jmol.util.BSUtil
-
this one slides bits to higher positions based on a pattern.
- shiftRefsPPM - Variable in class org.jmol.quantum.NMRCalculation
- shininess - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- shm - Variable in class org.jmol.viewer.Viewer
- SHORT_BINSTRING - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- shortSceneFilename(String) - Method in class org.jmol.io.JmolUtil
- show - Static variable in class org.jmol.script.T
- show - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- show() - Method in class org.jmol.scriptext.CmdExt
- show(int, int, boolean) - Method in class org.jmol.popup.GenericPopup
- show(String[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
- show(String[]) - Method in class org.jmol.console.ScriptEditor
- show(Component, int, int) - Method in class org.jmol.awtjs.swing.JPopupMenu
- show_alpha_checker - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- show_frame_rate - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- show_progress - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- showAtomSetIndex(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Show an atom set from the indexes array
- showAuxiliaryInfo(Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
- showaxes - Static variable in class org.jmol.script.T
- showAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- showboundbox - Static variable in class org.jmol.script.T
- showBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- showBox(JmolRendererInterface, short, int, int, int, int, int, int, float, boolean) - Static method in class org.jmol.render.TextRenderer
- showConsole(boolean) - Method in class org.jmol.viewer.Viewer
- showContourLines - Variable in class org.jmol.shape.Mesh
- showEditor(String[]) - Method in class org.jmol.viewer.Viewer
- showfrank - Static variable in class org.jmol.script.T
- showFrankMenu() - Method in class org.jmol.popup.JmolGenericPopup
- showFrankMenu() - Method in class org.jmol.popup.JmolPopup
- showGridInfo() - Method in class org.jmol.jvxl.readers.VolumeDataReader
- showHash(SB, String) - Method in class org.jmol.viewer.ChimeMessenger
-
#xxxx command output
- showHash(SB, String) - Method in interface org.jmol.viewer.JmolChimeMessenger
- showhiddenselectionhalos - Static variable in class org.jmol.script.T
- showHiddenSelectionHalos - Variable in class org.jmol.viewer.GlobalSettings
- showHide(boolean) - Method in class org.jmol.shape.Measures
- showHideM(Measurement, boolean) - Method in class org.jmol.shape.Measures
- showhydrogens - Static variable in class org.jmol.script.T
- showHydrogens - Variable in class org.jmol.viewer.GlobalSettings
- showHydrogens - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- showImage(String, Object) - Method in class org.jmol.viewer.StatusManager
-
called by Viewer.loadImageData to pop up a window with an image in it
- showInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
- showKey - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- showkeystrokes - Static variable in class org.jmol.script.T
- showKeyStrokes - Variable in class org.jmol.viewer.GlobalSettings
- showmeasurements - Static variable in class org.jmol.script.T
- showMeasurements - Variable in class org.jmol.viewer.GlobalSettings
- showMeasurements - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- showMenu(int, int) - Method in class org.jmol.modelkit.ModelKit
- showmodvecs - Static variable in class org.jmol.script.T
- showModVecs - Variable in class org.jmol.renderspecial.VectorsRenderer
- showModVecs - Variable in class org.jmol.viewer.GlobalSettings
- showMoleculesAndOrbitals - Static variable in class org.openscience.jmol.app.webexport.WebExport
- showmultiplebonds - Static variable in class org.jmol.script.T
- showMultipleBonds - Variable in class org.jmol.render.SticksRenderer
- showMultipleBonds - Variable in class org.jmol.viewer.GlobalSettings
- shownavigationpointalways - Static variable in class org.jmol.script.T
- showNavigationPointAlways - Variable in class org.jmol.viewer.GlobalSettings
- showNumbers - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- showNumbers - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- showPaintTime - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- showParameter(String, boolean, int) - Method in class org.jmol.viewer.Viewer
- showPlugin(String, String, Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- showPoints - Variable in class org.jmol.shape.Mesh
- showPovrayPathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Show a file selector when the savePath button is pressed.
- showProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
Shows the properties in the propertiesPane of the AtomSetChooser window
- showRebondTimes - Variable in class org.jmol.modelset.ModelSet
- showSaveDialog(Component, JFileChooser, File) - Method in class org.jmol.dialog.Dialog
- showSavePathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Show a file selector when the savePath button is pressed.
- showscript - Static variable in class org.jmol.script.T
- showSelected - Variable in class org.jmol.viewer.Viewer
- showSliceBoundaryPlanes(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- showSplashScreen() - Method in class org.openscience.jmol.app.jmolpanel.Splash
- showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.Splash
- showStatus(String) - Method in interface org.openscience.jmol.app.SplashInterface
- showString(String) - Method in class org.jmol.script.ScriptEval
- showString(String) - Method in class org.jmol.scriptext.ScriptExt
- showString(String, boolean) - Method in class org.jmol.viewer.Viewer
- showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptError
- showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptEval
- showSymop(Object) - Method in class org.jmol.modelkit.ModelKit
- showSymopInfo - Variable in class org.jmol.modelkit.ModelKit
- showTimeout(String) - Method in class org.jmol.viewer.Viewer
- showTimeout(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
- showTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- showtiming - Static variable in class org.jmol.script.T
- showTiming - Variable in class org.jmol.jvxl.readers.Parameters
- showTiming - Variable in class org.jmol.viewer.GlobalSettings
- showTrace - Variable in class org.jmol.util.Vibration
- showTriangles - Variable in class org.jmol.render.MeshRenderer
- showTriangles - Variable in class org.jmol.shape.Mesh
- showunitcell - Static variable in class org.jmol.script.T
- showunitcelldetails - Static variable in class org.jmol.script.T
- showUnitCellDetails - Variable in class org.jmol.viewer.GlobalSettings
- showUrl(String) - Method in interface org.jmol.api.JmolStatusListener
- showUrl(String) - Method in class org.jmol.api.JmolViewer
- showUrl(String) - Method in class org.jmol.util.GenericApplet
- showUrl(String) - Method in class org.jmol.viewer.StatusManager
- showUrl(String) - Method in class org.jmol.viewer.Viewer
-
syncCallback traps script synchronization messages and allows for cancellation (by returning "") or modification jmolSetCallback("syncCallback", "mySyncCallback") function mySyncCallback(app, script, appletName) { ...[modify script here]...
- showUrl(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- showXtalSymmetry() - Method in class org.jmol.modelkit.ModelKit
-
Draw the symmetry element
- showZBuffer() - Method in class org.jmol.g3d.PixelatorShaded
- sidechain - Static variable in class org.jmol.script.T
- siestaContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- SiestaReader - Class in org.jmol.adapter.readers.xtal
-
SIESTA http://www.icmab.es/siesta/
- SiestaReader() - Constructor for class org.jmol.adapter.readers.xtal.SiestaReader
- sigma - Variable in class org.jmol.adapter.readers.cif.MSRdr
- sigma - Variable in class org.jmol.jvxl.readers.Parameters
- sigma - Static variable in class org.jmol.script.T
- sigma - Variable in class org.jmol.symmetry.SymmetryOperation
- sigma - Variable in class org.jmol.util.ModulationSet
- sign - Static variable in class org.jmol.script.T
- sign(double) - Method in class org.jmol.quantum.NMRNoeMatrix
- sign(int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Just a simple signum for integers
- SignedOnly - Variable in class org.jmol.popup.GenericPopup
- signFactor - Variable in class org.jmol.modelset.TickInfo
- silent - Variable in class org.jmol.minimize.forcefield.Calculations
- silent - Static variable in class org.jmol.script.T
- SILVER - Static variable in class org.jmol.util.C
- SIMPLE_LINE - Static variable in class org.jmol.shapecgo.CGOMesh
- simpleCage - Variable in class org.jmol.modelset.Model
- SimpleEdge - Interface in org.jmol.util
-
minimal bond interface for SMILES and CIP
- simpleEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
- SimpleMarchingCubes - Class in org.openscience.jvxl.simplewriter
- SimpleMarchingCubes(VoxelDataCreator, VolumeData, Parameters, JvxlData, Lst<P3>, float[]) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- SimpleMarchingCubesOld - Class in org.openscience.jvxl.simplewriter
- SimpleMarchingCubesOld() - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
- SimpleNode - Interface in org.jmol.util
-
Just the bare minimum for CIP, and non-BioSMILES
- simpleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- SimpleUnitCell - Class in org.jmol.util
-
general-purpose simple unit cell for calculations and as a super-class of unitcell, which is only part of Symmetry allows one-dimensional (polymer) and two-dimensional (slab) periodicity
- SimpleUnitCell() - Constructor for class org.jmol.util.SimpleUnitCell
- simplify_display_lists - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SIMULATION_PROTOCOL - Static variable in class org.jmol.viewer.FileManager
- simulationPhase - Variable in class org.jmol.multitouch.ActionManagerMT
- simulator - Variable in class org.jmol.multitouch.ActionManagerMT
- sin - Static variable in class org.jmol.script.T
- sinAlpha - Variable in class org.jmol.util.SimpleUnitCell
- sinBeta - Variable in class org.jmol.util.SimpleUnitCell
- sinGamma - Variable in class org.jmol.util.SimpleUnitCell
- SINGLE - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- SINGLE - Static variable in class org.jmol.viewer.binding.Binding
- single_image - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SINGLE_POINT_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- SingleModelOnly - Variable in class org.jmol.popup.JmolPopup
- singleNet - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
-
storage for a single net from a non-looped data item
- SinglePointGesture - Class in org.jmol.multitouch.sparshui
-
SINGLE_POINT_GESTURE only passes single-touch gestures.
- SinglePointGesture() - Constructor for class org.jmol.multitouch.sparshui.SinglePointGesture
- sinPhi - Variable in class org.jmol.g3d.CylinderRenderer
- site - Static variable in class org.jmol.script.T
- site() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- SITE_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- SITE_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- SITE_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- SITE_INS_CODE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- SITE_MULT - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SITE_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- siteScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- sixdots - Static variable in class org.jmol.render.FontLineShapeRenderer
- size - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- size - Variable in class org.jmol.g3d.TextRenderer
- size - Static variable in class org.jmol.script.T
- size - Variable in class org.openscience.jmol.app.janocchio.TableSorter.Arrow
- sizeOf(T) - Static method in class org.jmol.script.SV
- sizes - Static variable in class org.jmol.shapecgo.CGOMesh
- sizes2D - Static variable in class org.jmol.shapecgo.CGOMesh
- skew() - Method in class org.jmol.util.Tensor
-
a measure of asymmetry.
- skip(long) - Method in class org.openscience.jvxl.MonitorInputStream
- skipAtomSet(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
- skipComments(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- skipData(int) - Method in class org.jmol.jvxl.readers.BCifDensityReader
- skipData(int) - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
- skipData(int) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
- skipData(int) - Method in class org.jmol.jvxl.readers.MrcBinaryReader
- skipData(int) - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
- skipData(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- skipData(int) - Method in class org.jmol.jvxl.readers.XsfReader
- skipDataVFR(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- skipFloats(int) - Method in class org.jmol.adapter.readers.more.MdCrdReader
- skipHeader() - Method in class org.jmol.jvxl.readers.MsmsReader
- skipKey(String) - Method in class org.jmol.adapter.readers.cif.CifReader
- skipLoop(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
- skipModel() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
- skipMOs - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- skipping - Variable in class org.jmol.adapter.readers.cif.CifReader
- skipping - Variable in class org.jmol.script.ScriptMathProcessor
- skipPoints(int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
- skipTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
- skipTo(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- skipTo(String) - Method in class org.jmol.jvxl.readers.XmlReader
- skipTo(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
- skipTo(String, String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
- skipToNextAtom() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- skipVoxels(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
- slab - Variable in class org.jmol.export.Export3D
- slab - Variable in class org.jmol.g3d.SphereRenderer
- slab - Static variable in class org.jmol.script.T
- slab - Variable in class org.jmol.thread.MoveToThread
- slab - Variable in class org.jmol.util.GData
- slabbing - Variable in class org.jmol.render.SticksRenderer
- slabbingObject - Variable in class org.jmol.shape.Mesh
- slabbingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
- slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSlicer
-
"slabs" an isosurface into the first Brillouin zone moving points as necessary.
- slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSurface
- slabbyatom - Static variable in class org.jmol.script.T
- slabByAtom - Variable in class org.jmol.render.SticksRenderer
- slabByAtom - Variable in class org.jmol.viewer.GlobalSettings
- slabbymolecule - Static variable in class org.jmol.script.T
- slabByMolecule - Variable in class org.jmol.viewer.GlobalSettings
- slabByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
- slabByPixels(int) - Method in class org.jmol.viewer.Viewer
- slabColix - Variable in class org.jmol.util.MeshSurface
- slabData - Variable in class org.jmol.shapespecial.Draw
- slabDepthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
- slabDepthByPixels(int) - Method in class org.jmol.viewer.Viewer
- slabDepthChanged() - Method in class org.jmol.viewer.TransformManager
- slabenabled - Static variable in class org.jmol.script.T
- slabEnabled - Variable in class org.jmol.viewer.TransformManager
- slabInfo - Variable in class org.jmol.jvxl.data.JvxlData
- slabInfo - Variable in class org.jmol.jvxl.readers.Parameters
- slabInternal(P4, boolean) - Method in class org.jmol.viewer.TransformManager
- slabIsosurface(Lst<Object[]>) - Method in class org.jmol.jvxl.readers.SurfaceReader
- slabMeshType - Variable in class org.jmol.util.MeshSurface
- slabOptions - Variable in class org.jmol.util.MeshSurface
- slabPercentSetting - Variable in class org.jmol.viewer.TransformManager
- slabPlane - Variable in class org.jmol.viewer.TransformManager
- slabPlaneOffset - Variable in class org.jmol.jvxl.readers.Parameters
- slabPolygons(Object[]) - Method in class org.jmol.shapesurface.Isosurface
- slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSlicer
- slabPolygonsList(Lst<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
- slabrange - Static variable in class org.jmol.script.T
- slabRange - Variable in class org.jmol.viewer.TransformManager
- slabReset() - Method in class org.jmol.viewer.TransformManager
- slabToPercent(int) - Method in class org.jmol.viewer.TransformManager
- slabValue - Variable in class org.jmol.jvxl.data.JvxlData
- slabValue - Variable in class org.jmol.viewer.TransformManager
- slabXY - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- slabZ - Variable in class org.jmol.export.___Exporter
- slaterArray - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- slaterCount - Variable in class org.jmol.adapter.readers.xml.XmlMOReader
- SlaterData - Class in org.jmol.quantum
- SlaterData(int, int, int, int, int, double, double) - Constructor for class org.jmol.quantum.SlaterData
- SlaterReader - Class in org.jmol.adapter.readers.quantum
- SlaterReader() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader
- SlaterReader.OrbitalSorter - Class in org.jmol.adapter.readers.quantum
- SlaterReader.SlaterSorter - Class in org.jmol.adapter.readers.quantum
- slaters - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- slaters - Variable in class org.jmol.quantum.MOCalculation
- SlaterSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
- sleepTime - Variable in class org.jmol.thread.JmolThread
- sLeft - Variable in class org.jmol.g3d.HermiteRenderer
- slen - Variable in class org.jmol.script.ScriptParam
- slen - Variable in class org.jmol.scriptext.ScriptExt
- slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- Slice - Class in org.openscience.jmol.app.surfacetool
- Slice() - Constructor for class org.openscience.jmol.app.surfacetool.Slice
- slice_dynamic_grid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- slice_dynamic_grid_resolution - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- slice_grid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- slice_height_map - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- slice_height_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- slice_track_camera - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sliceObject(String, int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- slicer - Variable in class org.jmol.util.MeshCapper
-
source of edges; consumer of triangles
- slicer - Variable in class org.jmol.util.MeshSurface
- slicer - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- slicerFrame - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- sliceSelected() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- SLIDE_ZOOM_X_PERCENT - Static variable in class org.jmol.viewer.ActionManager
- slider - Variable in class org.jmol.dialog.Dialog.QualityListener
- Slider(float, float) - Constructor for class org.jmol.thread.MoveToThread.Slider
- sliderPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- SLIM - Static variable in class org.jmol.util.Shader
- slm - Variable in class org.jmol.viewer.Viewer
- SLOP - Static variable in class org.jmol.util.SimpleUnitCell
- SLOP0001 - Static variable in class org.jmol.symmetry.SpaceGroupFinder
-
tolerance for fractional coord and
- SLOP001 - Static variable in class org.jmol.symmetry.SpaceGroupFinder
-
tolerance for fractional coord and
- SLOP0014 - Static variable in class org.jmol.symmetry.SpaceGroupFinder
-
maximum allowable distance fx, fy ,fz for atom finder
- SLOP1 - Static variable in class org.jmol.util.SimpleUnitCell
- SLOP2 - Static variable in class org.jmol.util.SimpleUnitCell
-
allowance for rounding in [0,1)
- slope - Variable in class org.jmol.g3d.LineRenderer
- slopeKey - Variable in class org.jmol.g3d.LineRenderer
- slow_idle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sm - Variable in class org.jmol.modelset.ModelSet
- sm - Variable in class org.jmol.script.ScriptEval
- sm - Variable in class org.jmol.smiles.SmilesGenerator
- sm - Variable in class org.jmol.viewer.Viewer
- SMALL_RING_MAX - Static variable in class org.jmol.symmetry.CIPChirality
-
maximum ring size that can have a double bond with no E/Z designation; also used for identifying aromatic rings and bridgehead nitrogens
- smallmoleculemaxatoms - Static variable in class org.jmol.script.T
- smallMoleculeMaxAtoms - Variable in class org.jmol.viewer.GlobalSettings
- smap - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
- smartaromatic - Static variable in class org.jmol.script.T
- smartAromatic - Variable in class org.jmol.viewer.GlobalSettings
- SmarterJmolAdapter - Class in org.jmol.adapter.smarter
- SmarterJmolAdapter() - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter
- smarts - Variable in class org.jmol.shapespecial.Polyhedron
- smartsCode - Variable in class org.jmol.minimize.forcefield.AtomType
- smiles - Static variable in class org.jmol.script.T
- smiles - Variable in class org.jmol.shapespecial.Polyhedron
- smiles - Variable in class org.jmol.symmetry.CIPDataSmiles
- SMILES_2D - Static variable in class org.jmol.viewer.JC
- SMILES_AROMATIC_DEFINED - Static variable in class org.jmol.viewer.JC
-
AROMATIC_DEFINED draws all aromatic bonds from connection definitions It is deprecated, because a=a will set it by itself.
- SMILES_AROMATIC_DOUBLE - Static variable in class org.jmol.viewer.JC
-
AROMATIC_DOUBLE allows a distinction between single and double, as for example is necessary to distinguish between n=cNH2 and ncNH2 (necessary for MMFF94 atom typing)
- SMILES_AROMATIC_MMFF94 - Static variable in class org.jmol.viewer.JC
-
AROMATIC_MMFF94 also raises the strictness level to force all 6- and 7-membered rings to have exactly three double bonds.
- SMILES_AROMATIC_PLANAR - Static variable in class org.jmol.viewer.JC
-
AROMATIC_PLANAR only invokes planarity (Jmol default through 14.5)
- SMILES_AROMATIC_STRICT - Static variable in class org.jmol.viewer.JC
-
AROMATIC_STRICT enforces Hueckel 4+2 rule, not allowing acyclic double bonds
- SMILES_BONDS - Static variable in class org.jmol.smiles.SmilesBond
- SMILES_FIRST_MATCH_ONLY - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_ATOM_COMMENT - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_COMMENT - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_COV_CROSSLINK - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_HH_CROSSLINK - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_BIO_NOCOMMENTS - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_EXPLICIT_H_ALL - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_EXPLICIT_H2_ONLY - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_NO_BRANCHES - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_POLYHEDRAL - Static variable in class org.jmol.viewer.JC
- SMILES_GEN_TOPOLOGY - Static variable in class org.jmol.viewer.JC
- SMILES_GROUP_BY_MODEL - Static variable in class org.jmol.viewer.JC
- SMILES_IGNORE_ATOM_CLASS - Static variable in class org.jmol.viewer.JC
- SMILES_IGNORE_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
- SMILES_INVERT_STEREOCHEMISTRY - Static variable in class org.jmol.viewer.JC
- SMILES_MAP_UNIQUE - Static variable in class org.jmol.viewer.JC
- SMILES_NO_AROMATIC - Static variable in class org.jmol.viewer.JC
- SMILES_TYPE_OPENSMARTS - Static variable in class org.jmol.viewer.JC
- SMILES_TYPE_OPENSMILES - Static variable in class org.jmol.viewer.JC
- SMILES_TYPE_SMARTS - Static variable in class org.jmol.viewer.JC
- SMILES_TYPE_SMILES - Static variable in class org.jmol.viewer.JC
- smiles2dimageformat - Static variable in class org.jmol.script.T
- SmilesAromatic - Class in org.jmol.smiles
- SmilesAromatic() - Constructor for class org.jmol.smiles.SmilesAromatic
- SmilesAtom - Class in org.jmol.smiles
-
This class represents an atom in a
SmilesMolecule
. - SmilesAtom() - Constructor for class org.jmol.smiles.SmilesAtom
- SmilesBond - Class in org.jmol.smiles
-
Bond in a SmilesMolecule
- SmilesBond(SmilesAtom, SmilesAtom, int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
-
SmilesBond constructor
- smilesExt - Variable in class org.jmol.script.ScriptExpr
- SmilesExt - Class in org.jmol.scriptext
- SmilesExt() - Constructor for class org.jmol.scriptext.SmilesExt
- SmilesGenerator - Class in org.jmol.smiles
-
Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal.
- SmilesGenerator() - Constructor for class org.jmol.smiles.SmilesGenerator
- smilesMatcher - Variable in class org.jmol.viewer.Viewer
- SmilesMatcher - Class in org.jmol.smiles
-
Originating author: Nicholas Vervelle A class to handle a variety of SMILES/SMARTS-related functions, including: -- determining if two SMILES strings are equivalent -- determining the molecular formula of a SMILES or SMARTS string -- searching for specific runs of atoms in a 3D model -- searching for specific runs of atoms in a SMILES description -- generating valid (though not canonical) SMILES and bioSMILES strings -- getting atom-atom correlation maps to be used with biomolecular alignment methods
- SmilesMatcher() - Constructor for class org.jmol.smiles.SmilesMatcher
- SmilesMatcherInterface - Interface in org.jmol.api
- SmilesMeasure - Class in org.jmol.smiles
- SmilesMeasure(SmilesSearch, int, int, boolean, float[]) - Constructor for class org.jmol.smiles.SmilesMeasure
- SmilesParser - Class in org.jmol.smiles
-
Parses a SMILES string or SMARTS pattern to create a
SmilesSearch
. - SmilesParser(boolean, boolean) - Constructor for class org.jmol.smiles.SmilesParser
- SmilesRing - Class in org.jmol.smiles
-
Ring of (tentatively) aromatic nodes and edges
- SmilesRing(int, BS, Lst<Edge>, boolean) - Constructor for class org.jmol.smiles.SmilesRing
- SmilesRingSet - Class in org.jmol.smiles
-
a list of fused rings
- SmilesRingSet() - Constructor for class org.jmol.smiles.SmilesRingSet
- SmilesSearch - Class in org.jmol.smiles
-
A class to build and carry out a SMILES or SMARTS match
- SmilesSearch() - Constructor for class org.jmol.smiles.SmilesSearch
- smilesStereo - Variable in class org.jmol.smiles.SmilesGenerator
- SmilesStereo - Class in org.jmol.smiles
-
This class relates to stereochemical issues
- SmilesStereo(int, int, int, String, String) - Constructor for class org.jmol.smiles.SmilesStereo
- smilesurlformat - Static variable in class org.jmol.script.T
- smilesUrlFormat - Variable in class org.jmol.viewer.GlobalSettings
- smooth_color_triangle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- smooth_half_bonds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- smoothingPower - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
- snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
- snapshotAnaglyphChannelBytes() - Method in class org.jmol.util.GData
- Snn - Static variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
- solid - Static variable in class org.jmol.script.T
- solidOnly - Variable in class org.jmol.export.___Exporter
- solvent - Static variable in class org.jmol.script.T
- solvent_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
- solvent_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
- solvent_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- solventAccessible - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- solventDistance(float, float, float, float, float, float) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- solventExtendedAtomRadius - Variable in class org.jmol.jvxl.readers.Parameters
- solventprobe - Static variable in class org.jmol.script.T
- solventproberadius - Static variable in class org.jmol.script.T
- solventProbeRadius - Variable in class org.jmol.viewer.GlobalSettings
- solventRadius - Variable in class org.jmol.jvxl.readers.Parameters
- someModelsAreModulated - Variable in class org.jmol.modelset.ModelLoader
- someModelsHaveAromaticBonds - Variable in class org.jmol.modelset.ModelSet
- someModelsHaveFractionalCoordinates - Variable in class org.jmol.modelset.ModelSet
- someModelsHaveSymmetry - Variable in class org.jmol.modelset.ModelSet
- someModelsHaveUnitcells - Variable in class org.jmol.modelset.ModelLoader
- sort - Static variable in class org.jmol.g3d.Graphics3D
- sort - Static variable in class org.jmol.script.T
- sort(int) - Method in class org.jmol.bspt.Leaf
- Sort(int, String) - Constructor for class org.jmol.script.SV.Sort
- SortableHeaderRenderer(TableCellRenderer) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter.SortableHeaderRenderer
- sortAndNormalize() - Method in class org.jmol.util.Tensor
-
The expression: |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso| simply sorts the values from largest to smallest or smallest to largest, depending upon the direction of the asymmetry, always setting the last value to be the farthest from the mean.
- sortAssemblyModels() - Method in class org.jmol.adapter.readers.cif.MMCifReader
-
issue here is that mmCIF assembly atoms can be in different blocks by chain: Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ...
- sorter - Variable in class org.jmol.smiles.SmilesStereo
- sortingColumns - Variable in class org.openscience.jmol.app.janocchio.TableSorter
- sortingStatusChanged() - Method in class org.openscience.jmol.app.janocchio.TableSorter
- sortInorganic(SimpleNode, Lst<Edge>, VTemp) - Method in class org.jmol.smiles.SmilesGenerator
-
We must sort the bond vector such that a diaxial pair is first and last.
- sortIso - Variable in class org.jmol.util.Tensor
- sortMapArray(String) - Method in class org.jmol.script.SV
- sortMOs() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
- sortOop(int[]) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
sorts coefficients by atomic number for speed later
- sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.SlaterReader
-
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- sortOrReverse(int) - Method in class org.jmol.script.SV
- sortPolyBonds(SimpleNode, SimpleNode, P3) - Method in class org.jmol.smiles.SmilesGenerator
- sortPolyBondsByStereo(SimpleNode, SimpleNode, T3, SimpleEdge[], V3) - Method in class org.jmol.smiles.SmilesStereo
-
Sort bond array as ccw rotation around the axis connecting the atom and the reference point (polyhedron center) as seen from outside the polyhedron looking in.
- SortSet() - Constructor for class org.jmol.jvxl.data.MeshData.SortSet
- sortSubstituents(int) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
Deep-Sort the substituents of an atom, setting the node's atoms[] and priorities[] arrays.
- source - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- sourceIndices - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- sourcePNGJ - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- sources - Variable in class org.jmol.util.MeshSlicer
- SOUTH - Static variable in class org.jmol.awtjs.swing.BorderLayout
- sp - Variable in class org.jmol.bspt.CubeIterator
- SP - Static variable in class org.jmol.quantum.QS
- SP_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- spacebeforesquare - Static variable in class org.jmol.script.T
- spacefill - Static variable in class org.jmol.script.T
- spacegroup - Static variable in class org.jmol.script.T
- spaceGroup - Variable in class org.jmol.symmetry.Symmetry
- SpaceGroup - Class in org.jmol.symmetry
- SpaceGroup(int, String, boolean) - Constructor for class org.jmol.symmetry.SpaceGroup
- SpaceGroupFinder - Class in org.jmol.symmetry
-
A relatively simple space group finder given a unit cell.
- SpaceGroupFinder() - Constructor for class org.jmol.symmetry.SpaceGroupFinder
- SpaceGroupFinder.SGAtom - Class in org.jmol.symmetry
- spaceGroupName - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- SPACES - Static variable in class org.jmol.util.JSONWriter
- span() - Method in class org.jmol.util.Tensor
-
width of the signal; |e2 - e0|
- spardirCache - Variable in class org.jmol.viewer.FileManager
- SparseArray(String) - Constructor for class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- spartanArchive - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- SpartanArchive - Class in org.jmol.adapter.readers.spartan
- SpartanArchive(BasisFunctionReader, String, String, int) - Constructor for class org.jmol.adapter.readers.spartan.SpartanArchive
- spartanBinaryContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- spartanContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- spartanDoc - Variable in class org.jmol.viewer.FileManager
- spartanFileList(String, String) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
-
Special loading for file directories.
- spartanGetObjectAsSections(String, String, Map<String, String>) - Method in class org.jmol.adapter.readers.spartan.SpartanUtil
-
delivers file contents and directory listing for a ZIP/JAR file into sb
- SpartanInputReader - Class in org.jmol.adapter.readers.spartan
- SpartanInputReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanInputReader
- SpartanReader - Class in org.jmol.adapter.readers.spartan
- SpartanReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanReader
- spartanSmolLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- SpartanSmolReader - Class in org.jmol.adapter.readers.spartan
- SpartanSmolReader() - Constructor for class org.jmol.adapter.readers.spartan.SpartanSmolReader
- spartanUtil() - Method in class org.jmol.viewer.FileManager
-
An isolated class to retrieve Spartan file data from compound documents, zip files, and directories
- SpartanUtil - Class in org.jmol.adapter.readers.spartan
-
A class to isolate Spartan file reading methods from the rest of Jmol.
- SpartanUtil() - Constructor for class org.jmol.adapter.readers.spartan.SpartanUtil
- spec_alternate - Static variable in class org.jmol.script.T
- spec_atom - Static variable in class org.jmol.script.T
- spec_chain - Static variable in class org.jmol.script.T
- spec_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- spec_direct - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- spec_direct_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- spec_model - Static variable in class org.jmol.script.T
- spec_model2 - Static variable in class org.jmol.script.T
- spec_name_pattern - Static variable in class org.jmol.script.T
- spec_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- spec_reflect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- spec_resid - Static variable in class org.jmol.script.T
- spec_seqcode - Static variable in class org.jmol.script.T
- spec_seqcode_range - Static variable in class org.jmol.script.T
- Special - Variable in class org.jmol.popup.JmolPopup
- SPECIAL_COLIX_MAX - Static variable in class org.jmol.util.C
- specialAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
- specialAtomNames - Static variable in class org.jmol.modelset.Group
- specialAtomNames - Static variable in class org.jmol.modelsetbio.BioResolver
- specialDetails - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- specialLabel - Variable in class org.jmol.shape.Hover
- specialposition - Static variable in class org.jmol.script.T
- specialTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
- specular - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- specular - Static variable in class org.jmol.script.T
- specular_intensity - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- specularexponent - Static variable in class org.jmol.script.T
- specularExponent - Variable in class org.jmol.util.Shader
- specularFactor - Variable in class org.jmol.util.Shader
- specularOn - Variable in class org.jmol.util.Shader
- specularpercent - Static variable in class org.jmol.script.T
- specularPercent - Variable in class org.jmol.util.Shader
- specularpower - Static variable in class org.jmol.script.T
- specularPower - Variable in class org.jmol.util.Shader
- SPG - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- sphere - Static variable in class org.jmol.script.T
- sphere - Variable in class org.jmol.symmetry.CIPChirality.CIPAtom
-
bond distance from the root atom to this atom
- sphere - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- SPHERE - Static variable in class org.jmol.shapecgo.CGOMesh
- sphere_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sphere_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sphere_point_max_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sphere_point_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sphere_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sphere_radiusAngstroms - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- sphere_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sphere_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sphere_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sphere_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sphere3d - Variable in class org.jmol.g3d.Graphics3D
- sphereColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- sphereMatrix - Variable in class org.jmol.export.__CartesianExporter
- sphereNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- spherePoint - Variable in class org.jmol.modelkit.ModelKit
- SphereRenderer - Class in org.jmol.g3d
-
Implements high performance rendering of shaded spheres.
- SphereRenderer(Graphics3D) - Constructor for class org.jmol.g3d.SphereRenderer
- sphereScale - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- sphereShadeIndexes - Variable in class org.jmol.util.Shader
- sphereShapeCache - Variable in class org.jmol.util.Shader
- sphereTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- sphericalDValues - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- spheroid_fill - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- spheroid_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- spheroid_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- spin - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
- spin - Static variable in class org.jmol.script.T
- SPIN_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- SPIN_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- SPIN_SAW_AX - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- SPIN_SAW_AY - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- SPIN_SAW_AZ - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- SPIN_SAW_C - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- SPIN_SAW_W - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- SPIN_SPEC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- spine - Static variable in class org.jmol.script.T
- spinfps - Static variable in class org.jmol.script.T
- spinFps - Variable in class org.jmol.viewer.TransformManager
- spinIsGesture - Variable in class org.jmol.viewer.TransformManager
- spinOn - Variable in class org.jmol.viewer.TransformManager
- spinOn - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- SpinOnWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
- spinOp - Variable in class org.jmol.util.ModulationSet
-
the spin operation for this atom: +1/0/-1
- spinThread - Variable in class org.jmol.viewer.TransformManager
- SpinThread - Class in org.jmol.thread
- SpinThread() - Constructor for class org.jmol.thread.SpinThread
- spinx - Static variable in class org.jmol.script.T
- spinX - Variable in class org.jmol.viewer.TransformManager
- spinXYBy(int, int, float) - Method in class org.jmol.viewer.TransformManager
- spinXYBy(int, int, float) - Method in class org.jmol.viewer.Viewer
- spiny - Static variable in class org.jmol.script.T
- spinY - Variable in class org.jmol.viewer.TransformManager
- spinz - Static variable in class org.jmol.script.T
- spinZ - Variable in class org.jmol.viewer.TransformManager
- splash - Variable in class org.openscience.jmol.app.janocchio.Nmr
- splash - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- Splash - Class in org.openscience.jmol.app.jmolpanel
- Splash(Frame, ImageIcon) - Constructor for class org.openscience.jmol.app.jmolpanel.Splash
- Splash.WindowListener - Class in org.openscience.jmol.app.jmolpanel
- splashEnabled - Variable in class org.openscience.jmol.app.JmolApp
- splashImage - Variable in class org.openscience.jmol.app.jmolpanel.Splash
- SplashInterface - Interface in org.openscience.jmol.app
- split - Variable in class org.jmol.awtjs.swing.JSplitPane
- split - Static variable in class org.jmol.script.T
- split(String, int) - Static method in class org.jmol.adapter.smarter.Resolver
- splitCommandLine(String) - Static method in class org.jmol.console.GenericConsole
-
separate a command line into three sections: prefix....;cmd ........
- sppm - Variable in class org.jmol.render.LabelsRenderer
- sprintf(String, SV) - Static method in class org.jmol.script.SV
- sprintf(String, SV, Object[], int[], float[], double[], boolean, boolean, boolean) - Static method in class org.jmol.script.SV
- SPS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- sptRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- sqrt - Static variable in class org.jmol.script.T
- sqrt3_2 - Static variable in class org.jmol.modelset.AtomCollection
- SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesStereo
- squareCount - Variable in class org.jmol.script.ScriptMathProcessor
- squared - Static variable in class org.jmol.script.T
- sr - Variable in class org.jmol.jvxl.data.VolumeData
- sr - Variable in class org.jmol.jvxl.readers.AtomDataReader
-
solvent radius
- sRight - Variable in class org.jmol.g3d.HermiteRenderer
- ss_helix_phi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_helix_phi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_helix_phi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_helix_psi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_helix_psi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_helix_psi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_strand_phi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_strand_phi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_strand_phi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_strand_psi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_strand_psi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ss_strand_psi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- ssbond - Static variable in class org.jmol.script.T
- ssbondsbackbone - Static variable in class org.jmol.script.T
- ssbondsBackbone - Variable in class org.jmol.render.SticksRenderer
- ssbondsBackbone - Variable in class org.jmol.viewer.GlobalSettings
- SSet(BS) - Constructor for class org.jmol.jvxl.data.MeshData.SSet
- ssMapAtom - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- ssMapSeq - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- SSTYPE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- st - Variable in class org.jmol.script.ScriptParam
- st - Variable in class org.jmol.scriptext.ScriptExt
- stack - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- stack - Variable in class org.jmol.bspt.CubeIterator
- STAND_ALONE - Static variable in class org.openscience.jmol.app.webexport.WebExport
- STANDARD_LABEL - Static variable in class org.jmol.modelset.LabelToken
- standardGroupList - Static variable in class org.jmol.modelset.Group
- standardLevel - Static variable in class org.jmol.util.Geodesic
-
3 levels, 0 through 3
- standardVector - Variable in class org.jmol.renderspecial.VectorsRenderer
- star - Static variable in class org.jmol.script.T
- Stars - Class in org.jmol.shape
- Stars() - Constructor for class org.jmol.shape.Stars
- StarsRenderer - Class in org.jmol.render
- StarsRenderer() - Constructor for class org.jmol.render.StarsRenderer
- start - Variable in class org.jmol.thread.MoveToThread.Slider
- start() - Method in class org.jmol.thread.JmolThread
- start() - Method in class org.openscience.jmol.app.InputScannerThread
- start() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- start(JFrame, Viewer, Map<String, Object>) - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- start(JFrame, Viewer, Map<String, Object>) - Method in interface org.openscience.jmol.app.JmolPlugin
- start(Viewer) - Method in interface org.jmol.api.JmolAppConsoleInterface
- start(Viewer) - Method in class org.jmol.console.AppletConsole
- start(Viewer) - Method in class org.jmol.consolejs.AppletConsole
- start(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- START - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- startApp() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- startByteArrayReaderThread() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
- startChainID - Variable in class org.jmol.adapter.smarter.Structure
- startCommandWatcher(boolean) - Method in interface org.jmol.api.JmolScriptManager
- startCommandWatcher(boolean) - Method in class org.jmol.script.ScriptManager
- startConsoleReaderThread(InputStream) - Method in class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
- startCoord - Variable in class org.jmol.shapespecial.Dipoles
- startDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
- started - Variable in class org.openscience.jmol.app.janocchio.NmrPlugin
- startedByCommandThread - Variable in class org.jmol.script.ScriptQueueThread
- startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- startGestureServer() - Method in interface org.jmol.api.JmolGestureServerInterface
- startHoverWatcher(boolean) - Method in class org.jmol.util.GenericApplet
- startHoverWatcher(boolean) - Method in class org.jmol.viewer.ActionManager
- startHoverWatcher(boolean) - Method in class org.jmol.viewer.Viewer
- startIndexPending - Variable in class org.jmol.renderbio.RocketRenderer
- startInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
- startJmol(JmolApp) - Static method in class org.openscience.jmol.app.Jmol
- startMinimization() - Method in class org.jmol.minimize.Minimizer
- startNBO(String) - Method in class org.jmol.viewer.Viewer
- startNBO(Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- startPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- startPlugin(String) - Method in class org.jmol.viewer.Viewer
-
startup -U nbo option
- startRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- startScriptQueue(boolean) - Method in class org.jmol.script.ScriptManager
- startSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
- startServerService() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- startService(int, JsonNioClient, Viewer, String, int) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
- startService(int, JsonNioClient, Viewer, String, int) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- startSimulator(Object) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- startSparshUIService(boolean) - Method in class org.jmol.multitouch.ActionManagerMT
- startSpinningAxis(T3, T3, boolean) - Method in class org.jmol.viewer.Viewer
- startTime - Variable in class org.jmol.thread.JmolThread
- startTimer(String) - Static method in class org.jmol.util.Logger
- startTrace(int) - Method in class org.jmol.util.Vibration
- startupDim - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- startupHeight - Variable in class org.openscience.jmol.app.JmolApp
- startupHeight - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- startupWidth - Variable in class org.openscience.jmol.app.JmolApp
- startupWidth - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- startViewer(JmolViewer, SplashInterface, boolean) - Method in class org.openscience.jmol.app.JmolApp
- starwidth - Static variable in class org.jmol.script.T
- starWidth - Variable in class org.jmol.viewer.GlobalSettings
- state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- state - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- state - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- state - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- state - Variable in class org.jmol.console.ScriptEditor
- state - Variable in class org.jmol.jvxl.readers.Parameters
- state - Variable in class org.jmol.modelkit.ModelKit
- state - Static variable in class org.jmol.script.T
- STATE_BITS_SYM_EDIT - Static variable in class org.jmol.modelkit.ModelKit
- STATE_BITS_SYM_VIEW - Static variable in class org.jmol.modelkit.ModelKit
- STATE_BITS_UNITCELL - Static variable in class org.jmol.modelkit.ModelKit
- STATE_BITS_XTAL - Static variable in class org.jmol.modelkit.ModelKit
- state_counter_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- STATE_DATA_COLORED - Static variable in class org.jmol.jvxl.readers.Parameters
- STATE_DATA_READ - Static variable in class org.jmol.jvxl.readers.Parameters
- STATE_EDITING - Static variable in class org.jmol.console.ScriptEditor
- STATE_FREQ - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
- STATE_INITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
- STATE_INPUT - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
- STATE_INPUT - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- STATE_INPUT_FROM - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
- STATE_MOLECULAR - Static variable in class org.jmol.modelkit.ModelKit
- STATE_NONE - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
- STATE_OPT_FINAL - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
- STATE_OPT_POINT - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
- STATE_OUTPUT - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- STATE_PAUSED - Static variable in class org.jmol.console.ScriptEditor
- STATE_RUNNING - Static variable in class org.jmol.console.ScriptEditor
- STATE_SYM_APPLYFULL - Static variable in class org.jmol.modelkit.ModelKit
- STATE_SYM_APPLYLOCAL - Static variable in class org.jmol.modelkit.ModelKit
- STATE_SYM_NONE - Static variable in class org.jmol.modelkit.ModelKit
- STATE_SYM_RETAINLOCAL - Static variable in class org.jmol.modelkit.ModelKit
- STATE_SYM_SHOW - Static variable in class org.jmol.modelkit.ModelKit
- STATE_UNINITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
- STATE_UNITCELL_EXTEND - Static variable in class org.jmol.modelkit.ModelKit
- STATE_UNITCELL_PACKED - Static variable in class org.jmol.modelkit.ModelKit
- STATE_UNKNOWN - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- STATE_VERSION_STAMP - Static variable in class org.jmol.viewer.JC
- STATE_WAVEFUNCTION - Static variable in class org.jmol.adapter.readers.xtal.CrystalReader
- STATE_XTALEDIT - Static variable in class org.jmol.modelkit.ModelKit
- STATE_XTALVIEW - Static variable in class org.jmol.modelkit.ModelKit
- stateButton - Variable in class org.jmol.console.GenericConsole
- stateButton - Variable in class org.jmol.console.ScriptEditor
- StateButton - Variable in class org.openscience.jmol.app.webexport.Test
- stateChanged(ChangeEvent) - Method in class org.jmol.dialog.Dialog.QualityListener
- stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.webexport.PopInJmol
- stateCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- stateCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- StateCreator - Class in org.jmol.viewer
-
StateCreator handles all aspects of working with the "state" as generally defined, including -- creating the state script -- general output, including logging -- handling undo/redo -- processing SYNC directives Called by reflection only; all state generation script here, for modularization in JavaScript
- StateCreator() - Constructor for class org.jmol.viewer.StateCreator
- StateManager - Class in org.jmol.viewer
- StateManager(Viewer) - Constructor for class org.jmol.viewer.StateManager
- statement - Variable in class org.jmol.script.ScriptContext
- statementAsString(Viewer, T[], int, boolean) - Static method in class org.jmol.script.ScriptEval
- statementLength - Variable in class org.jmol.script.ScriptContext
- StateScript - Class in org.jmol.modelset
- StateScript(int, String, BS, BS, BS, String, boolean) - Constructor for class org.jmol.modelset.StateScript
- stateScripts - Variable in class org.jmol.modelset.ModelSet
- stateScriptVersionInt - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- stateScriptVersionInt - Variable in class org.jmol.viewer.Viewer
- stateSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- static_singletons - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- staticFunctions - Static variable in class org.jmol.viewer.Viewer
- staticGetAtomSetCollection(AtomSetCollectionReader) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
- staticGetAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
-
The primary file or string reader -- returns just the reader now
- staticid - Static variable in class org.jmol.quantum.NMRNoeMatrix
- stats() - Method in class org.jmol.bspt.Bspf
- stats() - Method in class org.jmol.bspt.Bspt
-
prints some simple stats to stdout
- status - Variable in class org.jmol.thread.TimeoutThread
- status - Variable in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- status - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- status - Variable in class org.openscience.jmol.app.jmolpanel.Splash
- status - Variable in class org.openscience.jmol.app.jmolpanel.StatusBar
- STATUS_COORD - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
- STATUS_TEXT - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
- STATUS_TIME - Static variable in class org.openscience.jmol.app.jmolpanel.StatusBar
- StatusBar - Class in org.openscience.jmol.app.jmolpanel
- StatusBar(int) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusBar
- statusForm - Variable in class org.jmol.util.GenericApplet
- statusList - Variable in class org.jmol.viewer.StatusManager
- statusListener - Variable in class org.jmol.awt.FileDropper
- statusListener - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- StatusListener - Class in org.openscience.jmol.app.jmolpanel
- StatusListener(JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusListener
- StatusManager - Class in org.jmol.viewer
-
The StatusManager class handles all details of status reporting, including: 1) saving the message in a queue that replaces the "callback" mechanism, 2) sending messages off to the console, and 3) delivering messages back to the main Jmol.java class in app or applet to handle differences in capabilities, including true callbacks.
- StatusManager(Viewer) - Constructor for class org.jmol.viewer.StatusManager
- statusPtr - Variable in class org.jmol.viewer.StatusManager
- statusreporting - Static variable in class org.jmol.script.T
- statusReporting - Variable in class org.jmol.viewer.GlobalSettings
- STATUSSIZE - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
- statusText - Variable in class org.jmol.util.GenericApplet
- statusText - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
- statusTextarea - Variable in class org.jmol.util.GenericApplet
- statusTop - Variable in class org.openscience.jmol.app.jmolpanel.Splash
- STD_ORIENTATION_ATOMIC_NUMBER_OFFSET - Static variable in class org.jmol.adapter.readers.quantum.GaussianReader
-
Word index of atomic number in line with atom coordinates in an orientation block.
- stddev - Static variable in class org.jmol.script.T
- stdinchi - Static variable in class org.jmol.script.T
- stdinchikey - Static variable in class org.jmol.script.T
- steepestDescentInitialize(int, double, double) - Method in class org.jmol.minimize.forcefield.ForceField
- steepestDescentTakeNSteps(int) - Method in class org.jmol.minimize.forcefield.ForceField
- step - Static variable in class org.jmol.script.T
- stepAxisCoordinates() - Method in class org.jmol.render.SticksRenderer
- stepBohr - Variable in class org.jmol.quantum.QuantumCalculation
- stepButton - Variable in class org.jmol.console.ScriptEditor
- stepButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- stepMax - Variable in class org.jmol.minimize.forcefield.ForceField
- stepMinimization() - Method in class org.jmol.minimize.Minimizer
- stepNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
- stepPausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
- stepPausedExecution() - Method in class org.jmol.script.ScriptEval
- steps - Variable in class org.jmol.jvxl.readers.Parameters
- steps - Variable in class org.jmol.minimize.Minimizer
- steps - Variable in class org.jmol.modelset.Trajectory
- STER - Enum in org.jmol.c
- STER(String, boolean) - Constructor for enum org.jmol.c.STER
- stereo - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stereo - Static variable in class org.jmol.script.T
- stereo - Variable in class org.jmol.smiles.SmilesAtom
- stereo - Variable in class org.jmol.smiles.SmilesSearch
- stereo() - Method in class org.jmol.scriptext.CmdExt
- stereo_angle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- STEREO_BOTH_EZ - Static variable in class org.jmol.symmetry.CIPChirality
- STEREO_BOTH_RS - Static variable in class org.jmol.symmetry.CIPChirality
- stereo_double_pump_mono - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stereo_dynamic_strength - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- STEREO_E - Static variable in class org.jmol.symmetry.CIPChirality
- STEREO_M - Static variable in class org.jmol.symmetry.CIPChirality
- stereo_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- STEREO_P - Static variable in class org.jmol.symmetry.CIPChirality
- STEREO_R - Static variable in class org.jmol.symmetry.CIPChirality
- STEREO_S - Static variable in class org.jmol.symmetry.CIPChirality
- stereo_shift - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- STEREO_Z - Static variable in class org.jmol.symmetry.CIPChirality
- stereoColors - Variable in class org.jmol.viewer.TransformManager
- stereodegrees - Static variable in class org.jmol.script.T
- stereoDegrees - Variable in class org.jmol.viewer.TransformManager
- stereodir - Variable in class org.jmol.modelset.ModelLoader
- stereoDoubleDTI - Variable in class org.jmol.viewer.TransformManager
- stereoDoubleFull - Variable in class org.jmol.viewer.TransformManager
- stereoFrame - Variable in class org.jmol.viewer.TransformManager
- stereoMode - Variable in class org.jmol.viewer.TransformManager
- stereoRadians - Variable in class org.jmol.viewer.TransformManager
- stereoState - Variable in class org.jmol.viewer.GlobalSettings
- stereoSync - Variable in class org.jmol.viewer.StatusManager
- StereoViewWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
- stick_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_ball - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_ball_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_ball_ratio - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_fixed_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_good_geometry - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_h_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_nub - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_overlap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_round_nub - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stick_valence_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- Sticks - Class in org.jmol.shape
- Sticks() - Constructor for class org.jmol.shape.Sticks
- SticksRenderer - Class in org.jmol.render
- SticksRenderer() - Constructor for class org.jmol.render.SticksRenderer
- stickTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- stm - Variable in class org.jmol.viewer.Viewer
- STO_EXP - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- stop - Static variable in class org.jmol.script.T
- STOP - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- STOP - Static variable in class org.jmol.shapecgo.CGOMesh
- stop_on_exceptions - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- stopAudio(String) - Method in class org.jmol.viewer.StatusManager
- stopMinimization() - Method in class org.jmol.viewer.Viewer
- stopMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
- stopMotion() - Method in class org.jmol.viewer.TransformManager
- stopPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- stopped - Variable in class org.jmol.thread.JmolThread
- stopScriptThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
- stopScriptThreads() - Method in class org.jmol.script.ScriptEval
- stopThread(boolean) - Method in class org.jmol.viewer.AnimationManager
- storedFrameNumber - Variable in class org.openscience.jmol.app.janocchio.PopulationDisplay
- STR - Enum in org.jmol.c
- STR(int, int) - Constructor for enum org.jmol.c.STR
- STR_SG - Static variable in class org.jmol.symmetry.SpaceGroup
-
intlNo:options;nOps;schoenflies;hermannMauguin;Hall;BilbaoFlag 530 settings, some with multiple names
- straightness - Variable in class org.jmol.modelsetbio.Monomer
- straightness - Static variable in class org.jmol.script.T
- STRAIGHTNESS - Enum constant in enum org.jmol.c.PAL
- STRAND_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- strandcount - Static variable in class org.jmol.script.T
- strandCount - Variable in class org.jmol.adapter.smarter.Structure
- strandCount - Variable in class org.jmol.modelsetbio.ProteinStructure
- strandCount - Variable in class org.jmol.renderbio.StrandsRenderer
- strandcountformeshribbon - Static variable in class org.jmol.script.T
- strandCountForMeshRibbon - Variable in class org.jmol.viewer.GlobalSettings
- strandcountforstrands - Static variable in class org.jmol.script.T
- strandCountForStrands - Variable in class org.jmol.viewer.GlobalSettings
- strands - Static variable in class org.jmol.script.T
- Strands - Class in org.jmol.shapebio
- Strands() - Constructor for class org.jmol.shapebio.Strands
- strandSeparation - Variable in class org.jmol.renderbio.StrandsRenderer
- StrandsRenderer - Class in org.jmol.renderbio
- StrandsRenderer() - Constructor for class org.jmol.renderbio.StrandsRenderer
- strAtomicNumbers - Variable in class org.jmol.adapter.readers.quantum.CsfReader
- strCommand - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ExecuteCommandThread
- strCoord(SymmetryOperation, T3, boolean) - Static method in class org.jmol.symmetry.SymmetryDesc
- strFormat - Variable in class org.jmol.modelset.Measurement
- strFormat - Variable in class org.jmol.modelset.MeasurementData
- strFormat - Variable in class org.jmol.shape.Measures
- strFractionTemp - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- strID - Variable in class org.jmol.shapesurface.MolecularOrbital
- string - Static variable in class org.jmol.script.T
- stringAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- stringClass - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- stringCount - Variable in class org.jmol.g3d.Graphics3D
- stringParameter(int) - Method in class org.jmol.script.ScriptParam
- stringParameter(int) - Method in class org.jmol.scriptext.ScriptExt
- stringParameterSet(int) - Method in class org.jmol.script.ScriptParam
- strings - Variable in class org.jmol.g3d.Graphics3D
- strings - Variable in class org.jmol.shape.Labels
- stringSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
- stringsResourceBundle - Variable in class org.openscience.jmol.app.janocchio.NmrResourceHandler
- stringsResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
- StringtoScriptButton - Variable in class org.openscience.jmol.app.webexport.Test
- stringWidth(Object, String) - Static method in class org.jmol.awt.AwtFont
- stringWidth(String) - Method in class org.jmol.modelset.Text
- stringWidth(String) - Method in class org.jmol.util.Font
- stringWidth(Font, Object, String) - Static method in class org.jmol.awtjs2d.JSFont
- stripPath(String) - Static method in class org.jmol.viewer.FileManager
- stripTypePrefix(String) - Static method in class org.jmol.viewer.FileManager
-
Stip PDB::file://...
- strJavaVendor - Static variable in class org.jmol.viewer.Viewer
- strJavaVersion - Static variable in class org.jmol.viewer.Viewer
- strListValue(T) - Static method in class org.jmol.script.SV
- strMeasurement - Variable in class org.jmol.modelset.Measurement
- strMenuStructure - Variable in class org.jmol.popup.GenericPopup
- strokeBasic - Variable in class org.jmol.awt.AwtG2D
- strokeBold - Variable in class org.jmol.awt.AwtG2D
- strop - Variable in class org.jmol.util.ModulationSet
-
a string description of the atom's symmetry operator
- strOSName - Static variable in class org.jmol.viewer.Viewer
- strparam - Static variable in class org.jmol.script.T
- strproperty - Static variable in class org.jmol.script.T
- strSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- strucid - Static variable in class org.jmol.script.T
- strucno - Static variable in class org.jmol.script.T
- strucNo - Variable in class org.jmol.modelsetbio.ProteinStructure
- STRUCT_CONN_ALT1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_ALT2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_ASYM1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_ASYM2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_ATOM1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_ATOM2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_COMP1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_COMP2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_ORDER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_SEQ1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_SEQ2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_SYMM1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_SYMM2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_CONN_TYPE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_REF_G1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- STRUCT_REF_G3 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- structConfFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- structConnFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- structConnList - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- structConnMap - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- structRefFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- structSheetRangeFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- structSiteFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
- structure - Variable in class org.jmol.adapter.smarter.StructureIterator
- structure - Variable in class org.jmol.popup.PopupResource
- structure - Static variable in class org.jmol.script.T
- structure() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- Structure - Class in org.jmol.adapter.smarter
- Structure - Interface in org.jmol.modelset
- Structure(int, STR, STR, String, int, int, BS[]) - Constructor for class org.jmol.adapter.smarter.Structure
- STRUCTURE - Enum constant in enum org.jmol.c.PAL
- structureContents - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
- structureContents - Static variable in class org.jmol.popup.MainPopupResourceBundle
- structureCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- structureCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- structureCount - Variable in class org.jmol.adapter.smarter.StructureIterator
- structureID - Variable in class org.jmol.adapter.smarter.Structure
- structureID - Variable in class org.jmol.modelsetbio.ProteinStructure
- StructureIterator - Class in org.jmol.adapter.smarter
- StructureIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.StructureIterator
- structureList - Variable in class org.jmol.modelsetbio.AminoPolymer
- structureList - Variable in class org.jmol.viewer.GlobalSettings
- STRUCTUREMODIFIED - Enum constant in enum org.jmol.c.CBK
- structures - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- structures - Variable in class org.jmol.adapter.smarter.StructureIterator
- structuresDefinedInFile - Variable in class org.jmol.modelset.ModelLoader
- structureTainted - Variable in class org.jmol.modelset.Model
- structureType - Variable in class org.jmol.adapter.smarter.Structure
- structureTypes - Variable in class org.jmol.renderbio.BioShapeRenderer
- STRUT - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- strutdefaultradius - Static variable in class org.jmol.script.T
- strutDefaultRadius - Variable in class org.jmol.viewer.GlobalSettings
- strutlengthmaximum - Static variable in class org.jmol.script.T
- strutLengthMaximum - Variable in class org.jmol.viewer.GlobalSettings
- strutPoint(int, int, int) - Static method in class org.jmol.modelsetbio.BioExt
- struts - Static variable in class org.jmol.script.T
- struts() - Method in class org.jmol.scriptext.CmdExt
- strutsmultiple - Static variable in class org.jmol.script.T
- strutsMultiple - Variable in class org.jmol.viewer.GlobalSettings
- strutspacing - Static variable in class org.jmol.script.T
- strutSpacing - Variable in class org.jmol.viewer.GlobalSettings
- stub - Variable in class org.jmol.console.JmolConsole.FileChecker
- sType - Variable in class org.jmol.minimize.MinAtom
- sub - Static variable in class org.jmol.script.T
- sub(double[], double[], V3d) - Static method in class org.jmol.minimize.Util
- subAtoms - Variable in class org.jmol.smiles.SmilesAtom
- sublistAt(Lst<Object>, int...) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
- SUBMODE_NESTED - Static variable in class org.jmol.smiles.SmilesSearch
- SUBMODE_OR - Static variable in class org.jmol.smiles.SmilesSearch
- SUBMODE_RINGCHECK - Static variable in class org.jmol.smiles.SmilesSearch
- subParser - Variable in class org.jmol.adapter.readers.cif.CifReader
- subsearch(SmilesSearch, int) - Method in class org.jmol.smiles.SmilesSearch
- subSearches - Variable in class org.jmol.smiles.SmilesSearch
- subset - Static variable in class org.jmol.script.T
- subsetString(BS) - Static method in class org.jmol.jvxl.data.JvxlCoder
- substructure - Static variable in class org.jmol.script.T
- substructureType - Variable in class org.jmol.adapter.smarter.Structure
- SUBSYS_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
- subsystem - Static variable in class org.jmol.script.T
- Subsystem - Class in org.jmol.adapter.readers.cif
- Subsystem(MSRdr, String, Matrix) - Constructor for class org.jmol.adapter.readers.cif.Subsystem
- subsystemCode - Variable in class org.jmol.symmetry.SymmetryOperation
- subtype - Variable in class org.jmol.modelsetbio.ProteinStructure
- subzones - Variable in class org.jmol.util.BZone
- sum - Variable in class org.jmol.quantum.MOCalculation
- sum - Static variable in class org.jmol.script.T
- sum2 - Static variable in class org.jmol.script.T
- sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shape.Mesh
- sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
- sumVertexNormals2(Mesh, T3[], V3[]) - Static method in class org.jmol.shape.Mesh
- supercell - Static variable in class org.jmol.script.T
- supercellSymmetry - Variable in class org.jmol.adapter.readers.cif.MSRdr
- supportedRecordTypes - Static variable in class org.jmol.adapter.readers.xtal.ShelxReader
- suppress_hidden - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface - Static variable in class org.jmol.script.T
- SURFACE - Enum constant in enum org.jmol.c.PAL
- SURFACE_ATOMICORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
- surface_best - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_carve_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_carve_normal_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_carve_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_carve_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_cavity_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_cavity_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_cavity_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_circumscribe - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_clear_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_clear_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_clear_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_color_smoothing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_color_smoothing_threshold - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SURFACE_DISTANCE_FOR_CALCULATION - Static variable in class org.jmol.shapespecial.Dots
- SURFACE_ELLIPSOID2 - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_ELLIPSOID3 - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_FUNCTIONXY - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_FUNCTIONXYZ - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_GEODESIC - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_INTERSECT_ATOM - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_INTERSECT_FILE - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_LCAOCARTOON - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_LOBE - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_LONEPAIR - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_MEP - Static variable in class org.jmol.jvxl.readers.Parameters
- surface_miserable - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SURFACE_MLP - Static variable in class org.jmol.jvxl.readers.Parameters
- surface_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SURFACE_MOLECULAR - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_MOLECULARORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_NCI - Static variable in class org.jmol.jvxl.readers.Parameters
- surface_negative_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_negative_visible - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SURFACE_NOMAP - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_NONE - Static variable in class org.jmol.jvxl.readers.Parameters
- surface_normal - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_optimize_subsets - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_poor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SURFACE_PROPERTY - Static variable in class org.jmol.jvxl.readers.Parameters
- surface_proximity - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SURFACE_RADICAL - Static variable in class org.jmol.jvxl.readers.Parameters
- surface_ramp_above_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_residue_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SURFACE_SASURFACE - Static variable in class org.jmol.jvxl.readers.Parameters
- surface_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SURFACE_SOLVENT - Static variable in class org.jmol.jvxl.readers.Parameters
- SURFACE_SPHERE - Static variable in class org.jmol.jvxl.readers.Parameters
- surface_trim_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_trim_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_type - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surface_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- surfaceAtoms - Variable in class org.jmol.jvxl.readers.Parameters
- surfaceAtoms - Variable in class org.jmol.util.MeshSurface
- surfaceColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- surfaceDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- surfacedistance - Static variable in class org.jmol.script.T
- surfaceDistance100s - Variable in class org.jmol.modelset.AtomCollection
- surfaceDistanceMax - Variable in class org.jmol.modelset.AtomCollection
- surfaceDone - Variable in class org.jmol.jvxl.readers.IsoShapeReader
- SurfaceFileReader - Class in org.jmol.jvxl.readers
-
PolygonFileReader or VolumeFileReader
- SurfaceFileReader() - Constructor for class org.jmol.jvxl.readers.SurfaceFileReader
- SurfaceGenerator - Class in org.jmol.jvxl.readers
- SurfaceGenerator(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
- surfaceInfoName - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- surfaceList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- SurfaceListCellRenderer() - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
- surfaceMode - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- surfaceName - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- surfaceNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- surfacePoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingCubes
- surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingSquares
- surfaceReader - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- SurfaceReader - Class in org.jmol.jvxl.readers
- SurfaceReader() - Constructor for class org.jmol.jvxl.readers.SurfaceReader
- surfaces - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- surfaceScrollPane - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- surfaceSet - Variable in class org.jmol.util.MeshSurface
- surfacesOnly - Variable in class org.jmol.export._ObjExporter
-
Flag to cause only surfaces to be output.
- SurfaceStatus - Class in org.openscience.jmol.app.surfacetool
-
Class that holds the surface status information that the surface tool needs.
- SurfaceStatus(Mesh, int) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceStatus
- surfaceTool - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- SurfaceTool - Class in org.openscience.jmol.app.surfacetool
- SurfaceTool(JmolViewer, HistoryFile, String, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceTool
- SURFACETOOL_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- surfaceToolAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- SurfaceToolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
- surfaceToolActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- SurfaceToolGUI - Class in org.openscience.jmol.app.surfacetool
-
GUI for the Jmol surfaceTool
- SurfaceToolGUI(boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- SurfaceToolGUI(LayoutManager) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- SurfaceToolGUI(LayoutManager, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- SurfaceToolGUI(JmolViewer, HistoryFile, String, SurfaceTool) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
Builds and opens a GUI to control slicing.
- SurfaceToolGUI.SurfaceListCellRenderer - Class in org.openscience.jmol.app.surfacetool
- surfaceType - Variable in class org.jmol.jvxl.readers.Parameters
- suspend_undo - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- suspend_undo_atom_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- suspend_updates - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SV - Class in org.jmol.script
-
ScriptVariable class
- SV() - Constructor for class org.jmol.script.SV
- SV.Sort - Class in org.jmol.script
- sVal - Variable in class org.jmol.minimize.forcefield.FFParam
- sValue(T) - Static method in class org.jmol.script.SV
- sValueAddKeys(SB, String, Map<String, SV>, String, boolean, boolean, int, boolean) - Static method in class org.jmol.script.SV
- sValueArray(SB, SV, String, String, boolean, boolean, boolean, int, boolean) - Static method in class org.jmol.script.SV
- swap(int[], int, int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- swap_dsn6_bytes - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- swapArray(SimpleNode[], int, int, int) - Method in class org.jmol.smiles.SmilesGenerator
-
swap slices of an array [i0 i1) with [i1 i2)
- swapXZ() - Method in class org.jmol.jvxl.readers.VolumeFileReader
- sweep_angle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sweep_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sweep_phase - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- sweep_speed - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- SwingConstants - Class in org.jmol.awtjs.swing
- SwingConstants() - Constructor for class org.jmol.awtjs.swing.SwingConstants
- SwingController - Interface in org.jmol.awtjs.swing
-
SwingController is an interface that org.jmol.awtjs.swing classes will need.
- swipeCount - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- swipeCutoff - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- swipeDelayMs - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- swipeFactor - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- swipeStartTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- switchAtoms() - Method in class org.jmol.smiles.SmilesBond
-
Ensure that atom ordering is proper.
- switchAtoms() - Method in class org.jmol.util.ContactPair
- switchcmd - Static variable in class org.jmol.script.T
- sX - Variable in class org.jmol.util.Point3fi
-
screen X
- sY - Variable in class org.jmol.util.Point3fi
-
screen Y
- sym - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- sym - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
- SYM - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- SYM - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- SYM_EQ_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_MAGN_CENTERING - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_MAGN_REV - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_MAGN_REV_PRELIM - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_MAGN_SSG_ALG - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_MAGN_SSG_CENT_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_MAGN_SSG_CENTERING - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_MAGN_SSG_REV - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_MAGN_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_SSG_ALG - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_SSG_EQ_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
- SYM_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
- sym2 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- symbol - Static variable in class org.jmol.script.T
- symbol - Variable in class org.jmol.smiles.SmilesAtom
- symbolicMap - Variable in class org.jmol.adapter.readers.simple.InputReader
- symLine - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- symMatrix - Variable in class org.jmol.util.Tensor
- symmetries - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
- symmetry - Variable in class org.jmol.adapter.readers.cif.MSRdr
- symmetry - Variable in class org.jmol.adapter.readers.cif.Subsystem
- symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- symmetry - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- symmetry - Static variable in class org.jmol.script.T
- symmetry - Variable in class org.jmol.util.ModulationSet
-
the space group appropriate to this atom
- symmetry() - Method in class org.jmol.adapter.readers.xtal.JanaReader
- Symmetry - Class in org.jmol.symmetry
- Symmetry() - Constructor for class org.jmol.symmetry.Symmetry
- SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
-
state constants
- SYMMETRY_OPTIONS - Static variable in class org.jmol.modelkit.ModelKit
- symmetryAddAtoms(int, int, int, int, int, int, P3[], MSInterface, BS, int[]) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- SymmetryData(int, String) - Constructor for class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
- SymmetryDesc - Class in org.jmol.symmetry
-
A class to handle requests for information about space groups and symmetry operations.
- SymmetryDesc() - Constructor for class org.jmol.symmetry.SymmetryDesc
- symmetryInfo - Variable in class org.jmol.symmetry.Symmetry
- SymmetryInfo - Class in org.jmol.symmetry
- SymmetryInfo() - Constructor for class org.jmol.symmetry.SymmetryInfo
- SymmetryInterface - Interface in org.jmol.api
- SymmetryOnly - Variable in class org.jmol.popup.JmolPopup
- SymmetryOperation - Class in org.jmol.symmetry
- SymmetryOperation(SymmetryOperation, int, boolean) - Constructor for class org.jmol.symmetry.SymmetryOperation
- symmetryOperations - Variable in class org.jmol.symmetry.SymmetryInfo
- symmetryOperationsFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
- symmetryRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- symmetryRange - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- symop - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- symop - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- symop - Variable in class org.jmol.modelkit.ModelKit
- symop - Static variable in class org.jmol.script.T
- symopColixes - Variable in class org.jmol.shape.Mesh
- symopNormixes - Variable in class org.jmol.shape.Mesh
- symops - Variable in class org.jmol.adapter.readers.cif.CifReader
- symops - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- symops - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- symops - Variable in class org.jmol.shape.Mesh
- sync - Static variable in class org.jmol.script.T
- SYNC - Enum constant in enum org.jmol.c.CBK
- SYNC_DISABLE - Static variable in class org.jmol.viewer.StatusManager
- SYNC_DRIVER - Static variable in class org.jmol.viewer.StatusManager
- SYNC_ENABLE - Static variable in class org.jmol.viewer.StatusManager
- SYNC_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
- SYNC_NO_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
- SYNC_OFF - Static variable in class org.jmol.viewer.StatusManager
- SYNC_SLAVE - Static variable in class org.jmol.viewer.StatusManager
- SYNC_STEREO - Static variable in class org.jmol.viewer.StatusManager
- syncDisabled - Variable in class org.jmol.viewer.StatusManager
- syncDone() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- syncId - Variable in class org.jmol.util.GenericApplet
- syncId - Variable in class org.jmol.viewer.Viewer
- syncingMouse - Variable in class org.jmol.viewer.StatusManager
- syncingScripts - Variable in class org.jmol.viewer.StatusManager
- syncLists() - Method in class org.openscience.jmol.app.webexport.WebPanel
- syncmouse - Static variable in class org.jmol.script.T
- syncscript - Static variable in class org.jmol.script.T
- syncScript(String) - Method in interface org.jmol.api.JmolSyncInterface
- syncScript(String) - Method in class org.jmol.util.GenericApplet
- syncScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- syncScript(String, String, int) - Method in class org.jmol.api.JmolViewer
- syncScript(String, String, int) - Method in class org.jmol.viewer.StatusManager
- syncScript(String, String, int) - Method in class org.jmol.viewer.Viewer
- syncScript(Viewer, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- syncSend(String, Object, int) - Method in class org.jmol.viewer.StatusManager
- syncToJmol(String) - Method in interface org.jmol.api.JSVInterface
- syncToJmol(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
- sZ - Variable in class org.jmol.util.Point3fi
-
screen Z
T
- t - Variable in class org.jmol.symmetry.UnitCellIterator
- t - Variable in class org.openscience.jmol.app.InputScannerThread
- t(int) - Static method in class org.jmol.script.T
- T - Class in org.jmol.script
-
Script token class.
- T() - Constructor for class org.jmol.script.T
- T_SHAPED - Static variable in class org.jmol.smiles.SmilesStereo
- t0 - Static variable in class org.jmol.scriptext.MathExt
- T1 - Variable in class org.jmol.g3d.HermiteRenderer
- T2 - Variable in class org.jmol.g3d.HermiteRenderer
- tableCellRenderer - Variable in class org.openscience.jmol.app.janocchio.TableSorter.SortableHeaderRenderer
- TableCellRenderer - Interface in org.jmol.awtjs.swing
- tableChanged(TableModelEvent) - Method in class org.openscience.jmol.app.janocchio.TableSorter.TableModelHandler
- TableColumn - Interface in org.jmol.awtjs.swing
- tableHeader - Variable in class org.openscience.jmol.app.janocchio.TableSorter
- tableModel - Variable in class org.jmol.awtjs.swing.JTable
- tableModel - Variable in class org.openscience.jmol.app.janocchio.TableSorter
- TableModelHandler() - Constructor for class org.openscience.jmol.app.janocchio.TableSorter.TableModelHandler
- tableModelListener - Variable in class org.openscience.jmol.app.janocchio.TableSorter
- TableSorter - Class in org.openscience.jmol.app.janocchio
- TableSorter() - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
- TableSorter(TableModel) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
- TableSorter(TableModel, JTableHeader) - Constructor for class org.openscience.jmol.app.janocchio.TableSorter
- TableSorter.Arrow - Class in org.openscience.jmol.app.janocchio
- TableSorter.Directive - Class in org.openscience.jmol.app.janocchio
- TableSorter.MouseHandler - Class in org.openscience.jmol.app.janocchio
- TableSorter.Row - Class in org.openscience.jmol.app.janocchio
- TableSorter.SortableHeaderRenderer - Class in org.openscience.jmol.app.janocchio
- TableSorter.TableModelHandler - Class in org.openscience.jmol.app.janocchio
- tabPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- tags - Static variable in class org.jmol.adapter.readers.xtal.GulpReader
- tags - Static variable in class org.jmol.quantum.QS
- tags2 - Static variable in class org.jmol.quantum.QS
- TAINT_ATOMNAME - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_ATOMNO - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_ATOMTYPE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_BONDINGRADIUS - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_CHAIN - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_COORD - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_ELEMENT - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_FORMALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_HYDROPHOBICITY - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_MAX - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_OCCUPANCY - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_PARTIALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_RESNO - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_SEQID - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_SITE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_TEMPERATURE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_VALENCE - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_VANDERWAALS - Static variable in class org.jmol.modelset.AtomCollection
- TAINT_VIBRATION - Static variable in class org.jmol.modelset.AtomCollection
- taintAtom(int, int) - Method in class org.jmol.modelset.AtomCollection
- taintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
- tainted - Variable in class org.jmol.awtjs.swing.JPopupMenu
- tainted - Variable in class org.jmol.modelset.AtomCollection
- tainted - Variable in class org.jmol.modelset.Measurement
- tainted - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- taintModelCoord(int) - Method in class org.jmol.modelset.AtomCollection
- target - Variable in class org.jmol.modelset.Text
- targetAtomCount - Variable in class org.jmol.smiles.SmilesSearch
- targetAtoms - Variable in class org.jmol.smiles.SmilesSearch
- targetTime - Variable in class org.jmol.thread.JmolThread
- taskNumber - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
-
The number of the task begin interpreted.
- TAtom() - Constructor for class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- tatoms - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- tatoms - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- tau - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
-
the correlation time in seconds.
- tau - Variable in class org.jmol.util.ModulationSet
- tau - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- tauField - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- tauFieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- tauLabel - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- TBI_AB - Static variable in class org.jmol.minimize.forcefield.ForceField
- TBI_BC - Static variable in class org.jmol.minimize.forcefield.ForceField
- TBI_CD - Static variable in class org.jmol.minimize.forcefield.ForceField
- tButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- TEAL - Static variable in class org.jmol.util.C
- temp - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- temp - Variable in class org.jmol.viewer.StateCreator
- TEMP - Enum constant in enum org.jmol.c.PAL
- TEMP - Enum constant in enum org.jmol.c.VDW
- temp1 - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- temp2 - Variable in class org.jmol.adapter.readers.cif.TopoCifParser
- temp2 - Variable in class org.jmol.viewer.StateCreator
- temp3 - Variable in class org.jmol.viewer.StateCreator
- tempArray - Variable in class org.jmol.viewer.Viewer
- TempArray - Class in org.jmol.util
- TempArray() - Constructor for class org.jmol.util.TempArray
- tempC - Variable in class org.jmol.export.___Exporter
- tempDataXml - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- tempDipole - Variable in class org.jmol.shapespecial.Dipoles
- temperature - Static variable in class org.jmol.script.T
- TemperatureOnly - Variable in class org.jmol.popup.JmolPopup
- templateAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- tempP1 - Variable in class org.jmol.export.___Exporter
- tempP2 - Variable in class org.jmol.export.___Exporter
- tempP3 - Variable in class org.jmol.export.___Exporter
- tempQ1 - Variable in class org.jmol.export._VrmlExporter
- tempQ2 - Variable in class org.jmol.export._VrmlExporter
- tempQ3 - Variable in class org.jmol.export._VrmlExporter
- tempStatement - Variable in class org.jmol.script.ScriptExpr
- tempV1 - Variable in class org.jmol.export.___Exporter
- tempV2 - Variable in class org.jmol.export.___Exporter
- tempXY - Variable in class org.jmol.render.HoverRenderer
- tensor - Static variable in class org.jmol.script.T
- tensor - Variable in class org.jmol.shapespecial.Ellipsoid
- Tensor - Class in org.jmol.util
- Tensor() - Constructor for class org.jmol.util.Tensor
-
Although this constructor is public, to be a valid tensor, one must invoke one of the "setFrom" methods.
- tensors - Variable in class org.jmol.adapter.smarter.Atom
- term - Variable in class org.jmol.export.UseTable
- Test - Class in org.openscience.jmol.app.webexport
- Test(Viewer) - Constructor for class org.openscience.jmol.app.webexport.Test
- test1 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- test1 - Variable in class org.jmol.quantum.NciCalculation
- test2 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- testAsync - Variable in class org.jmol.viewer.Viewer
- testDiff(P3, P3, P3, P3) - Method in class org.jmol.shapespecial.Polyhedra
- testflag1 - Static variable in class org.jmol.script.T
- testFlag1 - Variable in class org.jmol.viewer.GlobalSettings
- testflag2 - Static variable in class org.jmol.script.T
- testFlag2 - Variable in class org.jmol.viewer.GlobalSettings
- testflag3 - Static variable in class org.jmol.script.T
- testFlag3 - Variable in class org.jmol.viewer.GlobalSettings
- testflag4 - Static variable in class org.jmol.script.T
- testFlag4 - Variable in class org.jmol.viewer.GlobalSettings
- testFlags - Variable in class org.jmol.jvxl.readers.Parameters
- testing - Variable in class org.jmol.quantum.MOCalculation
- testLinear - Static variable in class org.jmol.jvxl.readers.IsoSolventReader
- testRule6Full - Variable in class org.jmol.symmetry.CIPData
-
A flag that, if set, returns rr for bicyclo[2.2.2]octane
- TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesStereo
- tEvenDiameter - Variable in class org.jmol.g3d.CylinderRenderer
- text - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- text - Variable in class org.jmol.awt.AwtClipboard
- text - Variable in class org.jmol.awtjs.swing.Component
- text - Variable in class org.jmol.g3d.TextString
- text - Variable in class org.jmol.modelset.LabelToken
- text - Variable in class org.jmol.modelset.Measurement
- text - Variable in class org.jmol.modelset.MeasurementData
- text - Variable in class org.jmol.modelset.Text
- text - Variable in class org.jmol.shape.Hover
- Text - Class in org.jmol.modelset
- Text() - Constructor for class org.jmol.modelset.Text
- TEXT_ALIGN_CENTER - Static variable in class org.jmol.viewer.JC
- TEXT_ALIGN_FLAGS - Static variable in class org.jmol.viewer.JC
- TEXT_ALIGN_LEFT - Static variable in class org.jmol.viewer.JC
- TEXT_ALIGN_NONE - Static variable in class org.jmol.viewer.JC
- TEXT_ALIGN_RIGHT - Static variable in class org.jmol.viewer.JC
- TEXT_ALIGN_SHIFT - Static variable in class org.jmol.viewer.JC
- textAlign - Variable in class org.jmol.awtjs.swing.Cell
- textAlign - Variable in class org.jmol.render.LabelsRenderer
- TEXTCOLOR - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
- textHeight - Variable in class org.jmol.modelset.Text
- textInfo - Variable in class org.jmol.symmetry.PointGroup
- TextRenderer - Class in org.jmol.g3d
-
implementation for text rendering
- TextRenderer - Class in org.jmol.render
- TextRenderer() - Constructor for class org.jmol.render.TextRenderer
- TextRenderer(String, Font) - Constructor for class org.jmol.g3d.TextRenderer
- TextShape - Class in org.jmol.shape
- TextShape() - Constructor for class org.jmol.shape.TextShape
- TextString - Class in org.jmol.g3d
- TextString() - Constructor for class org.jmol.g3d.TextString
- TEXTTYPE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- textUnformatted - Variable in class org.jmol.modelset.Text
- texture_fonts - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- textureCode - Variable in class org.jmol.export._TachyonExporter
- textureFiles - Variable in class org.jmol.export._ObjExporter
-
List of texture files created.
- textures - Variable in class org.jmol.export._ObjExporter
-
HashSet for textures.
- textures - Variable in class org.jmol.export._TachyonExporter
- textWidth - Variable in class org.jmol.modelset.Text
- textY - Variable in class org.jmol.util.GData
- textY - Variable in class org.openscience.jmol.app.jmolpanel.Splash
- tFactorInv - Variable in class org.jmol.util.ModulationSet
- tHemisphere - Variable in class org.jmol.bspt.CubeIterator
- thePlane - Variable in class org.jmol.jvxl.data.VolumeData
- thePlane - Variable in class org.jmol.jvxl.readers.Parameters
- thePlane - Variable in class org.jmol.render.MeshRenderer
- thePlaneNormalMag - Variable in class org.jmol.jvxl.data.VolumeData
- theProperty - Variable in class org.jmol.jvxl.readers.AtomDataReader
- theProperty - Variable in class org.jmol.jvxl.readers.Parameters
- THERMAL_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
- theta - Variable in class org.jmol.minimize.forcefield.Calculation
- theta - Variable in class org.jmol.modelsetbio.Monomer
- theta - Static variable in class org.jmol.script.T
- theta0 - Variable in class org.jmol.minimize.MinAngle
- theTok - Variable in class org.jmol.script.ScriptContext
- theTok - Variable in class org.jmol.script.ScriptParam
- theTok - Variable in class org.jmol.script.ScriptTokenParser
- theToken - Variable in class org.jmol.script.ScriptContext
- theToken - Variable in class org.jmol.script.ScriptParam
- theToken - Variable in class org.jmol.script.ScriptTokenParser
- theValue - Variable in class org.jmol.script.ScriptTokenParser
- theWidgets - Variable in class org.openscience.jmol.app.webexport.WebPanel
- THICK_LINE - Static variable in class org.jmol.symmetry.SymmetryDesc
- thickness - Variable in class org.openscience.jmol.app.surfacetool.Slice
- thickness - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- thicknessMax - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- thicknessSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- THIN_LINE - Static variable in class org.jmol.symmetry.SymmetryDesc
- thisArgb - Variable in class org.jmol.shapespecial.Dots
- thisAtom - Variable in class org.jmol.quantum.QuantumCalculation
- thisAtom - Variable in class org.jmol.shapespecial.Dots
- thisAtomSet - Variable in class org.jmol.jvxl.readers.AtomDataReader
- thisBiomolecule - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- thisChain - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- thisCommand - Variable in class org.jmol.script.ScriptEval
- thisContext - Variable in class org.jmol.script.ScriptParam
- thisContour - Variable in class org.jmol.jvxl.calc.MarchingSquares
- thisContour - Variable in class org.jmol.jvxl.data.JvxlData
- thisContour - Variable in class org.jmol.jvxl.readers.Parameters
- thisData - Variable in class org.jmol.jvxl.readers.BCifDensityReader
- thisDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
- thisFontID - Variable in class org.jmol.shapespecial.Draw
- thisFormula - Variable in class org.jmol.adapter.readers.cif.CifReader
- thisFunction - Variable in class org.jmol.script.ScriptCompiler
- thisID - Variable in class org.jmol.modelset.Measurement
- thisID - Variable in class org.jmol.modelset.MeasurementData
- thisID - Variable in class org.jmol.shape.Mesh
- thisID - Variable in class org.jmol.shape.TextShape
- thisID - Variable in class org.jmol.shapespecial.Dipole
- thisID - Variable in class org.jmol.shapespecial.Polyhedra
- thisInside - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- thisMesh - Variable in class org.jmol.shapespecial.Draw
- thisMesh - Variable in class org.jmol.shapesurface.Isosurface
- thismodel - Static variable in class org.jmol.script.T
- thisModel - Variable in class org.jmol.shapesurface.MolecularOrbital
- thisModelID - Variable in class org.jmol.jsv.JDXMOLParser
- thisName - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- thisName - Variable in class org.jmol.util.ColorEncoder
- thisPlane - Variable in class org.jmol.jvxl.readers.AtomDataReader
- thisPlaneB - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- thisPlaneB - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
- thisPopup - Variable in class org.jmol.popup.GenericPopup
- thisRadius - Variable in class org.jmol.shapespecial.Dots
- thisReader - Variable in class org.jmol.adapter.readers.xml.XmlReader
- thisScale - Variable in class org.jmol.util.ColorEncoder
- thisSection - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- thisSet - Variable in class org.jmol.jvxl.data.JvxlData
- thisSet - Variable in class org.jmol.shapesurface.LcaoCartoon
- thisState - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- thisStateModel - Variable in class org.jmol.modelset.ModelSet
- thisStructuralFormula - Variable in class org.jmol.adapter.readers.cif.CifReader
- thisSub - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- thisType - Variable in class org.jmol.dialog.Dialog.TypeFilter
- thisType - Variable in class org.jmol.shapesurface.LcaoCartoon
- thisx - Variable in class org.jmol.popup.GenericPopup
- thisX - Variable in class org.jmol.jvxl.readers.AtomDataReader
- thisy - Variable in class org.jmol.popup.GenericPopup
- threadIndex - Static variable in class org.jmol.thread.JmolThread
- threadSafe - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- threeVertices - Variable in class org.jmol.export._VrmlExporter
- throwcmd - Static variable in class org.jmol.script.T
- tickA - Variable in class org.jmol.render.FontLineShapeRenderer
- tickAs - Variable in class org.jmol.render.FontLineShapeRenderer
- tickB - Variable in class org.jmol.render.FontLineShapeRenderer
- tickBs - Variable in class org.jmol.render.FontLineShapeRenderer
- tickEdges - Variable in class org.jmol.render.CageRenderer
- tickInfo - Variable in class org.jmol.modelset.Measurement
- tickInfo - Variable in class org.jmol.modelset.MeasurementData
- tickInfo - Variable in class org.jmol.render.FontLineShapeRenderer
- tickInfo - Variable in class org.jmol.shape.Measures
- TickInfo - Class in org.jmol.modelset
- TickInfo(P3) - Constructor for class org.jmol.modelset.TickInfo
- tickInfos - Variable in class org.jmol.shape.FontLineShape
- tickLabelFormats - Variable in class org.jmol.modelset.TickInfo
- tickParamAsStr(int, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptParam
- ticks - Variable in class org.jmol.modelset.TickInfo
- ticks - Static variable in class org.jmol.script.T
- TIED - Static variable in class org.jmol.symmetry.CIPChirality
- time - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- time - Variable in class org.jmol.viewer.MotionPoint
- time - Variable in class org.jmol.viewer.MouseState
- time0 - Variable in class org.jmol.viewer.Gesture
- timeBegin - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- timeBegin - Variable in class org.openscience.jvxl.MonitorInputStream
- timeBeginExecution - Variable in class org.jmol.script.ScriptEval
- timeCount - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- timeEndExecution - Variable in class org.jmol.script.ScriptEval
- timeLast - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- timeout - Static variable in class org.jmol.script.T
- timeouts - Variable in class org.jmol.viewer.Viewer
- TimeoutThread - Class in org.jmol.thread
- TimeoutThread(Viewer, String, int, String) - Constructor for class org.jmol.thread.TimeoutThread
- timePerStep - Variable in class org.jmol.thread.MoveToThread
- timeReversal - Variable in class org.jmol.symmetry.SymmetryOperation
- times - Static variable in class org.jmol.script.T
- TimeStamp_WebLink() - Static method in class org.openscience.jmol.app.webexport.WebExport
- timestimes - Static variable in class org.jmol.script.T
- timeTotal - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- TinkerReader - Class in org.jmol.adapter.readers.simple
-
simple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu
- TinkerReader() - Constructor for class org.jmol.adapter.readers.simple.TinkerReader
- title - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- title - Variable in class org.jmol.adapter.readers.quantum.DgridReader
- title - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- title - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- title - Variable in class org.jmol.awtjs.swing.JDialog
- title - Variable in class org.jmol.console.ImageDialog
- title - Variable in class org.jmol.console.ScriptEditor
- title - Variable in class org.jmol.jvxl.data.JvxlData
- title - Variable in class org.jmol.jvxl.readers.Parameters
- title - Static variable in class org.jmol.script.T
- title - Variable in class org.jmol.shape.Mesh
- title - Variable in class org.jmol.shape.MeshCollection
- title - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
- title() - Method in class org.jmol.adapter.readers.pdb.PdbReader
- TITLE - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- titleAtomSet - Variable in class org.jmol.adapter.readers.cif.CifReader
- titleColor - Variable in class org.jmol.shapespecial.Draw
- titleColor - Variable in class org.jmol.shapespecial.DrawMesh
- titleformat - Static variable in class org.jmol.script.T
- titleLabel - Variable in class org.openscience.jmol.app.janocchio.CoupleParameterSelectionPanel
- titleLabel - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- titleMsg - Variable in class org.jmol.adapter.readers.more.AFLOWReader
- titleRecords - Static variable in class org.jmol.adapter.readers.cif.CifReader
- titles - Variable in class org.jmol.adapter.readers.spartan.SpartanSmolReader
- titleWidthMax - Variable in class org.jmol.popup.JmolPopup
- TLink() - Constructor for class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- TLnn - Static variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
- tlsAddError(String) - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
- tlsAddError(String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
- tlsDataOnlyFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- TlsDataOnlyReader - Class in org.jmol.adapter.readers.more
- TlsDataOnlyReader() - Constructor for class org.jmol.adapter.readers.more.TlsDataOnlyReader
- tlsGroupID - Variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
- tlsGroupID - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- tlsU - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- tm - Variable in class org.jmol.export.___Exporter
- tm - Variable in class org.jmol.navigate.Navigator
- tm - Variable in class org.jmol.render.ShapeRenderer
- tm - Variable in class org.jmol.renderbio.NucleicRenderer
- tm - Variable in class org.jmol.renderbio.RocketRenderer
- tm - Variable in class org.jmol.viewer.Viewer
- tmap - Variable in class org.jmol.g3d.TextRenderer
- tMix - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- tMix - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- tMixField - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- tMixFieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- tMixLabel - Variable in class org.openscience.jmol.app.janocchio.NoeParameterSelectionPanel
- tmp - Variable in class org.jmol.g3d.PixelatorShaded
- TNet(int, String, String, String) - Constructor for class org.jmol.adapter.readers.cif.TopoCifParser.TNet
- TNode() - Constructor for class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- TNode(int, Atom, TopoCifParser.TNet, int, P3) - Constructor for class org.jmol.adapter.readers.cif.TopoCifParser.TNode
-
Constructor from TLink
- to - Static variable in class org.jmol.script.T
- toArray() - Method in class org.jmol.script.SV
- toCanonical - Static variable in class org.jmol.util.BoxInfo
- toCap(String, int) - Static method in class org.jmol.symmetry.SpaceGroup
- toCartesian(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
- toCartesian(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
- toCartesian(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
- toCartesian(T3, boolean) - Method in class org.jmol.viewer.Viewer
-
absolute or relative to origin of UNITCELL {x y z}
- toCartesianUC(SymmetryInterface, T3, boolean) - Method in class org.jmol.viewer.Viewer
- toDivisor(float, int) - Static method in class org.jmol.symmetry.SymmetryOperation
- toFloat(String) - Static method in class org.jmol.script.SV
- toFloatArray(double[]) - Method in class org.jmol.adapter.readers.quantum.QCJSONReader
- toFloatArray(List<Number>, float[]) - Static method in class org.jmol.adapter.readers.xtal.OptimadeReader
- toFractional(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
- toFractional(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
- toFractional(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
- toFractional(T3, boolean) - Method in class org.jmol.viewer.Viewer
- toFractional(Atom, SymmetryInterface) - Method in class org.jmol.symmetry.SpaceGroupFinder
- toFractionalM(M4) - Method in interface org.jmol.api.SymmetryInterface
- toFractionalM(M4) - Method in class org.jmol.symmetry.Symmetry
- toFractionalM(M4) - Method in class org.jmol.util.SimpleUnitCell
- toFractionalUC(SymmetryInterface, T3, boolean) - Method in class org.jmol.viewer.Viewer
- toFromPrimitive(boolean, char, T3[], M3) - Method in interface org.jmol.api.SymmetryInterface
- toFromPrimitive(boolean, char, T3[], M3) - Method in class org.jmol.symmetry.Symmetry
- toFromPrimitive(boolean, char, T3[], M3) - Method in class org.jmol.symmetry.UnitCell
- toFront() - Method in class org.jmol.awtjs.swing.JDialog
- toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
-
Brings the surfaceTool to the front and updates sliders, etc...
- toFrontOrGotFocus() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- toggle(Measurement) - Method in class org.jmol.shape.Measures
- toggleInPlace(BS, BS) - Static method in class org.jmol.util.BSUtil
-
a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.
- togglelabel - Static variable in class org.jmol.script.T
- toggleMeasurement() - Method in class org.jmol.viewer.ActionManager
- toggleMode() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
- toggleOn(int[]) - Method in class org.jmol.shape.Measures
- toHTML() - Method in class org.jmol.awtjs.swing.Component
- toHTML() - Method in class org.jmol.awtjs.swing.JButton
- toHTML() - Method in class org.jmol.awtjs.swing.JCheckBox
- toHTML() - Method in class org.jmol.awtjs.swing.JComboBox
- toHTML() - Method in class org.jmol.awtjs.swing.JComponentImp
- toHTML() - Method in class org.jmol.awtjs.swing.JContentPane
- toHTML() - Method in class org.jmol.awtjs.swing.JDialog
- toHTML() - Method in class org.jmol.awtjs.swing.JEditorPane
- toHTML() - Method in class org.jmol.awtjs.swing.JLabel
- toHTML() - Method in class org.jmol.awtjs.swing.JMenu
- toHTML() - Method in class org.jmol.awtjs.swing.JMenuItem
- toHTML() - Method in class org.jmol.awtjs.swing.JPanel
- toHTML() - Method in class org.jmol.awtjs.swing.JPopupMenu
- toHTML() - Method in class org.jmol.awtjs.swing.JScrollPane
- toHTML() - Method in class org.jmol.awtjs.swing.JSplitPane
- toHTML() - Method in class org.jmol.awtjs.swing.JTable
- toHTML() - Method in class org.jmol.awtjs.swing.JTextField
- toHTML() - Method in class org.jmol.awtjs.swing.JTextPane
- toHTML(String) - Method in class org.jmol.awtjs.swing.Cell
- toHTML(String) - Method in class org.jmol.awtjs.swing.Grid
- toHTML(SB, String, BS) - Method in interface org.jmol.awtjs.swing.AbstractTableModel
- toInt2(boolean, Object) - Method in class org.jmol.shapespecial.Polyhedron
- toIntARGB(int[]) - Static method in class org.jmol.awtjs2d.Image
- toJSON() - Method in class org.jmol.script.SV
- toJSONBytes(Map<String, Object>) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
-
Guaranteed to create a clean no-whitespace JSON stream terminated by a single \n.
- tok - Variable in class org.jmol.modelset.LabelToken
- tok - Variable in class org.jmol.script.ScriptFunction
- tok - Variable in class org.jmol.script.T
- tok0 - Variable in class org.jmol.script.ScriptFlowContext
- tokAction - Variable in class org.jmol.modelset.MeasurementData
- tokAction - Variable in class org.jmol.shape.Measures
- tokAt(int) - Method in class org.jmol.script.ScriptCompiler
- tokAt(int) - Method in class org.jmol.script.ScriptParam
- tokAt(int) - Method in class org.jmol.script.ScriptTokenParser
- tokAt(int) - Method in class org.jmol.scriptext.ScriptExt
- tokAtArray(int, T[]) - Static method in class org.jmol.scriptext.CmdExt
- tokAttr(int, int) - Static method in class org.jmol.script.T
- tokAttrOr(int, int, int) - Static method in class org.jmol.script.T
- tokCommand - Variable in class org.jmol.script.ScriptTokenParser
- token - Variable in class org.jmol.script.ScriptContext
- token - Variable in class org.jmol.script.ScriptFlowContext
- TOKEN_AROMATIC - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- TOKEN_ELEMENT_ALLYLIC - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- TOKEN_ELEMENT_CHARGED - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- TOKEN_ELEMENT_CONNECTED - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- TOKEN_ELEMENT_ONLY - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- TOKEN_ELEMENT_SP - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- tokenAll - Static variable in class org.jmol.script.T
- tokenAnd - Static variable in class org.jmol.script.T
- tokenAndEquals - Variable in class org.jmol.script.ScriptTokenParser
- tokenAndFALSE - Static variable in class org.jmol.script.T
- tokenAndSpec - Static variable in class org.jmol.script.T
- tokenArrayClose - Static variable in class org.jmol.script.T
- tokenArrayOpen - Static variable in class org.jmol.script.T
- tokenArraySquare - Static variable in class org.jmol.script.T
- tokenAt(int) - Method in class org.jmol.script.ScriptCompiler
- tokenAt(int, T[]) - Method in class org.jmol.scriptext.CmdExt
- tokenAttr(T, int) - Static method in class org.jmol.script.ScriptTokenParser
- tokenColon - Static variable in class org.jmol.script.T
- tokenComma - Static variable in class org.jmol.script.T
- tokenCommand - Variable in class org.jmol.script.ScriptTokenParser
- tokenConnected - Static variable in class org.jmol.script.T
- tokenCoordinateBegin - Static variable in class org.jmol.script.T
- tokenCoordinateEnd - Static variable in class org.jmol.script.T
- tokenCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- tokenDefineString - Static variable in class org.jmol.script.T
- tokenDivide - Static variable in class org.jmol.script.T
- tokenEquals - Static variable in class org.jmol.script.T
- tokenExpressionBegin - Static variable in class org.jmol.script.T
- tokenExpressionEnd - Static variable in class org.jmol.script.T
- tokenIf - Static variable in class org.jmol.script.T
- tokenize(String) - Static method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
-
Take the given string and chop it up into a series of strings on whitespace boundries.
- tokenizeCastepCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
- tokenizePlusPlus(int, boolean) - Method in class org.jmol.script.ScriptCompiler
- tokenLeftBrace - Static variable in class org.jmol.script.T
- tokenLeftParen - Static variable in class org.jmol.script.T
- tokenMap - Static variable in class org.jmol.script.T
- tokenMinus - Static variable in class org.jmol.script.T
- tokenMul3 - Static variable in class org.jmol.script.T
- tokenNext() - Method in class org.jmol.script.ScriptTokenParser
-
increments the pointer; does NOT set theToken or theValue
- tokenNextTok(int) - Method in class org.jmol.script.ScriptTokenParser
- tokenOff - Static variable in class org.jmol.script.T
- tokenOn - Static variable in class org.jmol.script.T
- tokenOpIf - Static variable in class org.jmol.script.T
- tokenOr - Static variable in class org.jmol.script.T
- tokenOrTRUE - Static variable in class org.jmol.script.T
- tokenPlus - Static variable in class org.jmol.script.T
- tokenRightBrace - Static variable in class org.jmol.script.T
- tokenRightParen - Static variable in class org.jmol.script.T
- tokens - Variable in class org.jmol.adapter.readers.simple.InputReader
- tokens - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- tokens - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- tokens - Variable in class org.jmol.adapter.readers.xtal.CgdReader
- tokens - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
- tokens - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- tokens - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
- tokens - Variable in class org.jmol.jvxl.readers.PmeshReader
- tokenScript - Static variable in class org.jmol.script.T
- tokenSet - Static variable in class org.jmol.script.T
- tokenSetArray - Static variable in class org.jmol.script.T
- tokenSetCmd - Static variable in class org.jmol.script.T
- tokenSetProperty - Static variable in class org.jmol.script.T
- tokenSetVar - Static variable in class org.jmol.script.T
- tokenSpaceBeforeSquare - Static variable in class org.jmol.script.T
- tokenSwitch - Static variable in class org.jmol.script.T
- tokenTimes - Static variable in class org.jmol.script.T
- tokenTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- tokInitialPlusPlus - Variable in class org.jmol.script.ScriptCompiler
- tokLastMath - Variable in class org.jmol.script.ScriptCompiler
- tokPeek() - Method in class org.jmol.script.ScriptTokenParser
- tokPeekIs(int) - Method in class org.jmol.script.ScriptTokenParser
- toMap(byte[]) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- toOABC(P3[], T3) - Static method in class org.jmol.util.BoxInfo
-
Delivers [center a b c] for generation of unit cells from a boundbox
- toolbar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- toolbarButtonGroup - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- top - Variable in class org.jmol.awtjs.swing.Insets
- top - Static variable in class org.jmol.script.T
- top - Variable in class org.jmol.smiles.SmilesSearch
- toP3(double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
- topAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- topButton - Variable in class org.jmol.console.ScriptEditor
- topButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- TopoCifParser - Class in org.jmol.adapter.readers.cif
-
see https://github.com/COMCIFS/TopoCif Basic idea: We have TLinks, TNodes, and TAtoms TLinks each have two TNodes and may also be associated with bridging TAtom sets.
- TopoCifParser() - Constructor for class org.jmol.adapter.readers.cif.TopoCifParser
- TopoCifParser.TAtom - Class in org.jmol.adapter.readers.cif
- TopoCifParser.TLink - Class in org.jmol.adapter.readers.cif
-
A class to hold the TOPOL_LINK data item information and transform it as needed.
- TopoCifParser.TNet - Class in org.jmol.adapter.readers.cif
- TopoCifParser.TNode - Class in org.jmol.adapter.readers.cif
- TopoCifParser.TPoint - Interface in org.jmol.adapter.readers.cif
- topol_atom_atom_label - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_element_symbol - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_fract_x - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_fract_y - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_fract_z - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_link_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_node_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_symop_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_translation - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_translation_x - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_translation_y - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_atom_translation_z - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- TOPOL_GROUP - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- TOPOL_LINK - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_distance - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_multiplicity - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_net_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_node_id_1 - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_node_id_2 - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_node_label_1_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_node_label_2_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_order - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_symop_1_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_symop_2_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_translation_1_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_translation_1_x_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_translation_1_y_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_translation_1_z_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_translation_2_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_translation_2_x_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_translation_2_y_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_site_symmetry_translation_2_z_DEPRECATED - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_symop_id_1 - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_symop_id_2 - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_translation_1 - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_translation_1_x - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_translation_1_y - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_translation_1_z - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_translation_2 - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_translation_2_x - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_translation_2_y - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_translation_2_z - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_type - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_link_voronoi_solidangle - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_net_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_net_label - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_net_special_details - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- TOPOL_NODE - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_fract_x - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_fract_y - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_fract_z - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_label - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_net_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_symop_id - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_translation - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_translation_x - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_translation_y - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topol_node_translation_z - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topolFields - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- topologyOnly - Variable in class org.jmol.smiles.SmilesGenerator
- topoOrder - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- topoType - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
- topPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- toRadians - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- toRadians - Static variable in class org.jmol.util.SimpleUnitCell
- toReadable(String, Object) - Static method in class org.jmol.util.Escape
-
Used only for getProperty("readable",...)
- torsion - Static variable in class org.jmol.script.T
- torsionCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- torsionCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
- torsionCount - Variable in class org.jmol.minimize.forcefield.Calculations
- toScript(P4) - Method in class org.jmol.util.BZone
- toStdAmino3(String) - Method in class org.jmol.modelsetbio.BioResolver
- toString() - Method in class org.jmol.adapter.readers.cif.Subsystem
- toString() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- toString() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- toString() - Method in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- toString() - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
- toString() - Method in class org.jmol.adapter.smarter.Bond
- toString() - Method in class org.jmol.adapter.writers.CIFWriter
- toString() - Method in class org.jmol.adapter.writers.CMLWriter
- toString() - Method in class org.jmol.adapter.writers.PDBWriter
- toString() - Method in class org.jmol.adapter.writers.PWMATWriter
- toString() - Method in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- toString() - Method in class org.jmol.adapter.writers.QCJSONWriter
- toString() - Method in class org.jmol.adapter.writers.XSFWriter
- toString() - Method in class org.jmol.atomdata.RadiusData
- toString() - Method in class org.jmol.awtjs.swing.Color
- toString() - Method in class org.jmol.dssx.Bridge
- toString() - Method in class org.jmol.g3d.TextString
- toString() - Method in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
- toString() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- toString() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Face
- toString() - Method in class org.jmol.minimize.MinAtom
- toString() - Method in class org.jmol.minimize.MinObject
- toString() - Method in class org.jmol.modelset.Atom
- toString() - Method in class org.jmol.modelset.Bond
- toString() - Method in class org.jmol.modelset.Group
- toString() - Method in class org.jmol.modelset.Measurement
- toString() - Method in class org.jmol.modelset.StateScript
- toString() - Method in class org.jmol.modelset.Text
- toString() - Method in class org.jmol.modelsetbio.BasePair
- toString() - Method in class org.jmol.modelsetbio.BioPolymer
- toString() - Method in class org.jmol.modelsetbio.Monomer
- toString() - Method in class org.jmol.modelsetbio.ProteinStructure
- toString() - Method in class org.jmol.quantum.NMRNoeMatrix.NOEParams
- toString() - Method in class org.jmol.quantum.NMRNoeMatrix
- toString() - Method in class org.jmol.quantum.SlaterData
- toString() - Method in class org.jmol.script.ScriptEval
- toString() - Method in exception org.jmol.script.ScriptException
- toString() - Method in class org.jmol.script.ScriptFlowContext
- toString() - Method in class org.jmol.script.ScriptFunction
- toString() - Method in class org.jmol.script.SV
- toString() - Method in class org.jmol.script.T
- toString() - Method in class org.jmol.smiles.SmilesAtom
- toString() - Method in class org.jmol.smiles.SmilesBond
- toString() - Method in class org.jmol.smiles.SmilesMeasure
- toString() - Method in class org.jmol.smiles.SmilesSearch
- toString() - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
- toString() - Method in class org.jmol.symmetry.HallInfo
- toString() - Method in class org.jmol.symmetry.SpaceGroup
- toString() - Method in class org.jmol.symmetry.SymmetryOperation
- toString() - Method in class org.jmol.thread.JmolThread
- toString() - Method in class org.jmol.thread.TimeoutThread
- toString() - Method in class org.jmol.util.BoxInfo
- toString() - Method in class org.jmol.util.ContactPair
- toString() - Method in class org.jmol.util.Font
- toString() - Method in class org.jmol.util.MeshCapper.CapVertex
- toString() - Method in class org.jmol.util.Modulation
- toString() - Method in class org.jmol.util.Rgb16
- toString() - Method in class org.jmol.util.SimpleUnitCell
- toString() - Method in class org.jmol.util.Tensor
- toString() - Method in class org.jmol.viewer.Gesture
- toString() - Method in class org.jmol.viewer.MotionPoint
- toString() - Method in class org.openscience.jmol.app.janocchio.Measure
- toString() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
- toString(JniInchiStructure) - Static method in class org.jmol.inchi.InChIJNI
- toString2() - Method in class org.jmol.script.T
- toStringNormRow() - Method in class org.jmol.quantum.NMRNoeMatrix
- toSupercell(P3) - Method in interface org.jmol.api.SymmetryInterface
- toSupercell(P3) - Method in class org.jmol.symmetry.Symmetry
- toSupercell(P3) - Method in class org.jmol.util.SimpleUnitCell
-
convenience return only after changing fpt
- toTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
- totalArea - Variable in class org.jmol.util.BZone
- totalAtomCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- totalfield - Variable in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- totalSteps - Variable in class org.jmol.navigate.Navigator
- totalSteps - Variable in class org.jmol.thread.MoveToThread
- totE - Variable in class org.jmol.adapter.readers.xtal.DmolReader
- totEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- totEnergy - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
- totEnergy - Variable in class org.jmol.adapter.readers.xtal.GulpReader
- TOUCH_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- TOUCH_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- touchHandler - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- TouchHandler() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- toUnicode(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
There is no need to convert to unicode in CIF 2.0.
- toUnitCell(P3, P3) - Method in class org.jmol.viewer.Viewer
-
Returns the relative to origin without regard to offset created using the UNITCELL command.
- toUnitCell(T3, T3) - Method in interface org.jmol.api.SymmetryInterface
- toUnitCell(T3, T3) - Method in class org.jmol.symmetry.Symmetry
- toUnitCell(T3, T3) - Method in class org.jmol.symmetry.UnitCell
-
when offset is null, use the current cell, otherwise use the original unit cell
- toUnitCellRnd(T3, T3) - Method in interface org.jmol.api.SymmetryInterface
- toUnitCellRnd(T3, T3) - Method in class org.jmol.symmetry.Symmetry
- toUnitCellRnd(T3, T3) - Method in class org.jmol.symmetry.UnitCell
-
when offset is null, use the current cell, otherwise use the original unit cell
- toUnits(double, String) - Method in class org.jmol.minimize.forcefield.ForceField
- toUnits(float, String, boolean) - Static method in class org.jmol.modelset.Measurement
- toUserUnits(double) - Method in class org.jmol.minimize.forcefield.ForceField
- toWebAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ToWebAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
- toWebActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- tPending - Variable in class org.jmol.renderbio.RocketRenderer
- tQuiet - Variable in class org.jmol.script.ScriptEval
- trace - Static variable in class org.jmol.script.T
- trace - Variable in class org.jmol.util.Vibration
- Trace - Class in org.jmol.shapebio
- Trace() - Constructor for class org.jmol.shapebio.Trace
- trace_atoms_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- tracealpha - Static variable in class org.jmol.script.T
- traceAlpha - Variable in class org.jmol.viewer.GlobalSettings
- tracePt - Variable in class org.jmol.util.Vibration
- TraceRenderer - Class in org.jmol.renderbio
- TraceRenderer() - Constructor for class org.jmol.renderbio.TraceRenderer
- traceX - Variable in class org.jmol.modelset.Measurement
- traceY - Variable in class org.jmol.modelset.Measurement
- track(CIPChirality, CIPChirality.CIPAtom, CIPChirality.CIPAtom, int, int, boolean) - Method in class org.jmol.symmetry.CIPData
-
Track this decision - CIPDataTracker only
- track(CIPChirality, CIPChirality.CIPAtom, CIPChirality.CIPAtom, int, int, boolean) - Method in class org.jmol.symmetry.CIPDataTracker
- trackTerminal - Variable in class org.jmol.symmetry.CIPDataTracker.CIPTracker
- trajectory - Variable in class org.jmol.modelset.AtomCollection
- trajectory - Static variable in class org.jmol.script.T
- Trajectory - Class in org.jmol.modelset
- Trajectory() - Constructor for class org.jmol.modelset.Trajectory
- trajectoryBaseIndex - Variable in class org.jmol.modelset.Model
- trajectoryNames - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- trajectoryPtr - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- trajectoryStep - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- trajectoryStepCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- trajectoryUnitCells - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- trans - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TAtom
- trans - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TNode
- trans - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- transferStateFromJmol() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- transferStateToJmol() - Method in class org.openscience.jmol.app.janocchio.NmrPlugin
- transform - Static variable in class org.jmol.script.T
- transform(short, Atom, Vibration, JmolModulationSet) - Method in class org.jmol.renderspecial.VectorsRenderer
- transform(V3, V3) - Method in class org.jmol.jvxl.data.VolumeData
- transformedVectors - Variable in class org.jmol.render.MeshRenderer
- transformedVectors - Variable in class org.jmol.util.GData
- TransformFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
- transformManager - Variable in class org.jmol.thread.MoveToThread
- transformManager - Variable in class org.jmol.thread.SpinThread
- transformManager - Variable in class org.jmol.thread.VibrationThread
- TransformManager - Class in org.jmol.viewer
- TransformManager() - Constructor for class org.jmol.viewer.TransformManager
- TransformManager4D - Class in org.jmol.viewer
- TransformManager4D() - Constructor for class org.jmol.viewer.TransformManager4D
- TRANSFORMMAT - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- transformPoints(int, T3[], P3[]) - Method in class org.jmol.renderbio.NucleicRenderer
- transformPt(T3) - Method in class org.jmol.viewer.TransformManager
-
CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
- transformPt2D(T3) - Method in class org.jmol.viewer.TransformManager
- transformPt2Df(T3, P3) - Method in class org.jmol.viewer.TransformManager
- transformPt3f(T3, P3) - Method in class org.jmol.viewer.TransformManager
- transformPtNoClip(T3, T3) - Method in class org.jmol.viewer.TransformManager
- transformPtScr(T3, P3i) - Method in class org.jmol.viewer.TransformManager
- transformPtScrT3(T3, T3) - Method in class org.jmol.viewer.TransformManager
- transformPtScrT32D(T3, P3) - Method in class org.jmol.viewer.TransformManager
- transformPtVib(P3, Vibration) - Method in class org.jmol.viewer.TransformManager
- transformXYZ(M4, BS) - Method in class org.jmol.atomdata.AtomData
-
allow for transformed XYZ
- translate - Static variable in class org.jmol.script.T
- translate(char, float, char, BS) - Method in class org.jmol.viewer.Viewer
- translate(String) - Method in interface org.jmol.api.Translator
- translate(String) - Method in class org.jmol.i18n.GT
-
used in custom menu translation only
- translate(String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
- translateModel(int, T3) - Method in class org.jmol.modelset.ModelSet
-
move atoms by vector pt; used for co-centering with FRAME ALIGN {atoms} TRUE
- translateScale(Object, double, double, double) - Method in interface org.jmol.api.GenericGraphics
- translateScale(Object, double, double, double) - Method in class org.jmol.awt.AwtG2D
- translateScale(Object, double, double, double) - Method in class org.jmol.awtjs2d.JsG2D
- translateSelected - Static variable in class org.jmol.script.T
- translateToPercent(char, float) - Method in class org.jmol.viewer.TransformManager
- translateXYBy(int, int) - Method in class org.jmol.viewer.TransformManager
- translateXYBy(int, int) - Method in class org.jmol.viewer.Viewer
- translateZBy(int) - Method in class org.jmol.viewer.TransformManager
- translation - Variable in class org.jmol.modelset.Model
- translation - Static variable in class org.jmol.script.T
- translation - Variable in class org.jmol.symmetry.HallRotationTerm
- translation - Variable in class org.jmol.symmetry.UnitCellIterator
- translationCode - Variable in class org.jmol.symmetry.HallTranslation
- translations - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- translations - Variable in class org.jmol.modelset.ModelSet
- translations - Static variable in class org.openscience.jmol.app.jmolpanel.GuiMap
- translationString - Variable in class org.jmol.symmetry.HallRotationTerm
- Translator - Interface in org.jmol.api
- translucency - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- translucency - Static variable in class org.jmol.g3d.TextRenderer
- translucency - Variable in class org.jmol.jvxl.data.JvxlData
- translucency - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- translucencyFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
- translucencyLog - Variable in class org.jmol.g3d.Graphics3D
- translucencyMask - Variable in class org.jmol.g3d.Graphics3D
- translucent - Static variable in class org.jmol.script.T
- translucent - Variable in class org.jmol.viewer.GlobalSettings
- TRANSLUCENT_MASK - Static variable in class org.jmol.util.C
- TRANSLUCENT_SCREENED - Static variable in class org.jmol.util.C
- TRANSLUCENT_SHIFT - Static variable in class org.jmol.util.C
- translucentAllowed - Variable in class org.jmol.shape.Shape
- translucentCoverOnly - Variable in class org.jmol.util.GData
- translucentLevel - Variable in class org.jmol.shape.Shape
- transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- transparency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- transparency - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
- transparency_global_sort - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- transparency_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- transparency_picking_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- TRANSPARENT - Static variable in class org.jmol.util.C
- transX - Variable in class org.jmol.thread.MoveToThread
- transY - Variable in class org.jmol.thread.MoveToThread
- tree - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- treeDepth - Variable in class org.jmol.bspt.Bspt
- treeModel - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- triad(float, float, float) - Method in class org.jmol.export._TachyonExporter
- triad(T3) - Method in class org.jmol.export._TachyonExporter
- Triangle(int, int, int, int, int) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.Triangle
- triangle_max_passes - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- triangle3d - Variable in class org.jmol.g3d.Graphics3D
- triangleArea(int, int, int, V3, V3, V3) - Method in class org.jmol.shapespecial.Polyhedron
- triangleCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
- TriangleData - Class in org.jmol.util
-
An adaptation of Marching Cubes that allows for indicating edges on triangles.
- TriangleData() - Constructor for class org.jmol.util.TriangleData
- triangleFace - Variable in class org.jmol.export._IdtfExporter
- triangleNum - Variable in class org.jmol.export._ObjExporter
-
Number for the next mesh of this type.
- TriangleRenderer - Class in org.jmol.g3d
-
renders triangles
- TriangleRenderer() - Constructor for class org.jmol.g3d.TriangleRenderer
- triangles - Variable in class org.jmol.jvxl.calc.MarchingSquares
- triangles - Variable in class org.jmol.renderbio.NucleicRenderer
- triangles - Static variable in class org.jmol.script.T
- triangles - Variable in class org.jmol.shapespecial.Polyhedron
- triangleTable2 - Static variable in class org.jmol.util.TriangleData
-
The new triangle table developed specifically for Jmol.
- triangleVolume(int, int, int, V3, V3, V3) - Method in class org.jmol.shapespecial.Polyhedron
- triangulateFaces(int[][], P3[], int[][]) - Method in class org.jmol.util.MeshCapper
-
generic entry for a set of faces
- triangulatePolygon(P3[], int) - Method in class org.jmol.util.MeshCapper
-
generic entry for a polygon
- triangulator - Variable in class org.jmol.viewer.Viewer
- Triangulator - Class in org.jmol.util
- Triangulator() - Constructor for class org.jmol.util.Triangulator
- TRICOLOR_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
- trigger(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
- triggered - Variable in class org.jmol.thread.TimeoutThread
- triggerTimeout(String) - Method in class org.jmol.viewer.Viewer
- TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
- TRIGONAL_PYRAMIDAL - Static variable in class org.jmol.smiles.SmilesStereo
- TRIGONALITY_MIN - Static variable in class org.jmol.symmetry.CIPData
-
measure of planarity in a trigonal system, in Angstroms
- trim - Static variable in class org.jmol.script.T
- trim_dots - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- trimAtomSet() - Method in class org.jmol.adapter.readers.cif.MSRdr
- trimGUI(String) - Method in class org.jmol.console.GenericConsole
- trimLine() - Method in class org.jmol.adapter.readers.xtal.MagresReader
-
All characters after hash ignored; lines are trimmed.
- trimPWPropertyNameTo(String, String) - Method in class org.jmol.adapter.readers.xtal.PWmatReader
- trimString(String) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
- trimToUnitCell(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
- TRIPLE - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- TRUE - Static variable in class org.jmol.viewer.SelectionManager
- truncate0(SB, float) - Static method in class org.jmol.viewer.TransformManager
- truncate2(SB, float) - Static method in class org.jmol.viewer.TransformManager
- trustRadius - Variable in class org.jmol.minimize.forcefield.ForceField
- trustRadius - Variable in class org.jmol.minimize.Minimizer
- trycmd - Static variable in class org.jmol.script.T
- tryPt - Variable in class org.jmol.script.ScriptContext
- tryPt - Variable in class org.jmol.viewer.Viewer
- tSort - Static variable in class org.jmol.util.Tensor
- tsType - Variable in class org.jmol.adapter.readers.xtal.CastepReader
- TUPLE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
- tuples - Variable in class org.jmol.bspt.Leaf
- Turn - Class in org.jmol.modelsetbio
- Turn(AlphaPolymer, int, int) - Constructor for class org.jmol.modelsetbio.Turn
- TURN - Enum constant in enum org.jmol.c.STR
- tv(int, int, Object) - Static method in class org.jmol.script.T
- twelfths - Static variable in class org.jmol.adapter.writers.XtlWriter
- twelfths - Static variable in class org.jmol.symmetry.SymmetryOperation
- twelfthsOf(float) - Static method in class org.jmol.adapter.writers.XtlWriter
- twelfthsOf(float) - Static method in class org.jmol.symmetry.SymmetryOperation
- twistedsheets - Static variable in class org.jmol.script.T
- twistedSheets - Variable in class org.jmol.modelsetbio.BioPolymer
- twistedSheets - Variable in class org.jmol.viewer.GlobalSettings
- TWO_PI - Static variable in class org.jmol.minimize.forcefield.Calculations
- TWO_POINT_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- two_sided_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- twoChar - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
- twoCharLabelTokenIds - Static variable in class org.jmol.modelset.LabelToken
- twoCharLabelTokenParams - Static variable in class org.jmol.modelset.LabelToken
- twodots - Static variable in class org.jmol.render.FontLineShapeRenderer
- twoP2 - Static variable in class org.jmol.symmetry.UnitCell
- twoPass - Variable in class org.jmol.g3d.Graphics3D
- twoPI - Static variable in class org.jmol.util.Vibration
- TWOPI - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
- TWOPI - Static variable in class org.jmol.util.Modulation
- TwoPointGesture - Class in org.jmol.multitouch.sparshui
-
TWO_POINT_GESTURE This gesture requires two points of contact, but its type is not initially defined.
- TwoPointGesture() - Constructor for class org.jmol.multitouch.sparshui.TwoPointGesture
- Txt - Class in org.jmol.util
- Txt() - Constructor for class org.jmol.util.Txt
- type - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- type - Variable in class org.jmol.adapter.readers.more.JcampdxReader
- type - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- type - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
- type - Variable in class org.jmol.adapter.writers.QCJSONWriter.SparseArray
- type - Variable in enum org.jmol.c.VDW
- type - Variable in class org.jmol.jvxl.readers.IsoMepReader
- type - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
- type - Variable in class org.jmol.jvxl.readers.PmeshReader
- type - Variable in class org.jmol.jvxl.readers.Ras3DReader
- type - Variable in class org.jmol.minimize.MinObject
- type - Variable in class org.jmol.minimize.MMConstraint
- type - Variable in class org.jmol.modelkit.ModelKit.Constraint
- type - Variable in class org.jmol.modelset.Measurement
- type - Variable in class org.jmol.modelset.TickInfo
- type - Variable in class org.jmol.modelsetbio.BioPolymer
- type - Variable in class org.jmol.modelsetbio.ProteinStructure
- type - Variable in class org.jmol.quantum.NciCalculation
- type - Static variable in class org.jmol.script.T
- type - Variable in class org.jmol.shapespecial.Dipole
- type - Variable in class org.jmol.smiles.SmilesMeasure
- type - Variable in class org.jmol.symmetry.PointGroup.Operation
- type - Variable in class org.jmol.util.Modulation
- type - Variable in class org.jmol.util.Tensor
- type - Variable in class org.openscience.jmol.app.janocchio.Measure
- TYPE - Enum constant in enum org.jmol.c.PAL
- TYPE_ADP - Static variable in class org.jmol.util.Tensor
- TYPE_ALL - Static variable in class org.jmol.quantum.NciCalculation
- TYPE_AMINO - Static variable in class org.jmol.modelsetbio.BioPolymer
- TYPE_ANGLE - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_ANGLE - Static variable in class org.jmol.minimize.MMConstraint
- TYPE_ANGLE - Static variable in class org.jmol.modelkit.ModelKit.Constraint
- TYPE_ANY - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_ATROPISOMER - Static variable in class org.jmol.util.Edge
- TYPE_ATROPISOMER_REV - Static variable in class org.jmol.util.Edge
- TYPE_BIO_CROSSLINK - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_BIO_SEQUENCE - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_BNDK - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_BOND - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_BUTTON - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_CARBOHYDRATE - Static variable in class org.jmol.modelsetbio.BioPolymer
- TYPE_CHARGE - Static variable in class org.jmol.util.Tensor
- TYPE_CHECKBOX - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_CHRG - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_CSA - Static variable in class org.jmol.util.Tensor
- TYPE_DIFF - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- TYPE_DIFF - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
- TYPE_DIFF_PAIR - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- TYPE_DIFF_PAIR - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
- TYPE_DIHEDRAL - Static variable in class org.jmol.minimize.MMConstraint
- TYPE_DIHEDRAL - Static variable in class org.jmol.modelkit.ModelKit.Constraint
- TYPE_DISP_FOURIER - Static variable in class org.jmol.util.Modulation
- TYPE_DISP_LEGENDRE - Static variable in class org.jmol.util.Modulation
- TYPE_DISP_SAWTOOTH - Static variable in class org.jmol.util.Modulation
- TYPE_DISTANCE - Static variable in class org.jmol.minimize.MMConstraint
- TYPE_DISTANCE - Static variable in class org.jmol.modelkit.ModelKit.Constraint
- TYPE_DISTANCE - Static variable in class org.openscience.jmol.app.janocchio.Measure
- TYPE_EFG - Static variable in class org.jmol.util.Tensor
- TYPE_EXP_NOE - Static variable in class org.openscience.jmol.app.janocchio.Measure
- TYPE_FUNCTION - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- TYPE_FUNCTION - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
- TYPE_GENERAL - Static variable in class org.jmol.modelkit.ModelKit.Constraint
- TYPE_INTER - Static variable in class org.jmol.quantum.NciCalculation
- TYPE_INTRA - Static variable in class org.jmol.quantum.NciCalculation
- TYPE_ISC - Static variable in class org.jmol.util.Tensor
- TYPE_ISO - Static variable in class org.jmol.util.Tensor
- TYPE_J - Static variable in class org.openscience.jmol.app.janocchio.Measure
- TYPE_LIGAND - Static variable in class org.jmol.quantum.NciCalculation
- TYPE_LOCKED - Static variable in class org.jmol.modelkit.ModelKit.Constraint
- TYPE_MAX - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- TYPE_MAX - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
- TYPE_MENU - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_MS - Static variable in class org.jmol.util.Tensor
- TYPE_NOBONDING - Static variable in class org.jmol.modelsetbio.BioPolymer
- TYPE_NOE - Static variable in class org.openscience.jmol.app.janocchio.Measure
- TYPE_NONE - Static variable in class org.jmol.modelkit.ModelKit.Constraint
- TYPE_NONE - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_NUCLEIC - Static variable in class org.jmol.modelsetbio.BioPolymer
- TYPE_OCC_CRENEL - Static variable in class org.jmol.util.Modulation
- TYPE_OCC_FOURIER - Static variable in class org.jmol.util.Modulation
- TYPE_OOP - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_OTHER - Static variable in class org.jmol.util.Tensor
- TYPE_PBCI - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_PLANE - Static variable in class org.jmol.modelkit.ModelKit.Constraint
- TYPE_QUADRUPOLE - Static variable in class org.jmol.util.Tensor
- TYPE_RADIO - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_RAMAN - Static variable in class org.jmol.util.Tensor
- TYPE_RING - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_SB - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_SBDEF - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_SEPARATOR - Static variable in class org.jmol.awtjs.swing.JMenuItem
- TYPE_SPIN - Static variable in class org.jmol.util.Vibration
- TYPE_SPIN_FOURIER - Static variable in class org.jmol.util.Modulation
- TYPE_SPIN_SAWTOOTH - Static variable in class org.jmol.util.Modulation
- TYPE_SUM - Static variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- TYPE_SUM - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
- TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cif.CifReader
- TYPE_TLS_R - Static variable in class org.jmol.util.Tensor
- TYPE_TLS_U - Static variable in class org.jmol.util.Tensor
- TYPE_TORSION - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_U_FOURIER - Static variable in class org.jmol.util.Modulation
- TYPE_U_LEGENDRE - Static variable in class org.jmol.util.Modulation
- TYPE_UNKNOWN - Static variable in class org.jmol.smiles.SmilesBond
- TYPE_VDW - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- TYPE_VECTOR - Static variable in class org.jmol.modelkit.ModelKit.Constraint
- TYPE_VIBRATION - Static variable in class org.jmol.util.Vibration
- type2 - Variable in enum org.jmol.c.VDW
- typeAndOcc - Variable in class org.jmol.symmetry.SpaceGroupFinder.SGAtom
- typeArray - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
- typeBondOrder - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- typeData - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- typeFactor - Variable in class org.jmol.util.Tensor
- TypeFilter(String) - Constructor for class org.jmol.dialog.Dialog.TypeFilter
- typeName - Variable in class org.jmol.script.ScriptFunction
- typeNames - Static variable in class org.jmol.symmetry.PointGroup
- typeOf(int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
- typeOf(SV) - Static method in class org.jmol.script.ScriptMathProcessor
- typeOrder - Variable in class org.jmol.symmetry.PointGroup.Operation
- types - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- types - Static variable in class org.jmol.modelsetbio.BioResolver
- TYPES - Static variable in class org.jmol.smiles.SmilesMeasure
- TYPES - Static variable in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
- typeSelected - Variable in class org.jmol.shapespecial.Ellipsoids
- typeSymbol - Variable in class org.jmol.adapter.smarter.Atom
U
- U_ISO_OR_EQUIV - Static variable in class org.jmol.adapter.readers.cif.CifReader
- U_LIST - Static variable in class org.jmol.adapter.readers.cif.MSRdr
- U_LIST - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- uABsM(String) - Static method in class org.jmol.util.Escape
- uc - Variable in class org.jmol.adapter.writers.PWMATWriter
- uc - Variable in class org.jmol.adapter.writers.XSFWriter
- UC_TOLERANCE2 - Static variable in class org.jmol.viewer.JC
- Uccage - Class in org.jmol.shape
- Uccage() - Constructor for class org.jmol.shape.Uccage
- UccageRenderer - Class in org.jmol.render
- UccageRenderer() - Constructor for class org.jmol.render.UccageRenderer
- uccageTickEdges - Static variable in class org.jmol.util.BoxInfo
- ucItems - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- uff2DParams - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- UFFAngleCalc - Class in org.jmol.minimize.forcefield
- UFFAngleCalc() - Constructor for class org.jmol.minimize.forcefield.UFFAngleCalc
- UFFDistanceCalc - Class in org.jmol.minimize.forcefield
- UFFDistanceCalc() - Constructor for class org.jmol.minimize.forcefield.UFFDistanceCalc
- UFFOOPCalc - Class in org.jmol.minimize.forcefield
- UFFOOPCalc() - Constructor for class org.jmol.minimize.forcefield.UFFOOPCalc
- uffParams - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
- UFFTorsionCalc - Class in org.jmol.minimize.forcefield
- UFFTorsionCalc() - Constructor for class org.jmol.minimize.forcefield.UFFTorsionCalc
- UFFVDWCalc - Class in org.jmol.minimize.forcefield
- UFFVDWCalc() - Constructor for class org.jmol.minimize.forcefield.UFFVDWCalc
- uguideAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- UguideAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
- UhbdReader - Class in org.jmol.jvxl.readers
-
UHBD reader
- UhbdReader() - Constructor for class org.jmol.jvxl.readers.UhbdReader
- uicrcifContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- unaryMinus - Static variable in class org.jmol.script.T
- unbind - Static variable in class org.jmol.script.T
- unbindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
- unbindAction(String, String) - Method in class org.jmol.viewer.ActionManager
- unBindAction(String, String) - Method in class org.jmol.viewer.Viewer
- unbindJmolAction(int) - Method in class org.jmol.viewer.binding.Binding
- unbindMouseAction(int) - Method in class org.jmol.viewer.binding.Binding
- unbindName(int, String) - Method in class org.jmol.viewer.binding.Binding
- unbindUserAction(String) - Method in class org.jmol.viewer.binding.Binding
- UNBRACKETED_SET - Static variable in class org.jmol.smiles.SmilesAtom
- unCentered - Variable in class org.jmol.symmetry.SymmetryOperation
- undeleteAtom(int) - Method in class org.jmol.modelset.ModelLoader
-
called from org.jmol.modelsetbio.resolver when adding hydrogens.
- UNDETERMINED - Static variable in class org.jmol.symmetry.CIPChirality
- undo - Variable in class org.jmol.console.ScriptEditor.EditorDocument
- undo - Static variable in class org.jmol.script.T
- undo() - Method in class org.jmol.console.ScriptEditor.EditorDocument
- UNDO_CONSOLE - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- UNDO_NONE - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- UNDO_USER - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- undoableEditHappened(UndoableEditEvent) - Method in class org.jmol.console.ScriptEditor.EditorDocument.MyUndoableEditListener
- undoauto - Static variable in class org.jmol.script.T
- undoButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- undoClear() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- undomax - Static variable in class org.jmol.script.T
- undomove - Static variable in class org.jmol.script.T
- undoMoveAction(int, int) - Method in class org.jmol.viewer.JmolStateCreator
- undoMoveAction(int, int) - Method in class org.jmol.viewer.StateCreator
- undoMoveAction(int, int) - Method in class org.jmol.viewer.Viewer
- undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.JmolStateCreator
- undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.StateCreator
- undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.Viewer
- undoPointer - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- undoRedo(boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- undoSave(boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- undoSaved - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- undoStack - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- undoStateStack - Variable in class org.jmol.viewer.StateManager
- undoWorking - Variable in class org.jmol.viewer.StateCreator
- unEscapeBitSet(SV, BS) - Static method in class org.jmol.script.SV
-
Turn the string "({3:5})" into a bitset
- unEscapeBitSetArray(Lst<SV>, boolean) - Static method in class org.jmol.script.SV
-
Turn an array of strings in the form of "{n,n,n:n...} or an array of integers into a bitset.
- unescapeMatrix(String) - Static method in class org.jmol.util.Escape
- unescapePointOrBitsetAsVariable(Object) - Static method in class org.jmol.script.SV
- unescapeString(String, int, int) - Static method in class org.jmol.script.ScriptCompiler
- unescapeStringArray(String) - Static method in class org.jmol.util.Escape
- unescapeUnicode(String) - Static method in class org.jmol.util.Escape
- uniqueAtomMap - Variable in class org.jmol.adapter.readers.quantum.PsiReader
- uniqueAxis - Variable in class org.jmol.symmetry.SpaceGroup
- uniqueID - Variable in class org.jmol.adapter.smarter.Bond
- UNIQUEID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- uniqueIDs - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- uniqueList - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- uniqueList - Variable in class org.jmol.smiles.SmilesSearch
- uniqueSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- uniqueSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- unitAxisVectors - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
- unitAxisVectors - Static variable in class org.jmol.viewer.JC
- unitBboxPoints - Static variable in class org.jmol.util.BoxInfo
- unitcell - Variable in class org.jmol.render.UccageRenderer
- unitcell - Static variable in class org.jmol.script.T
- unitcell(int, boolean) - Method in class org.jmol.scriptext.CmdExt
- unitCell - Variable in class org.jmol.shape.Mesh
- unitCell - Variable in class org.jmol.symmetry.Symmetry
- unitCell - Variable in class org.jmol.symmetry.UnitCellIterator
- UnitCell - Class in org.jmol.symmetry
-
a class private to the org.jmol.symmetry package to be accessed only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.
- UnitCell() - Constructor for class org.jmol.symmetry.UnitCell
-
Indicate that this is a new unit cell, not one from a file.
- UNITCELL_OPTIONS - Static variable in class org.jmol.modelkit.ModelKit
- unitcellcolor - Static variable in class org.jmol.script.T
- unitCellData - Variable in class org.jmol.adapter.readers.xtal.DmolReader
- unitCellData - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
- unitCellData - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
- unitCellEquals(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
- unitCellEquals(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
- UnitCellIterator - Class in org.jmol.symmetry
- UnitCellIterator() - Constructor for class org.jmol.symmetry.UnitCellIterator
- unitCellMultiplied - Variable in class org.jmol.symmetry.UnitCell
-
the multiplied, offset UnitCell derived from this UnitCell
- unitCellMultiplier - Variable in class org.jmol.symmetry.UnitCell
-
a P3 or P4; the raw multiplier for the cell from UNITCELL {ijk ijk scale} UNITCELL {1iiijjjkkk 1iiijjjkkk scale} (encoded as a P4: {1iiijjjkkk 1iiijjjkkk scale 1kkkkkk} )
- unitCellOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- unitCellOffsetFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- UnitcellOnly - Variable in class org.jmol.popup.JmolPopup
- unitCellParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- unitCellParams - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- unitCellParams - Variable in class org.jmol.util.SimpleUnitCell
- unitCellParamsS - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- unitCellParamTags - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
- unitCells - Variable in class org.jmol.modelset.ModelSet
- unitCellTranslations - Variable in class org.jmol.adapter.smarter.XtalSymmetry
- unitCellVectors - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
- unitCubePoints - Static variable in class org.jmol.util.BoxInfo
- unitFactor - Variable in class org.jmol.quantum.QuantumCalculation
- UNITID_ATOM - Static variable in class org.jmol.viewer.JC
- UNITID_INSCODE - Static variable in class org.jmol.viewer.JC
- UNITID_MODEL - Static variable in class org.jmol.viewer.JC
- UNITID_RESIDUE - Static variable in class org.jmol.viewer.JC
- UNITID_TRIM - Static variable in class org.jmol.viewer.JC
- unitIdSets - Variable in class org.jmol.modelsetbio.BioModelSet
- unitize(T3) - Method in interface org.jmol.api.SymmetryInterface
- unitize(T3) - Method in class org.jmol.symmetry.Symmetry
- unitize(T3) - Method in class org.jmol.symmetry.UnitCell
-
returns [0,1)
- unitizeDim(int, T3) - Static method in class org.jmol.util.SimpleUnitCell
- unitizeDimRnd(int, T3) - Static method in class org.jmol.util.SimpleUnitCell
- unitizeRnd(T3) - Method in class org.jmol.symmetry.UnitCell
-
returns [0,1) with rounding to 0.0001
- unitizeX(float) - Static method in class org.jmol.util.SimpleUnitCell
- unitizeXRnd(float) - Static method in class org.jmol.util.SimpleUnitCell
- unitList - Variable in class org.jmol.symmetry.UnitCellIterator
- units - Variable in class org.jmol.adapter.readers.simple.FAHReader
- units - Variable in class org.jmol.minimize.Minimizer
- units - Variable in class org.jmol.modelset.Measurement
- units - Variable in class org.jmol.modelset.MeasurementData
- UNITS_PI - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- unitVector - Variable in class org.jmol.modelkit.ModelKit.Constraint
- unitVectors - Static variable in class org.jmol.symmetry.UnitCell
- unitVectorX - Variable in class org.jmol.modelsetbio.BioPolymer
- unitVolumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
- unitx - Static variable in class org.jmol.script.T
- unitxyz - Static variable in class org.jmol.script.T
- unity - Static variable in class org.jmol.script.T
- unitz - Static variable in class org.jmol.script.T
- UNKNOWN - Enum constant in enum org.jmol.c.HB
- UNKNOWN - Enum constant in enum org.jmol.c.PAL
- UNKNOWN - Static variable in class org.jmol.viewer.SelectionManager
- unlikeDuplicates(CIPChirality.CIPAtom) - Method in class org.jmol.symmetry.CIPChirality.CIPAtom
-
This check is not technically one of those listed in the rules, but it is useful when preparing to check substituents because if one of the atoms has substituents and the other doesn't, we are done -- there is no reason to check substituents.
- UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.util.C
- unquoted(String) - Method in class org.jmol.adapter.readers.cif.Cif2DataParser
-
Handle unquoted value as Integer or Float if we can.
- unreportedProperties - Static variable in class org.jmol.viewer.GlobalSettings
- unscaleToScreen(float, float) - Method in class org.jmol.viewer.TransformManager
- UNSET - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
- unsetProperty(String) - Method in class org.jmol.viewer.Viewer
- unsetUserVariable(String) - Method in class org.jmol.viewer.GlobalSettings
- unsetVariables(Map<String, SV>, Lst<SV>) - Method in class org.jmol.script.ScriptFunction
- unsetVoxelData() - Method in class org.jmol.jvxl.readers.AtomDataReader
- unsetVoxelData() - Method in class org.jmol.jvxl.readers.IsoSolventReader
- unsetVoxelData2() - Method in class org.jmol.jvxl.readers.AtomDataReader
- UNSPECIFIED - Enum constant in enum org.jmol.util.Edge.EnumBondOrder
- unsupportedRecordTypes - Static variable in class org.jmol.adapter.readers.xtal.ShelxReader
- untaint(int, int) - Method in class org.jmol.modelset.AtomCollection
- unTaintAtoms(BS, int) - Method in class org.jmol.modelset.AtomCollection
- untransformedPoint - Variable in class org.jmol.viewer.TransformManager
- unTransformPoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
- untranslated - Variable in exception org.jmol.script.ScriptException
- unused_boolean_def_true - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- unwrapCdata(String) - Static method in class org.jmol.jvxl.readers.XmlReader
- uP(String) - Static method in class org.jmol.util.Escape
- UP - Static variable in class org.jmol.viewer.binding.Binding
- update() - Method in class org.jmol.util.GenericApplet
- update(String) - Method in class org.jmol.viewer.ChimeMessenger
-
called upon script exit and file opening
- update(String) - Method in interface org.jmol.viewer.JmolChimeMessenger
- update(LineEvent) - Method in class org.jmol.util.JmolAudio
- UPDATE_ALL - Static variable in class org.jmol.popup.JmolPopup
- UPDATE_CONFIG - Static variable in class org.jmol.popup.JmolPopup
- UPDATE_NEVER - Static variable in class org.jmol.popup.JmolPopup
- UPDATE_SHOW - Static variable in class org.jmol.popup.JmolPopup
- updateAboutSubmenu() - Method in class org.jmol.popup.JmolPopup
- updateAllXtalMenuOptions() - Method in class org.jmol.modelkit.ModelKitPopup
- updateAngleSliders() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- updateAtomXYZ() - Method in class org.jmol.minimize.Minimizer
- updateAwtMenus(String) - Method in class org.jmol.awt.AwtJmolPopup
- updateAwtMenus(String) - Method in class org.jmol.awt.AwtModelKitPopup
- updateBasisFromSite(int) - Method in class org.jmol.modelset.ModelSet
- updateBSAtoms() - Method in class org.jmol.adapter.smarter.XtalSymmetry
-
Update asc.bsAtoms to include all atoms, or at least all atoms that are still viable from the reader.
- updateButton(SC, String, String) - Method in class org.jmol.popup.GenericPopup
- updateCheckBoxesForModelKit(String) - Method in class org.jmol.modelkit.ModelKitPopup
- updateCheckBoxesForShow() - Method in class org.jmol.popup.GenericPopup
- updateCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- updateComponents() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- updateConfigurationComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateConsoleFont() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- updateCoordinates(M4, BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
-
bs will be null if this is a set from the new isosurface MOVE [mat4] command
- updateCoupleTableData() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- updateElementsComputedMenu(BS) - Method in class org.jmol.popup.JmolPopup
- updateExisting(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceStatus
- updateFileMenu() - Method in class org.jmol.popup.JmolPopup
- updateFileTypeDependentMenus() - Method in class org.jmol.popup.JmolPopup
- updateFont() - Method in class org.jmol.console.ScriptEditor
- updateFont() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- updateFontSize() - Method in class org.jmol.console.JmolConsole
- updateFontSize() - Method in class org.jmol.console.ScriptEditor
- updateFontSize() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- updateFRAMESbyModelComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateGroup3List(SC, String) - Method in class org.jmol.popup.JmolPopup
- updateHeteroComputedMenu(Map<String, String>) - Method in class org.jmol.popup.JmolPopup
- updateInvalidatedVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
- updateJS() - Method in class org.jmol.viewer.Viewer
-
for JavaScript only
- updateJSView(int, int) - Method in class org.jmol.viewer.Viewer
-
File has been loaded or model has been changed or atom picked.
- updateLabels() - Method in class org.jmol.console.GenericConsole
- updateLabels() - Method in class org.jmol.console.JmolConsole
- updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
- updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
- updateLanguageSubmenu() - Method in class org.jmol.popup.JmolPopup
- updateLocations(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- updateMeasurementTableData() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- updateMenu() - Method in class org.jmol.modelkit.ModelKit
- updateMenus() - Method in class org.jmol.popup.JmolPopup
- updateMeshInfo(Shape[], int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- updateMode - Variable in class org.jmol.popup.JmolPopup
- updateModel(int) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- updateModelIDs(String, int, boolean) - Method in class org.jmol.adapter.readers.more.JcampdxReader
-
The first model set is allowed to be a single model and given no extension.
- updateModelSetComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateNoeTableData() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- updateNoeTableStructure() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- updateOffsetsForAlternativeLocations(Atom[], BS) - Method in class org.jmol.modelsetbio.Monomer
- updateOperatorMenu() - Method in class org.jmol.modelkit.ModelKitPopup
- updateParameters() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
- updatePDBResidueComputedMenus() - Method in class org.jmol.popup.JmolPopup
- updatePositionSlider() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- updateSceneComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateScreen() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
-
Update screen informations
- updateSelectMenu() - Method in class org.jmol.popup.JmolPopup
- updateSignedAppletItems() - Method in class org.jmol.popup.GenericPopup
- updateSize(boolean) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- updateSlices() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- updateSpecialMenuItem(SC) - Method in class org.jmol.popup.JmolPopup
- updateSpectraMenu() - Method in class org.jmol.popup.JmolPopup
- updateSurfaceData() - Method in class org.jmol.jvxl.readers.SurfaceReader
- updateSurfaceData(String, float[], int, int, char) - Static method in class org.jmol.jvxl.data.JvxlData
- updateSurfaceInfo() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
- updateSurfaceList() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- updateSurfMoComputedMenu(Map<String, Object>) - Method in class org.jmol.popup.JmolPopup
- updateSYMMETRYComputedMenus() - Method in class org.jmol.popup.JmolPopup
- updateSYMMETRYSelectComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateSYMMETRYShowComputedMenu() - Method in class org.jmol.popup.JmolPopup
- updateTables() - Method in class org.openscience.jmol.app.janocchio.CoupleTable
- updateTables() - Method in class org.openscience.jmol.app.janocchio.NoeTable
- updateTables() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- updateThicknessSlider() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- updateTriangles() - Method in class org.jmol.jvxl.readers.SurfaceReader
- updateUI() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- updateVars() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- updateWindow(int, int) - Method in class org.jmol.viewer.Viewer
- updatingForShow - Variable in class org.jmol.popup.GenericPopup
- url - Static variable in class org.jmol.script.T
- url - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
- urlEncode(String) - Method in class org.jmol.viewer.FileManager
- urlPrefixPairs - Static variable in class org.jmol.awt.AwtFile
- use_display_lists - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- USE_PALETTE - Static variable in class org.jmol.util.C
- use_shaders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- useAbsolute - Variable in class org.jmol.quantum.NciCalculation
- useAltNames - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- useAuthorChainID - Variable in class org.jmol.adapter.readers.cif.CifReader
- useBananas - Variable in class org.jmol.render.SticksRenderer
- useColix - Variable in class org.jmol.shape.Mesh
- useColix - Variable in class org.jmol.shapecgo.CGO
- useCommandThread - Variable in class org.jmol.viewer.Viewer
- useCommandWatcherThread - Variable in class org.jmol.script.ScriptManager
- useDefaultLabel - Variable in class org.jmol.modelset.Measurement
- useFileModelNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- useGUI - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- useLight - Variable in class org.jmol.util.Shader
- useminimizationthread - Static variable in class org.jmol.script.T
- useMinimizationThread - Variable in class org.jmol.viewer.GlobalSettings
- useMinimizationThread() - Method in class org.jmol.viewer.Viewer
- useMolecular - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- usenumberlocalization - Static variable in class org.jmol.script.T
- useNumberLocalization - Variable in class org.jmol.viewer.GlobalSettings
- useOriginStepsPoints - Variable in class org.jmol.jvxl.readers.VolumeDataReader
- usePercent - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- usePhongExponent - Variable in class org.jmol.util.Shader
- usePropertyForColorRange - Variable in class org.jmol.jvxl.readers.Parameters
- user - Static variable in class org.jmol.script.T
- USER - Enum constant in enum org.jmol.c.VDW
- USER - Static variable in class org.jmol.util.ColorEncoder
- userAction(int, Object[]) - Method in class org.jmol.viewer.ActionManager
-
If the user has created a function to handle this action, run it and cancel action processing if that function returns an explicit FALSE;
- userActionEnabled(int) - Method in class org.jmol.viewer.ActionManager
- userAtomTypes - Variable in class org.jmol.adapter.readers.more.ForceFieldReader
- usercolorscheme - Static variable in class org.jmol.script.T
- userData - Variable in class org.jmol.adapter.readers.molxyz.V3000Rdr
- userDefinedVanDerWaalRadius - Variable in class org.jmol.modelset.Atom
- userPropsFile - Variable in class org.openscience.jmol.app.JmolApp
- userScale - Variable in class org.jmol.util.ColorEncoder
- userSettableValues - Static variable in class org.jmol.modelset.AtomCollection
- userStatusListener - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- userVdwMars - Variable in class org.jmol.viewer.Viewer
- userVdws - Variable in class org.jmol.viewer.Viewer
- useScriptQueue - Variable in class org.jmol.viewer.GlobalSettings
- useTable - Variable in class org.jmol.export._VrmlExporter
- useTable - Variable in class org.jmol.export.JSExporter
- UseTable - Class in org.jmol.export
- UseTable(String) - Constructor for class org.jmol.export.UseTable
- useThreads() - Method in class org.jmol.script.ScriptEval
- useTimeout - Variable in class org.jmol.thread.JmolThread
- useUnitCell - Variable in class org.jmol.shapespecial.Polyhedra
- useZoomLarge - Variable in class org.jmol.viewer.TransformManager
- utens - Variable in class org.jmol.util.Modulation
- Util - Class in org.jmol.minimize
- Util() - Constructor for class org.jmol.minimize.Util
V
- v - Variable in class org.jmol.console.JmolConsole.FileChecker
- v - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
- v - Variable in class org.jmol.smiles.SmilesSearch
- v - Variable in class org.jmol.smiles.SmilesStereo
- v0 - Variable in class org.jmol.util.ModulationSet
- v0Cart - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- v1 - Variable in class org.jmol.adapter.readers.simple.InputReader
- v1 - Variable in class org.jmol.minimize.forcefield.Calculations
- v1 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- v1 - Variable in class org.jmol.viewer.TransformManager4D
- v176 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- v176b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- v177 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- v177b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- v181 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- v181b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- v2 - Variable in class org.jmol.adapter.readers.simple.InputReader
- v2 - Variable in class org.jmol.minimize.forcefield.Calculations
- v2 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- v3 - Variable in class org.jmol.minimize.forcefield.Calculations
- v3 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
- V3000Rdr - Class in org.jmol.adapter.readers.molxyz
-
A reader for Accelrys V3000 files.
- V3000Rdr() - Constructor for class org.jmol.adapter.readers.molxyz.V3000Rdr
- v3temp - Variable in class org.jmol.renderspecial.DotsRenderer
- vA - Variable in class org.jmol.smiles.VTemp
- vAB - Static variable in class org.jmol.g3d.HermiteRenderer
- vAB - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- vAB - Variable in class org.jmol.modelsetbio.BioResolver
- vAB - Variable in class org.jmol.shape.Mesh
- vAB - Variable in class org.jmol.shapespecial.Draw
- vAB - Variable in class org.jmol.shapespecial.Polyhedra
- vAB - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- vAC - Static variable in class org.jmol.g3d.HermiteRenderer
- vAC - Variable in class org.jmol.shapespecial.Polyhedra
- vAC - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- val - Variable in class org.jmol.minimize.forcefield.AtomType
-
valence (number of bonds, generally 4 for neutral carbon, regardless of bonding, but 3 in the case of isonitrile)
- val - Static variable in class org.jmol.script.T
- valence - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- valence - Variable in class org.jmol.modelset.Atom
- valence - Static variable in class org.jmol.script.T
- valence - Variable in class org.jmol.smiles.SmilesAtom
- VALENCE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- valence_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- valence_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- validate() - Method in class org.jmol.awtjs.swing.JDialog
- validate(boolean) - Method in class org.jmol.shapespecial.Ellipsoid
- VALIDATE - Static variable in class org.jmol.util.Geodesic
- validate_object_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- validateAndAllocate(Chain, String, int, int, int) - Static method in class org.jmol.modelsetbio.CarbohydrateMonomer
- validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.NucleicMonomer
- validateAndAllocate(Chain, String, int, int, int, int[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
- validateAndAllocateA(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.AlphaMonomer
- validateAndAllocateP(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.PhosphorusMonomer
- validateBspf(boolean) - Method in class org.jmol.modelset.AtomCollection
- validateBspfForModel(int, boolean) - Method in class org.jmol.modelset.AtomCollection
- validateFace(int, int, int, IsoSolventReader.Edge, P3) - Method in class org.jmol.jvxl.readers.IsoSolventReader
- validateModel(int, boolean) - Method in class org.jmol.bspt.Bspf
- validatePolyhedron(P3, int) - Method in class org.jmol.shapespecial.Polyhedra
- validation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- validation - Static variable in class org.jmol.script.T
- validSpheres - Variable in class org.jmol.jvxl.readers.AtomDataReader
- valign - Variable in class org.jmol.modelset.Text
- value - Variable in class org.jmol.adapter.readers.xml.XmlReader.NVPair
- value - Variable in class org.jmol.atomdata.RadiusData
- value - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
- value - Variable in class org.jmol.minimize.MMConstraint
- value - Variable in class org.jmol.modelkit.ModelKit.Constraint
- value - Variable in class org.jmol.modelset.Measurement
- value - Variable in class org.jmol.script.T
- value - Variable in class org.jmol.thread.MoveToThread.Slider
- value - Variable in class org.jmol.util.Int2IntHashEntry
- valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
- valueChanged(TreeSelectionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- valueCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- valueExtended - Variable in class org.jmol.atomdata.RadiusData
- valueFor(float, float, int) - Method in class org.jmol.quantum.MepCalculation
- valueMappedToBlue - Variable in class org.jmol.jvxl.data.JvxlData
- valueMappedToBlue - Variable in class org.jmol.jvxl.readers.Parameters
- valueMappedToRed - Variable in class org.jmol.jvxl.data.JvxlData
- valueMappedToRed - Variable in class org.jmol.jvxl.readers.Parameters
- valueMax - Variable in class org.jmol.jvxl.calc.MarchingSquares
- valueMin - Variable in class org.jmol.jvxl.calc.MarchingSquares
- valueMin - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- valueOf(String) - Static method in enum org.jmol.atomdata.RadiusData.EnumType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.c.CBK
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.c.FIL
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.c.HB
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.c.PAL
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.c.STER
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.c.STR
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.c.VDW
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.util.Edge.EnumBondOrder
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.viewer.Viewer.ACCESS
-
Returns the enum constant of this type with the specified name.
- valuePeek() - Method in class org.jmol.script.ScriptTokenParser
- valueRange - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- values - Variable in class org.jmol.atomdata.RadiusData
- values - Variable in class org.jmol.jvxl.readers.BCifDensityReader
- values - Variable in class org.jmol.jvxl.readers.IsoFxyReader
- values - Variable in class org.jmol.jvxl.readers.IsoIntersectAtomReader
- values - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
- values - Variable in class org.jmol.util.MeshSlicer
- values() - Static method in enum org.jmol.atomdata.RadiusData.EnumType
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.c.CBK
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.c.FIL
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.c.HB
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.c.PAL
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.c.STER
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.c.STR
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.c.VDW
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.util.Edge.EnumBondOrder
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.jmol.viewer.Viewer.ACCESS
-
Returns an array containing the constants of this enum type, in the order they are declared.
- vanderwaals - Static variable in class org.jmol.script.T
- vanderwaalsMars - Static variable in class org.jmol.util.Elements
-
Default table of van der Waals Radii.
- var - Variable in class org.jmol.script.ScriptFlowContext
- var - Static variable in class org.jmol.script.T
- varButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- varClip(String, String, int) - Static method in class org.jmol.viewer.StateManager
- variable - Static variable in class org.jmol.script.T
- VARIABLE - Enum constant in enum org.jmol.c.PAL
- variables - Variable in class org.jmol.script.ScriptFunction
- variables - Static variable in class org.jmol.script.T
- varray - Static variable in class org.jmol.script.T
- vars - Variable in class org.jmol.script.ScriptContext
- VaspChgcarReader - Class in org.jmol.adapter.readers.xtal
-
http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.
- VaspChgcarReader - Class in org.jmol.jvxl.readers
- VaspChgcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspChgcarReader
- VaspChgcarReader() - Constructor for class org.jmol.jvxl.readers.VaspChgcarReader
- vaspOutcarLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- VaspOutcarReader - Class in org.jmol.adapter.readers.xtal
-
http://cms.mpi.univie.ac.at/vasp/
- VaspOutcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspOutcarReader
- VaspPoscarReader - Class in org.jmol.adapter.readers.xtal
-
adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/
- VaspPoscarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspPoscarReader
- vaspVersion - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
- vAtoms - Variable in class org.jmol.adapter.readers.simple.InputReader
- vB - Variable in class org.jmol.smiles.VTemp
- vBar - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
- vBC - Variable in class org.jmol.shapespecial.Polyhedra
- vBiomolecules - Variable in class org.jmol.adapter.readers.cif.MMCifReader
- vBiomolecules - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- vBraces - Variable in class org.jmol.script.ScriptCompiler
- vButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- vc - Variable in class org.jmol.util.MeshSurface
-
vertex count
- vCompnds - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- vConnect - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- vContours - Variable in class org.jmol.jvxl.data.JvxlData
- vcs - Variable in class org.jmol.util.MeshSurface
-
vertex color index "colix" array
- vData - Variable in class org.jmol.shapespecial.Draw
- vdc - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- vDist - Variable in class org.jmol.jvxl.readers.IsoMOReader
- VDW - Enum in org.jmol.c
- VDW - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- VDW(int, String, String) - Constructor for enum org.jmol.c.VDW
- vdw1 - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- vdwCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
- vdwCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
- vdwKey - Variable in class org.jmol.minimize.MinAtom
- vdwPercentSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- VdwPROBE - Static variable in class org.jmol.util.Elements
- vdws - Variable in class org.jmol.util.ContactPair
- vdwType - Variable in class org.jmol.atomdata.RadiusData
- vdwVolume - Variable in class org.jmol.util.ContactPair
- vecs - Static variable in class org.jmol.adapter.readers.xtal.CgdReader
- vector - Static variable in class org.jmol.script.T
- vector - Variable in class org.jmol.shapespecial.Dipole
- VECTOR - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
-
String for prefix/resource identifier for the vector area.
- vector12ths - Variable in class org.jmol.symmetry.HallInfo
- vectorAB - Variable in class org.jmol.g3d.Graphics3D
- vectorAC - Variable in class org.jmol.g3d.Graphics3D
- vectorAngleRadians(V3d, V3d) - Static method in class org.jmol.minimize.Util
- vectorCode - Variable in class org.jmol.symmetry.HallInfo
- vectorNormal - Variable in class org.jmol.g3d.Graphics3D
- vectorProjection - Variable in class org.jmol.modelsetbio.ProteinStructure
- vectors - Variable in class org.jmol.jvxl.readers.MapFileReader
- Vectors - Class in org.jmol.shapespecial
- Vectors() - Constructor for class org.jmol.shapespecial.Vectors
- vectorscale - Static variable in class org.jmol.script.T
- vectorScale - Variable in class org.jmol.renderspecial.VectorsRenderer
- vectorScale - Variable in class org.jmol.viewer.GlobalSettings
- vectorscentered - Static variable in class org.jmol.script.T
- vectorsCentered - Variable in class org.jmol.renderspecial.VectorsRenderer
- vectorsCentered - Variable in class org.jmol.viewer.GlobalSettings
- vectorShift12ths - Variable in class org.jmol.symmetry.HallTranslation
- VectorsRenderer - Class in org.jmol.renderspecial
- VectorsRenderer() - Constructor for class org.jmol.renderspecial.VectorsRenderer
- vectorsymmetry - Static variable in class org.jmol.script.T
- vectorSymmetry - Variable in class org.jmol.renderspecial.VectorsRenderer
- vectorSymmetry - Variable in class org.jmol.viewer.GlobalSettings
- vectorT - Variable in class org.jmol.render.FontLineShapeRenderer
- vectorT - Variable in class org.jmol.viewer.TransformManager
- vectorT2 - Variable in class org.jmol.render.FontLineShapeRenderer
- vectorT2 - Variable in class org.jmol.viewer.TransformManager
- vectorT3 - Variable in class org.jmol.render.FontLineShapeRenderer
- vectorTemp - Variable in class org.jmol.viewer.TransformManager
- vectortrail - Static variable in class org.jmol.script.T
- vectorTrail - Variable in class org.jmol.renderspecial.VectorsRenderer
- vectorTrail - Variable in class org.jmol.viewer.GlobalSettings
- vEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- version - Variable in class org.jmol.jvxl.data.JvxlData
- version - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- version - Static variable in class org.jmol.viewer.JC
- version - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- VERSION - Static variable in class org.openscience.jmol.app.janocchio.Nmr
- VERSION - Static variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- VERSION - Static variable in class org.openscience.jvxl.Jvxl
- version_date - Static variable in class org.jmol.viewer.Viewer
- versionInt - Static variable in class org.jmol.viewer.JC
- VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
- VERTEX_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
- vertexBase - Variable in class org.jmol.jvxl.readers.PmeshReader
- vertexColixes - Variable in class org.jmol.shapesurface.PMeshWriter
- vertexColorMap - Variable in class org.jmol.jvxl.data.JvxlData
- vertexColorMap - Variable in class org.jmol.shape.Mesh
- vertexColors - Variable in class org.jmol.jvxl.data.JvxlData
- vertexCount - Variable in class org.jmol.jvxl.data.JvxlData
- vertexCount - Variable in class org.jmol.render.MeshRenderer
- vertexCount - Variable in class org.jmol.shapesurface.PMeshWriter
- vertexCount0 - Variable in class org.jmol.util.MeshSurface
- vertexCounts - Static variable in class org.jmol.util.Geodesic
- vertexDataOnly - Variable in class org.jmol.jvxl.data.JvxlData
- vertexDataOnly - Variable in class org.jmol.jvxl.readers.SurfaceReader
- VertexDataServer - Interface in org.jmol.jvxl.api
- vertexIncrement - Variable in class org.jmol.jvxl.data.MeshData
- vertexIncrement - Variable in class org.jmol.shapesurface.IsosurfaceMesh
- vertexMap - Variable in class org.jmol.jvxl.readers.EfvetReader
- vertexMap - Variable in class org.jmol.jvxl.readers.NffReader
- vertexMap - Variable in class org.jmol.jvxl.readers.PmeshReader
- vertexNext - Static variable in class org.jmol.util.Geodesic
- vertexSets - Variable in class org.jmol.util.MeshSurface
- vertexSource - Variable in class org.jmol.jvxl.readers.Parameters
- vertexSource - Variable in class org.jmol.util.MeshSurface
- vertexTest - Variable in class org.jmol.geodesic.EnvelopeCalculation
- vertexValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
- vertexValues - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
- vertexValues - Variable in class org.jmol.shapesurface.PMeshWriter
- vertexVectors - Static variable in class org.jmol.util.Geodesic
- vertexVectors - Static variable in class org.jmol.util.Normix
- vertices - Variable in class org.jmol.render.MeshRenderer
- vertices - Static variable in class org.jmol.script.T
- vertices - Variable in class org.jmol.shapespecial.Polyhedron
- vertices - Variable in class org.jmol.symmetry.UnitCell
- vertices - Variable in class org.jmol.util.MeshCapper
- verticesT - Variable in class org.jmol.render.UccageRenderer
- vf - Variable in class org.jmol.shape.Shape
-
shape visibility flag
- vF - Static variable in class org.jmol.script.SV
- vFaces - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- vFunctionStack - Variable in class org.jmol.script.ScriptCompiler
- vH - Variable in class org.jmol.renderbio.RocketRenderer
- vHBonds - Variable in class org.jmol.dssx.DSSP
- vib - Variable in class org.jmol.adapter.smarter.Atom
- vib - Variable in class org.jmol.util.ModulationSet
-
vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.
- VIB_ENERGY - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- vibFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- vibFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- vibOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
- vibration - Static variable in class org.jmol.script.T
- Vibration - Class in org.jmol.util
-
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.
- Vibration() - Constructor for class org.jmol.util.Vibration
- VIBRATION_VECTOR_FLAG - Static variable in class org.jmol.modelset.Atom
- vibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- vibrationOn - Variable in class org.jmol.renderspecial.VectorsRenderer
- vibrationOn - Variable in class org.jmol.viewer.TransformManager
- VibrationOnly - Variable in class org.jmol.popup.JmolPopup
- vibrationperiod - Static variable in class org.jmol.script.T
- vibrationPeriod - Variable in class org.jmol.viewer.GlobalSettings
- vibrationPeriod - Variable in class org.jmol.viewer.TransformManager
- vibrationPeriodMs - Variable in class org.jmol.viewer.TransformManager
- vibrations - Variable in class org.jmol.modelset.AtomCollection
- vibrationscale - Static variable in class org.jmol.script.T
- vibrationScale - Variable in class org.jmol.viewer.GlobalSettings
- vibrationScale - Variable in class org.jmol.viewer.TransformManager
- vibrationSteps - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- vibrationSteps - Variable in class org.jmol.modelset.ModelSet
- vibrationT - Variable in class org.jmol.viewer.TransformManager
- vibrationThread - Variable in class org.jmol.viewer.TransformManager
- VibrationThread - Class in org.jmol.thread
- VibrationThread() - Constructor for class org.jmol.thread.VibrationThread
- vibs - Variable in class org.jmol.renderspecial.PolyhedraRenderer
- vibScale - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- vibScale - Variable in class org.jmol.jsv.JDXMOLParser
- vibsFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- vibTemp - Variable in class org.jmol.renderspecial.VectorsRenderer
- vibx - Static variable in class org.jmol.script.T
- vibxyz - Static variable in class org.jmol.script.T
- viby - Static variable in class org.jmol.script.T
- vibz - Static variable in class org.jmol.script.T
- viewButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
- viewCenterButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- ViewCoupleTableAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewCoupleTableAction
- viewer - Variable in class org.jmol.util.GenericApplet
- viewer - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- viewer - Variable in class org.openscience.jmol.app.janocchio.FrameCounter
- viewer - Variable in class org.openscience.jmol.app.janocchio.FrameDeltaDisplay
- viewer - Variable in class org.openscience.jmol.app.janocchio.LabelSetter
- viewer - Variable in class org.openscience.jmol.app.janocchio.NMR_DisplayPanel
- viewer - Variable in class org.openscience.jmol.app.janocchio.NmrMolecule
- viewer - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- viewer - Variable in class org.openscience.jmol.app.janocchio.PopulationDisplay
- Viewer - Class in org.jmol.viewer
- Viewer(Map<String, Object>) - Constructor for class org.jmol.viewer.Viewer
-
new way...
- Viewer.ACCESS - Enum in org.jmol.viewer
- viewMeasurementTableAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- ViewMeasurementTableAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
- ViewNoeTableAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.ViewNoeTableAction
- viewOffset - Variable in class org.jmol.modelkit.ModelKit
- viewpoint - Variable in class org.jmol.export.__CartesianExporter
- viewToModel - Variable in class org.openscience.jmol.app.janocchio.TableSorter
- virtual_trackball - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- VIS_BACKBONE_FLAG - Static variable in class org.jmol.viewer.JC
- VIS_BALLS_FLAG - Static variable in class org.jmol.viewer.JC
- VIS_BOND_FLAG - Static variable in class org.jmol.viewer.JC
- VIS_CARTOON_FLAG - Static variable in class org.jmol.viewer.JC
- VIS_LABEL_FLAG - Static variable in class org.jmol.viewer.JC
- VISIBILITY_CLIPPED - Static variable in class org.jmol.g3d.LineRenderer
- VISIBILITY_OFFSCREEN - Static variable in class org.jmol.g3d.LineRenderer
- VISIBILITY_UNCLIPPED - Static variable in class org.jmol.g3d.LineRenderer
- visibilityFlags - Variable in class org.jmol.shape.Mesh
- visibilityFlags - Variable in class org.jmol.shapespecial.Dipole
- visibilityFlags - Variable in class org.jmol.shapespecial.Polyhedron
- visible - Variable in class org.jmol.adapter.readers.pymol.JmolObject
- visible - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
- visible - Variable in class org.jmol.modelset.Text
- visible - Static variable in class org.jmol.script.T
- visible - Variable in class org.jmol.shape.Mesh
- visible - Variable in class org.jmol.shapespecial.Dipole
- visible - Variable in class org.jmol.shapespecial.Ellipsoid
- visible - Variable in class org.jmol.shapespecial.Polyhedron
- VISREP - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- visualrange - Static variable in class org.jmol.script.T
- visualRangeAngstroms - Variable in class org.jmol.viewer.TransformManager
- VK_ALT - Static variable in class org.jmol.awtjs.Event
- VK_BACK_SPACE - Static variable in class org.jmol.awtjs.Event
- VK_CONTROL - Static variable in class org.jmol.awtjs.Event
- VK_DELETE - Static variable in class org.jmol.awtjs.Event
- VK_DOWN - Static variable in class org.jmol.awtjs.Event
- VK_ESCAPE - Static variable in class org.jmol.awtjs.Event
- VK_LEFT - Static variable in class org.jmol.awtjs.Event
- VK_META - Static variable in class org.jmol.awtjs.Event
- VK_PAGE_DOWN - Static variable in class org.jmol.awtjs.Event
- VK_PAGE_UP - Static variable in class org.jmol.awtjs.Event
- VK_PERIOD - Static variable in class org.jmol.awtjs.Event
- VK_RIGHT - Static variable in class org.jmol.awtjs.Event
- VK_SHIFT - Static variable in class org.jmol.awtjs.Event
- VK_SPACE - Static variable in class org.jmol.awtjs.Event
- VK_UP - Static variable in class org.jmol.awtjs.Event
- vl0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
- vl1 - Variable in class org.jmol.jvxl.readers.AtomDataReader
- vl2 - Variable in class org.jmol.jvxl.readers.AtomDataReader
- vMax - Variable in class org.jmol.jvxl.readers.KinemageReader
- vMin - Variable in class org.jmol.jvxl.readers.KinemageReader
- vNaN - Static variable in class org.jmol.script.SV
- vNorm - Variable in class org.jmol.adapter.writers.MOLWriter
- vNorm - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- vNorm - Variable in class org.jmol.modelsetbio.BioResolver
- vNorm - Variable in class org.jmol.symmetry.CIPData
- vNorm2 - Variable in class org.jmol.smiles.VTemp
- vNorm3 - Variable in class org.jmol.smiles.VTemp
- vNorm4 - Variable in class org.jmol.smiles.VTemp
- vOcc - Variable in class org.jmol.util.ModulationSet
-
the current value of the occupancy modulation
- volume - Variable in class org.jmol.jvxl.readers.VaspChgcarReader
- volume - Variable in class org.jmol.quantum.QuantumCalculation
- volume - Static variable in class org.jmol.script.T
- volume - Variable in class org.jmol.shapespecial.Polyhedron
- volume - Variable in class org.jmol.util.BZone
- volume - Variable in class org.jmol.util.ContactPair
- volume - Variable in class org.jmol.util.SimpleUnitCell
- volume_bit_depth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- volume_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- volume_data_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- volume_layers - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- volumeData - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- volumeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
- volumeData - Variable in class org.jmol.jvxl.calc.MarchingSquares
- volumeData - Variable in class org.jmol.jvxl.readers.Parameters
- volumeData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- volumeData - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
- VolumeData - Class in org.jmol.jvxl.data
- VolumeData() - Constructor for class org.jmol.jvxl.data.VolumeData
- VolumeDataReader - Class in org.jmol.jvxl.readers
- VolumeDataReader() - Constructor for class org.jmol.jvxl.readers.VolumeDataReader
- volumeDataTemp - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
- VolumeFileReader - Class in org.jmol.jvxl.readers
- VolumeFileReader() - Constructor for class org.jmol.jvxl.readers.VolumeFileReader
- volumeRender - Variable in class org.jmol.render.MeshRenderer
- volumeRender(boolean) - Method in interface org.jmol.api.JmolRendererInterface
- volumeRender(boolean) - Method in class org.jmol.export.Export3D
- volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
- volumeRender4(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
- volumeRender4(int, int, int, int) - Method in class org.jmol.export.Export3D
- volumeRender4(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
- volumeRenderPointSize - Variable in class org.jmol.shape.Mesh
- volumetricMatrix - Variable in class org.jmol.jvxl.data.VolumeData
- volumetricOrigin - Variable in class org.jmol.jvxl.data.VolumeData
- volumetricOrigin - Variable in class org.jmol.jvxl.readers.SurfaceReader
- volumetricVectorLengths - Variable in class org.jmol.jvxl.data.VolumeData
- volumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
- volumetricVectors - Variable in class org.jmol.jvxl.readers.SurfaceReader
- vOrientations - Variable in class org.jmol.modelset.ModelSet
- voronoiAngle - Variable in class org.jmol.adapter.readers.cif.TopoCifParser.TLink
- voxelCount - Variable in class org.jmol.jvxl.readers.UhbdReader
- voxelCounts - Variable in class org.jmol.jvxl.data.VolumeData
- voxelCounts - Variable in class org.jmol.jvxl.readers.SurfaceReader
- voxelData - Variable in class org.jmol.jvxl.calc.MarchingCubes
- voxelData - Variable in class org.jmol.jvxl.data.VolumeData
- voxelData - Variable in class org.jmol.jvxl.readers.SurfaceReader
- voxelData - Variable in class org.jmol.quantum.QuantumCalculation
- VoxelDataCreator - Class in org.openscience.jvxl.simplewriter
- VoxelDataCreator(VolumeData) - Constructor for class org.openscience.jvxl.simplewriter.VoxelDataCreator
- voxelDataTemp - Variable in class org.jmol.quantum.QuantumCalculation
- voxelList - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
- voxelMap - Variable in class org.jmol.jvxl.data.VolumeData
- voxelPtToXYZ(int, int, int, T3) - Method in class org.jmol.jvxl.data.VolumeData
- voxelSource - Variable in class org.jmol.jvxl.readers.AtomDataReader
- voxelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
- voxelVolume - Variable in class org.jmol.jvxl.data.JvxlData
- voxelVolume - Variable in class org.jmol.jvxl.data.VolumeData
- vPush - Variable in class org.jmol.script.ScriptCompiler
- vr - Variable in class org.jmol.adapter.readers.molxyz.MolReader
- vR - Variable in class org.jmol.adapter.readers.xtal.JanaReader
- vRef - Static variable in class org.jmol.modelset.AtomCollection
- vRef - Variable in class org.jmol.smiles.PolyhedronStereoSorter
- vReturn - Variable in class org.jmol.smiles.SmilesSearch
- vRings - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
- vs - Variable in class org.jmol.util.MeshSurface
-
vertices
- vStereo - Variable in class org.jmol.modelset.ModelLoader
- vSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
- vT - Static variable in class org.jmol.script.SV
- vtemp - Variable in class org.jmol.renderbio.RocketRenderer
- vtemp - Static variable in class org.jmol.symmetry.SymmetryDesc
- vTemp - Variable in class org.jmol.adapter.writers.MOLWriter
- vTemp - Variable in class org.jmol.jvxl.readers.IsoMOReader
- vTemp - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- vTemp - Variable in class org.jmol.modelset.ModelSet
- vTemp - Variable in class org.jmol.renderspecial.DrawRenderer
- vTemp - Variable in class org.jmol.shape.Mesh
- vTemp - Variable in class org.jmol.smiles.PolyhedronStereoSorter
- vTemp - Variable in class org.jmol.smiles.SmilesGenerator
- vTemp - Variable in class org.jmol.smiles.VTemp
- vTemp - Variable in class org.jmol.symmetry.CIPData
- vTemp - Variable in class org.jmol.symmetry.PointGroup
- vTemp - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
- VTemp - Class in org.jmol.smiles
- VTemp() - Constructor for class org.jmol.smiles.VTemp
- vTemp1 - Variable in class org.jmol.smiles.VTemp
- vTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
- vTemp2 - Variable in class org.jmol.renderspecial.DrawRenderer
- vTemp2 - Variable in class org.jmol.smiles.VTemp
- vTlsModels - Variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
- vTlsModels - Variable in class org.jmol.adapter.readers.pdb.PdbReader
- vtrans - Static variable in class org.jmol.symmetry.SymmetryDesc
- vvs - Variable in class org.jmol.util.MeshSurface
-
vertex values
- vW - Variable in class org.jmol.renderbio.RocketRenderer
- vwr - Variable in class org.jmol.adapter.readers.pymol.PickleReader
- vwr - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
- vwr - Variable in class org.jmol.adapter.readers.quantum.NBOParser
- vwr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
- vwr - Variable in class org.jmol.adapter.writers.CIFWriter
- vwr - Variable in class org.jmol.adapter.writers.CMLWriter
- vwr - Variable in class org.jmol.adapter.writers.MOLWriter
- vwr - Variable in class org.jmol.adapter.writers.PDBWriter
- vwr - Variable in class org.jmol.adapter.writers.PWMATWriter
- vwr - Variable in class org.jmol.adapter.writers.QCJSONWriter
- vwr - Variable in class org.jmol.adapter.writers.XSFWriter
- vwr - Variable in class org.jmol.awt.FileDropper
- vwr - Variable in class org.jmol.awt.Mouse
- vwr - Variable in class org.jmol.awt.Platform
- vwr - Variable in class org.jmol.awtjs2d.Mouse
- vwr - Variable in class org.jmol.awtjs2d.Platform
- vwr - Variable in class org.jmol.console.GenericConsole
- vwr - Variable in class org.jmol.console.ImageDialog
- vwr - Variable in class org.jmol.console.ScriptEditor
- vwr - Variable in class org.jmol.dialog.Dialog
- vwr - Variable in class org.jmol.dialog.FilePreview.FPPanel
- vwr - Variable in class org.jmol.dialog.FilePreview
- vwr - Variable in class org.jmol.export.___Exporter
- vwr - Variable in class org.jmol.geodesic.EnvelopeCalculation
- vwr - Static variable in class org.jmol.i18n.GT
- vwr - Variable in class org.jmol.io.DOMReader
- vwr - Variable in class org.jmol.io.FileReader
- vwr - Variable in class org.jmol.io.FilesReader
- vwr - Variable in class org.jmol.jsv.JSpecView
- vwr - Variable in class org.jmol.minimize.Minimizer
- vwr - Variable in class org.jmol.modelkit.ModelKit
- vwr - Variable in class org.jmol.modelset.AtomCollection
- vwr - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- vwr - Variable in class org.jmol.modelset.Measurement
- vwr - Variable in class org.jmol.modelset.MeasurementData
- vwr - Variable in class org.jmol.modelset.ModelLoader
- vwr - Variable in class org.jmol.modelset.Orientation
- vwr - Variable in class org.jmol.modelset.Text
- vwr - Variable in class org.jmol.modelset.Trajectory
- vwr - Variable in class org.jmol.modelsetbio.BioExt
- vwr - Variable in class org.jmol.modelsetbio.BioModel
- vwr - Variable in class org.jmol.modelsetbio.BioModelSet
- vwr - Variable in class org.jmol.modelsetbio.BioResolver
- vwr - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
- vwr - Variable in class org.jmol.popup.JmolGenericPopup
- vwr - Variable in class org.jmol.quantum.MepCalculation
- vwr - Variable in class org.jmol.quantum.NMRCalculation
- vwr - Variable in class org.jmol.render.RepaintManager
- vwr - Variable in class org.jmol.render.ShapeRenderer
- vwr - Variable in class org.jmol.renderbio.NucleicRenderer
- vwr - Variable in class org.jmol.renderbio.RocketRenderer
- vwr - Variable in class org.jmol.script.ScriptError
- vwr - Variable in class org.jmol.script.ScriptManager
- vwr - Variable in class org.jmol.script.ScriptMathProcessor
- vwr - Variable in class org.jmol.script.ScriptParallelProcessor
- vwr - Variable in class org.jmol.script.ScriptTokenParser
- vwr - Variable in class org.jmol.scriptext.MathExt
- vwr - Variable in class org.jmol.scriptext.ScriptExt
- vwr - Variable in class org.jmol.shape.Shape
- vwr - Variable in class org.jmol.symmetry.CIPData
-
Jmol's viewer class
- vwr - Variable in class org.jmol.thread.JmolThread
- vwr - Variable in class org.jmol.util.BZone
- vwr - Variable in class org.jmol.util.ColorEncoder
- vwr - Variable in class org.jmol.util.GData
- vwr - Variable in class org.jmol.util.JmolAudio
- vwr - Variable in class org.jmol.util.MeshSurface
- vwr - Variable in class org.jmol.viewer.ActionManager
- vwr - Variable in class org.jmol.viewer.AnimationManager
- vwr - Variable in class org.jmol.viewer.ChimeMessenger
- vwr - Variable in class org.jmol.viewer.ColorManager
- vwr - Variable in class org.jmol.viewer.Connections
- vwr - Variable in class org.jmol.viewer.DataManager
- vwr - Variable in class org.jmol.viewer.FileManager
- vwr - Variable in class org.jmol.viewer.Gesture
- vwr - Variable in class org.jmol.viewer.GlobalSettings
- vwr - Variable in class org.jmol.viewer.ModelManager
- vwr - Variable in class org.jmol.viewer.OutputManager
- vwr - Variable in class org.jmol.viewer.PropertyManager
- vwr - Variable in class org.jmol.viewer.SelectionManager
- vwr - Variable in class org.jmol.viewer.ShapeManager
- vwr - Variable in class org.jmol.viewer.StateCreator
- vwr - Variable in class org.jmol.viewer.StateManager
- vwr - Variable in class org.jmol.viewer.StatusManager
- vwr - Variable in class org.jmol.viewer.TransformManager
- vwr - Variable in class org.openscience.jmol.app.InputScannerThread
- vwr - Variable in class org.openscience.jmol.app.JmolData
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
- vwr - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
- vwr - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
- vwr - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
- vwr - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- vwr - Variable in class org.openscience.jmol.app.webexport.Test
- vwr - Variable in class org.openscience.jmol.app.webexport.WebPanel
- vwrFrame - Variable in class org.jmol.console.JmolConsole
- vwrOptions - Variable in class org.jmol.util.GenericApplet
- vwrOptions - Variable in class org.jmol.viewer.Viewer
- vwrOptions - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- vX - Variable in class org.jmol.rendercgo.CGORenderer
-
UV mapping Cartesian origin, X, and Y
- vX - Variable in class org.jmol.shapesurface.Contact
- vY - Variable in class org.jmol.rendercgo.CGORenderer
-
UV mapping Cartesian origin, X, and Y
- vY - Variable in class org.jmol.shapesurface.Contact
- vZ - Variable in class org.jmol.shapesurface.Contact
W
- w - Variable in class org.jmol.adapter.readers.cif.Subsystem
- w - Static variable in class org.jmol.script.T
- waitForDisplay(Object, Object) - Method in interface org.jmol.api.GenericPlatform
-
can be ignored (return false) if platform cannot save images
- waitForDisplay(Object, Object) - Method in class org.jmol.awt.Platform
- waitForDisplay(Object, Object) - Method in class org.jmol.awtjs2d.Platform
- waitForDisplay(PlatformViewer, Object) - Static method in class org.jmol.awt.Image
- waitformoveto - Static variable in class org.jmol.script.T
- waitForMoveTo - Variable in class org.jmol.viewer.GlobalSettings
- waitForQueue() - Method in interface org.jmol.api.JmolScriptManager
- waitForQueue() - Method in class org.jmol.script.ScriptManager
- walkDOMTree() - Method in class org.jmol.adapter.readers.xml.XmlReader
- warn(String) - Method in class org.jmol.util.DefaultLogger
- warn(String) - Static method in class org.jmol.util.Logger
-
Writes a log at WARN level.
- warn(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at WARN level.
- warned - Variable in class org.jmol.quantum.MOCalculation
- warnEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
- warnEx(String, Throwable) - Static method in class org.jmol.util.Logger
-
Writes a log at WARN level with detail on exception.
- warnEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at WARN level with detail on exception.
- warning(int, String, String) - Method in class org.jmol.script.ScriptError
- warning(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
- warningAtom - Variable in class org.jmol.adapter.readers.xml.XmlChemDrawReader
- wasClicked(int, int) - Method in class org.jmol.shape.Frank
- wasClicked(int, int) - Method in class org.jmol.shape.Shape
- wasCubic - Variable in class org.jmol.jvxl.data.JvxlData
- wasImpliedScript() - Method in class org.jmol.script.ScriptCompiler
-
Check for improperly parsed implied script command: only two tokens: [implied script] xxx.SORT/REVERSE/PUSH/POP more than two tokens: xxxx.spt(3,4,5)
- wasJvxl - Variable in class org.jmol.jvxl.data.JvxlData
- wasmInchiHack(String) - Method in class org.jmol.viewer.Viewer
-
WASM inchi must be initialized asynchronously
- wasPerspective - Variable in class org.jmol.export.__RayTracerExporter
- wasRotating - Variable in class org.jmol.modelkit.ModelKit
-
set to TRUE after rotation has been turned off in order to turn highlight off in viewer.hoverOff()
- wasRotating() - Method in class org.jmol.modelkit.ModelKit
- wasScreened - Variable in class org.jmol.g3d.Graphics3D
- wasSpinOn - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioClient.TouchHandler
- wasSyntaxCheck - Variable in class org.jmol.script.ScriptMathProcessor
- wasX - Variable in class org.jmol.script.ScriptMathProcessor
- WB - Static variable in class org.jmol.util.ColorEncoder
- WEB_MAKER_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- webExport - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- webExport - Static variable in class org.openscience.jmol.app.webexport.WebExport
- WebExport - Class in org.openscience.jmol.app.webexport
- WebExport(Viewer, HistoryFile) - Constructor for class org.openscience.jmol.app.webexport.WebExport
- webFrame - Static variable in class org.openscience.jmol.app.webexport.WebExport
- webGL - Variable in class org.jmol.export.Export3D
- webmoFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- WebMOReader - Class in org.jmol.adapter.readers.quantum
-
A molecular orbital reader for WebMO files.
- WebMOReader() - Constructor for class org.jmol.adapter.readers.quantum.WebMOReader
- webPageTitle - Variable in class org.openscience.jmol.app.webexport.WebPanel
- webPanel - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
- WebPanel - Class in org.openscience.jmol.app.webexport
- WebPanel(Viewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.WebPanel
- WebPanel.InstanceCellRenderer - Class in org.openscience.jmol.app.webexport
- webPanels - Static variable in class org.openscience.jmol.app.webexport.WebExport
- webPanels - Variable in class org.openscience.jmol.app.webexport.WebPanel
- weightx - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- weighty - Variable in class org.jmol.awtjs.swing.GridBagConstraints
- WEST - Static variable in class org.jmol.awtjs.swing.BorderLayout
- WEST - Static variable in class org.jmol.awtjs.swing.GridBagConstraints
- whatsnewAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- WhatsNewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
- WhatsNewDialog - Class in org.openscience.jmol.app.jmolpanel
- WhatsNewDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
- WHEEL - Static variable in class org.jmol.viewer.binding.Binding
- wheeled(long, int, int) - Method in class org.jmol.awtjs2d.Mouse
- WHEELED - Static variable in class org.jmol.awtjs.Event
- wheeling - Variable in class org.jmol.awt.Mouse
- wheeling - Variable in class org.jmol.awtjs2d.Mouse
- whichOrigin - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- whichWidgets - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- whilecmd - Static variable in class org.jmol.script.T
- white - Variable in class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- WHITE - Static variable in class org.jmol.util.C
- whiteSpace - Variable in class org.jmol.util.JSONWriter
- why - Variable in class org.jmol.script.ScriptContext
- Widget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.Widget
- widgetCheckboxes - Variable in class org.openscience.jmol.app.webexport.WebPanel
- widgetList - Variable in class org.openscience.jmol.app.webexport.Widgets
- Widgets - Class in org.openscience.jmol.app.webexport
- Widgets() - Constructor for class org.openscience.jmol.app.webexport.Widgets
- Widgets.AnimationWidget - Class in org.openscience.jmol.app.webexport
- Widgets.BackgroundColorWidget - Class in org.openscience.jmol.app.webexport
- Widgets.ConsoleWidget - Class in org.openscience.jmol.app.webexport
- Widgets.DownLoadWidget - Class in org.openscience.jmol.app.webexport
- Widgets.SpinOnWidget - Class in org.openscience.jmol.app.webexport
- Widgets.StereoViewWidget - Class in org.openscience.jmol.app.webexport
- Widgets.Widget - Class in org.openscience.jmol.app.webexport
- width - Variable in class org.jmol.awtjs.swing.Component
- width - Variable in class org.jmol.awtjs.swing.Dimension
- width - Variable in class org.jmol.export.Export3D
- width - Variable in class org.jmol.g3d.Pixelator
- width - Variable in class org.jmol.g3d.SphereRenderer
- width - Variable in class org.jmol.g3d.TextRenderer
- width - Variable in class org.jmol.modelset.LabelToken
- width - Variable in class org.jmol.render.FontLineShapeRenderer
- width - Variable in class org.jmol.render.MeshRenderer
- width - Variable in class org.jmol.render.StarsRenderer
- width - Static variable in class org.jmol.script.T
- width - Variable in class org.jmol.shape.Mesh
- width - Variable in class org.jmol.shapespecial.Draw
- width - Variable in class org.jmol.util.GData
- width - Variable in class org.jmol.util.Rectangle
- width - Variable in class org.jmol.viewer.TransformManager
- width - Variable in class org.openscience.jmol.app.webexport.JmolInstance
- widthOffscreen - Variable in class org.jmol.g3d.Platform3D
- widths - Variable in class org.jmol.modelset.Text
- WIDTHSCALE - Static variable in class org.jmol.shapecgo.CGOMesh
- widthUnitVector - Variable in class org.jmol.modelsetbio.Sheet
- Wien2kReader - Class in org.jmol.adapter.readers.xtal
-
A reader for Wein2k DFT files.
- Wien2kReader() - Constructor for class org.jmol.adapter.readers.xtal.Wien2kReader
- wigner - Static variable in class org.jmol.script.T
- wildcard - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- wildID - Variable in class org.jmol.shapespecial.Dipoles
- window - Static variable in class org.jmol.script.T
- windowActivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowActivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowActivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.Splash.WindowListener
- windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowcentered - Static variable in class org.jmol.script.T
- windowCentered - Variable in class org.jmol.viewer.TransformManager
- windowCenteredFlag - Variable in class org.jmol.modelset.Orientation
- windowClosed(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowClosed(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowClosed(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowClosing(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowClosing(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowClosing(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.janocchio.CoupleTable.CoupleListWindowListener
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.janocchio.NoeTable.NoeListWindowListener
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementListWindowListener
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog.PovrayWindowListener
-
Closes the dialog when window closing event occurs.
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowClosing(HTMLElement) - Method in interface org.jmol.awtjs.swing.SwingController
-
Called by clicking the [x] in the corner of the dialog; send a notification back to the manager via processWindowClosing(key) var id = $("div.JDialog:has(#" + element.id + ")")[0].id var dialog = Jmol.Swing.htDialogs[id]; dialog.manager.processWindowClosing(dialog.registryKey);
- windowDeactivated(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowDeactivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowDeactivated(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowDeiconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowDeiconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowDeiconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowHeight - Variable in class org.jmol.awtjs2d.JsG2D
- windowHeight - Variable in class org.jmol.g3d.Platform3D
- windowHeight - Variable in class org.jmol.modelset.Text
- windowHeight - Variable in class org.jmol.util.GData
- windowIconified(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowIconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowIconified(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- WindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.Splash.WindowListener
- windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowName - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- windowName - Static variable in class org.openscience.jmol.app.webexport.WebExport
- windowOpened(WindowEvent) - Method in class org.jmol.console.ImageDialog
- windowOpened(WindowEvent) - Method in class org.jmol.console.JmolConsole
- windowOpened(WindowEvent) - Method in class org.jmol.console.ScriptEditor
- windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
- windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
- windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowSize - Variable in class org.jmol.g3d.Platform3D
- windowStateChanged(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
- windowWidth - Variable in class org.jmol.awtjs2d.JsG2D
- windowWidth - Variable in class org.jmol.g3d.Platform3D
- windowWidth - Variable in class org.jmol.modelset.Text
- windowWidth - Variable in class org.jmol.util.GData
- wing - Variable in class org.jmol.renderbio.BioMeshRenderer
- wing1 - Variable in class org.jmol.renderbio.BioMeshRenderer
- wingHermites - Variable in class org.jmol.renderbio.BioMeshRenderer
- wingT - Variable in class org.jmol.renderbio.BioMeshRenderer
- wingVectors - Variable in class org.jmol.modelsetbio.BioPolymer
- wingVectors - Variable in class org.jmol.renderbio.BioShapeRenderer
- wingVectors - Variable in class org.jmol.shapebio.BioShape
- wireframe - Static variable in class org.jmol.script.T
- wireframeOnly - Variable in class org.jmol.render.SticksRenderer
- wireframeOnly - Variable in class org.jmol.renderbio.BioShapeRenderer
- wireframerotation - Static variable in class org.jmol.script.T
- wireframeRotation - Variable in class org.jmol.viewer.GlobalSettings
- within - Static variable in class org.jmol.script.T
- within(float, P3, Lst<P3>) - Method in class org.jmol.util.BZone
- withinDistance2 - Variable in class org.jmol.shapesurface.Isosurface
- withinDistPoints(float, P3, P3[], P3[], BS, Object[]) - Static method in class org.jmol.bspt.PointIterator
-
carry out various functions of the within() script function
- withinPoints - Variable in class org.jmol.shapesurface.Isosurface
- wizard_prompt_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- WMATRIX - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- words - Variable in class org.jmol.popup.PopupResource
- working - Static variable in class org.jmol.g3d.TextRenderer
- wPlane - Variable in class org.jmol.util.MeshSlicer
- wrap_output - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
- wrapPathForAllFiles(String, String) - Method in class org.jmol.viewer.OutputManager
- write - Static variable in class org.jmol.script.T
- write(BS) - Method in class org.jmol.adapter.writers.CIFWriter
- write(BS) - Method in class org.jmol.adapter.writers.CMLWriter
- write(BS) - Method in class org.jmol.adapter.writers.PDBWriter
- write(BS) - Method in class org.jmol.adapter.writers.PWMATWriter
- write(BS) - Method in class org.jmol.adapter.writers.QCJSONWriter
- write(BS) - Method in class org.jmol.adapter.writers.XSFWriter
- write(BS) - Method in interface org.jmol.api.JmolWriter
- write(T[]) - Method in class org.jmol.scriptext.CmdExt
- write(IsosurfaceMesh, boolean) - Method in class org.jmol.shapesurface.PMeshWriter
- writeAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- WriteAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
- writeActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
- writeArray(Object) - Method in class org.jmol.util.JSONWriter
- writeAtoms(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeBonds(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeBoolean(Boolean) - Method in class org.jmol.util.JSONWriter
- writeChecked(SB, String) - Method in class org.jmol.adapter.writers.CIFWriter
-
see https://github.com/rcsb/ciftools-java/blob/master/src/main/java/org/rcsb/cif/text/TextCifWriter.java
- writeDataBlocks() - Method in class org.jmol.adapter.writers.PWMATWriter
- writeFacet(T3[], int[], int, int, int) - Method in class org.jmol.export._StlExporter
- writeFile(String, String) - Static method in class org.openscience.jvxl.Jvxl
- writeFile(String, String) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
- writeFileData(String, String, int, Object[]) - Method in class org.jmol.viewer.OutputManager
-
Generates file data and passes it on either to a FileOuputStream (Java) or via POSTing to a url using a ByteOutputStream (JavaScript)
- writeFileData(String, String, int, Object[]) - Method in class org.jmol.viewer.Viewer
- writeFileZipped(String[], byte[], int) - Static method in class org.openscience.jmol.app.webexport.WebPanel
- writeFloat(float) - Method in class org.jmol.export._StlExporter
- writeFrame(int, String[], Map<String, Object>, SB) - Method in class org.jmol.viewer.OutputManager
- writeGlobalBlocks() - Method in class org.jmol.adapter.writers.PWMATWriter
- writeGlobals - Variable in class org.jmol.adapter.writers.PWMATWriter
- writeHeader() - Method in class org.jmol.adapter.writers.PWMATWriter
- writeItem2(float[], String) - Method in class org.jmol.adapter.writers.PWMATWriter
- writeItems(String) - Method in class org.jmol.adapter.writers.PWMATWriter
- writeJob(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeJobMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeJobs() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeJSON() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeLattice() - Method in class org.jmol.adapter.writers.PWMATWriter
- writeLattice(String) - Method in class org.jmol.adapter.writers.XSFWriter
- writeList(List<Object>) - Method in class org.jmol.util.JSONWriter
- writeMacros() - Method in class org.jmol.export._PovrayExporter
- writeMacros2() - Method in class org.jmol.export._PovrayExporter
- writeMacrosAtom() - Method in class org.jmol.export._PovrayExporter
- writeMacrosBond() - Method in class org.jmol.export._PovrayExporter
- writeMacrosFinish() - Method in class org.jmol.export._PovrayExporter
- writeMagic() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeMagnetic() - Method in class org.jmol.adapter.writers.PWMATWriter
- writeMap(Map<String, Object>) - Method in class org.jmol.util.JSONWriter
- writeMapKeyValueUnits(String, Object, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeMOBases() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeMOData(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeModel(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeModelMetadata(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeModels() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeMoreData() - Method in class org.jmol.adapter.writers.PWMATWriter
- writeMsg(String) - Method in class org.jmol.scriptext.CmdExt
- writeMultiline(SB, String) - Method in class org.jmol.adapter.writers.CIFWriter
- writeNamfisAction - Static variable in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- WriteNamfisAction() - Constructor for class org.openscience.jmol.app.janocchio.NMR_JmolPanel.WriteNamfisAction
- writeNamfisFiles(String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- writeNmrData(File) - Method in class org.openscience.jmol.app.janocchio.NMR_JmolPanel
- writeNmrDataJSON(File) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- writeNull() - Method in class org.jmol.util.JSONWriter
- writeNullAsString - Variable in class org.jmol.util.JSONWriter
- writeNumber(Number) - Method in class org.jmol.util.JSONWriter
- writeObject(Object) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeObject(Object) - Method in class org.jmol.util.JSONWriter
- writePmeshHeader(int) - Method in class org.jmol.shapesurface.PMeshWriter
- writePoint(String, T3) - Method in class org.jmol.export._StlExporter
- writePositions() - Method in class org.jmol.adapter.writers.PWMATWriter
- writePrefix_Units(String, String) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeSchemaMetadata() - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeString(String) - Method in class org.jmol.util.JSONWriter
- writeString(String, SB) - Method in class org.jmol.util.JSONWriter
- writeTextFile(String, String) - Method in class org.jmol.api.JmolViewer
- writeTextFile(String, String) - Method in class org.jmol.viewer.Viewer
- writeToOutputChannel(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
-
From handleOutputToFile, write text, byte[], or image data to a file;
- writeTopology(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeVector(Vector<?>, PrintWriter) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- writeVectors(String) - Method in class org.jmol.adapter.writers.PWMATWriter
- writeVibrations(int) - Method in class org.jmol.adapter.writers.QCJSONWriter
- writeZip(Vector<String>, String) - Method in class org.openscience.jmol.app.janocchio.LoadMeasureThreadJSON
- writeZipFile(OC, Lst<Object>, String, String) - Method in class org.jmol.viewer.OutputManager
-
generic method to create a zip file based on http://www.exampledepot.com/egs/java.util.zip/CreateZip.html
- ws - Variable in class org.jmol.util.JSONWriter
- WV_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- WV_X - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- WV_Y - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
- WV_Z - Static variable in class org.jmol.adapter.readers.cif.MSCifParser
X
- x - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- x - Variable in class org.jmol.quantum.SlaterData
- x - Variable in class org.jmol.render.SticksRenderer
- x - Static variable in class org.jmol.script.T
- x - Variable in class org.jmol.shape.Frank
- x - Variable in class org.jmol.util.Rectangle
- x - Variable in class org.jmol.viewer.MotionPoint
- x - Variable in class org.jmol.viewer.MouseState
- X - Variable in class org.jmol.quantum.QuantumCalculation
- X - Static variable in class org.jmol.util.BoxInfo
- x0 - Variable in class org.jmol.rendercgo.CGORenderer
-
UV mapping min/max x and y
- x1 - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- x1t - Variable in class org.jmol.g3d.LineRenderer
- x2 - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- X2 - Variable in class org.jmol.quantum.QuantumCalculation
- x2t - Variable in class org.jmol.g3d.LineRenderer
- xa - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- xA - Variable in class org.jmol.g3d.CylinderRenderer
- xA - Variable in class org.jmol.render.SticksRenderer
- xAdj - Variable in class org.jmol.modelset.Text
- xAend - Variable in class org.jmol.g3d.CylinderRenderer
- xAf - Variable in class org.jmol.g3d.CylinderRenderer
- xAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
- xAxis1 - Variable in class org.jmol.render.SticksRenderer
- xAxis2 - Variable in class org.jmol.render.SticksRenderer
- xB - Variable in class org.jmol.render.SticksRenderer
- xBohr - Variable in class org.jmol.quantum.QuantumCalculation
- xcrysDenContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- XcrysdenReader - Class in org.jmol.adapter.readers.xtal
- XcrysdenReader() - Constructor for class org.jmol.adapter.readers.xtal.XcrysdenReader
- xEndcap - Variable in class org.jmol.g3d.CylinderRenderer
- xGT - Static variable in class org.jmol.util.GData
- xIndex - Variable in class org.jmol.jvxl.readers.MapFileReader
- xLast - Variable in class org.jmol.util.GData
- xlateAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- xLight - Variable in class org.jmol.util.Shader
- xLT - Static variable in class org.jmol.util.GData
- xMax - Variable in class org.jmol.quantum.QuantumCalculation
- xMin - Variable in class org.jmol.quantum.QuantumCalculation
- XmlArgusReader - Class in org.jmol.adapter.readers.xml
-
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
- XmlArgusReader() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
- XmlChem3dReader - Class in org.jmol.adapter.readers.xml
-
An chem3d c3xml reader
- XmlChem3dReader() - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader
- XmlChemDrawReader - Class in org.jmol.adapter.readers.xml
-
An chem3d c3xml reader
- XmlChemDrawReader() - Constructor for class org.jmol.adapter.readers.xml.XmlChemDrawReader
- XmlCmlReader - Class in org.jmol.adapter.readers.xml
-
A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.
- XmlCmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
- xmlContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- xmlData - Variable in class org.jmol.jvxl.data.VolumeData
- XmlHandler - Class in org.jmol.adapter.readers.xml
-
a SAX handler -- Java only
- XmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlHandler
- XmlMagResReader - Class in org.jmol.adapter.readers.xml
- XmlMagResReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMagResReader
- XmlMolproReader - Class in org.jmol.adapter.readers.xml
-
A Molpro 2005 reader
- XmlMolproReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader
- XmlMOReader - Class in org.jmol.adapter.readers.xml
-
An abstract class accessing MOReader -- currently just for XmlMolproReader only.
- XmlMOReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMOReader
- XmlOdysseyReader - Class in org.jmol.adapter.readers.xml
-
An Odyssey xodydata reader
- XmlOdysseyReader() - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader
- XmlQEReader - Class in org.jmol.adapter.readers.xml
-
QuantumEspresso XML reader
- XmlQEReader() - Constructor for class org.jmol.adapter.readers.xml.XmlQEReader
- xmlReader - Variable in class org.jmol.adapter.readers.xml.XmlHandler
- XmlReader - Class in org.jmol.adapter.readers.xml
-
A generic XML reader template -- by itself, does nothing.
- XmlReader - Class in org.jmol.jvxl.readers
- XmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlReader
- XmlReader(BufferedReader) - Constructor for class org.jmol.jvxl.readers.XmlReader
- XmlReader.NVPair - Class in org.jmol.adapter.readers.xml
- xmlStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
- XmlVaspReader - Class in org.jmol.adapter.readers.xml
-
Vasp vasprun.xml reader
- XmlVaspReader() - Constructor for class org.jmol.adapter.readers.xml.XmlVaspReader
- XmlXsdReader - Class in org.jmol.adapter.readers.xml
-
An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09
- XmlXsdReader() - Constructor for class org.jmol.adapter.readers.xml.XmlXsdReader
- xNav - Variable in class org.jmol.modelset.Orientation
- xNav - Variable in class org.jmol.thread.MoveToThread
- XplorReader - Class in org.jmol.jvxl.readers
- XplorReader() - Constructor for class org.jmol.jvxl.readers.XplorReader
- xpos - Variable in class org.jmol.render.UccageRenderer
- xPt - Variable in class org.jmol.script.ScriptMathProcessor
- xr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
- XsfReader - Class in org.jmol.jvxl.readers
- XsfReader() - Constructor for class org.jmol.jvxl.readers.XsfReader
- XSFWriter - Class in org.jmol.adapter.writers
-
An XCrysDen XSF writer.
- XSFWriter() - Constructor for class org.jmol.adapter.writers.XSFWriter
- xStack - Variable in class org.jmol.script.ScriptMathProcessor
- XTAL_MODE - Static variable in class org.jmol.modelkit.ModelKit
- xtalHoverLabel - Variable in class org.jmol.modelkit.ModelKit
- xtalSymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollection
- XtalSymmetry - Class in org.jmol.adapter.smarter
-
A class used by AtomSetCollection for building the symmetry of a model and generating new atoms based on that symmetry.
- XtalSymmetry() - Constructor for class org.jmol.adapter.smarter.XtalSymmetry
- xTip - Variable in class org.jmol.g3d.CylinderRenderer
- XtlWriter - Class in org.jmol.adapter.writers
- XtlWriter() - Constructor for class org.jmol.adapter.writers.XtlWriter
- xTrans - Variable in class org.jmol.modelset.Orientation
- xTrans - Variable in class org.jmol.navigate.Navigator
- xTrans - Variable in class org.jmol.thread.MoveToThread
- xTransDelta - Variable in class org.jmol.navigate.Navigator
- xTranslationFraction - Variable in class org.jmol.viewer.TransformManager
- xTransStart - Variable in class org.jmol.navigate.Navigator
- xVdwClash - Variable in class org.jmol.util.ContactPair
- xWhenPressed - Variable in class org.jmol.awt.Mouse
- xWhenPressed - Variable in class org.jmol.awtjs2d.Mouse
- xy - Variable in class org.jmol.render.LabelsRenderer
- xy - Variable in class org.jmol.shape.Hover
- XY_RANGE - Static variable in class org.jmol.viewer.ActionManager
- XY_THREASHOLD - Static variable in class org.jmol.shape.Sticks
- XY_ZTOP - Static variable in class org.jmol.viewer.JC
- xyCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
- xypParameter(int) - Method in class org.jmol.script.ScriptParam
- xyz - Variable in class org.jmol.adapter.readers.xtal.OptimadeReader
- xyz - Variable in class org.jmol.atomdata.AtomData
- xyz - Variable in class org.jmol.modelset.Text
- xyz - Static variable in class org.jmol.script.T
- xyz - Variable in class org.jmol.symmetry.SymmetryOperation
- XYZ - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
- XYZ - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
- XYZ - Static variable in class org.jmol.util.BoxInfo
- xyzBohr - Variable in class org.jmol.adapter.readers.quantum.OrcaReader
- xyzBohr - Variable in class org.jmol.adapter.readers.simple.OrcaReader
- xyzCanonical - Variable in class org.jmol.symmetry.SymmetryOperation
- xyzFraction12(float, int, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
- xyzfRaster - Variable in class org.jmol.g3d.CylinderRenderer
- xyzIsSlabbedInternal(T3) - Method in class org.jmol.viewer.TransformManager
- xyzList - Variable in class org.jmol.symmetry.SpaceGroup
- xyzMax - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- xyzMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
- xyzMin - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
- xyzMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
- xyzOriginal - Variable in class org.jmol.symmetry.SymmetryOperation
- xyzpParameter(int) - Method in class org.jmol.script.ScriptParam
- XyzReader - Class in org.jmol.adapter.readers.molxyz
-
Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c
- XyzReader() - Constructor for class org.jmol.adapter.readers.molxyz.XyzReader
- xyzStart - Variable in class org.jmol.jvxl.readers.MapFileReader
- xyzToVoxelPt(float, float, float, T3i) - Method in class org.jmol.jvxl.data.VolumeData
- xyztRaster - Variable in class org.jmol.g3d.CylinderRenderer
Y
- y - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- y - Variable in class org.jmol.quantum.SlaterData
- y - Variable in class org.jmol.render.SticksRenderer
- y - Static variable in class org.jmol.script.T
- y - Variable in class org.jmol.shape.Frank
- y - Variable in class org.jmol.util.Rectangle
- y - Variable in class org.jmol.viewer.MotionPoint
- y - Variable in class org.jmol.viewer.MouseState
- Y - Variable in class org.jmol.quantum.QuantumCalculation
- Y - Static variable in class org.jmol.util.BoxInfo
- y0 - Variable in class org.jmol.modelset.Text
- y0 - Variable in class org.jmol.rendercgo.CGORenderer
-
UV mapping min/max x and y
- y1 - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- y1t - Variable in class org.jmol.g3d.LineRenderer
- y2 - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- Y2 - Variable in class org.jmol.quantum.QuantumCalculation
- y2t - Variable in class org.jmol.g3d.LineRenderer
- ya - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- yA - Variable in class org.jmol.g3d.CylinderRenderer
- yA - Variable in class org.jmol.render.SticksRenderer
- yAdj - Variable in class org.jmol.modelset.Text
- yAend - Variable in class org.jmol.g3d.CylinderRenderer
- yAf - Variable in class org.jmol.g3d.CylinderRenderer
- yAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
- yAxis1 - Variable in class org.jmol.render.SticksRenderer
- yAxis2 - Variable in class org.jmol.render.SticksRenderer
- yB - Variable in class org.jmol.render.SticksRenderer
- yBohr - Variable in class org.jmol.quantum.QuantumCalculation
- yellow - Variable in class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- YELLOW - Static variable in class org.jmol.util.C
- yellowField - Variable in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- yellowField - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- yellowFieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- yellowFieldActionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- yellowLabel - Variable in class org.openscience.jmol.app.janocchio.CoupleColourSelectionPanel
- yellowLabel - Variable in class org.openscience.jmol.app.janocchio.NoeColourSelectionPanel
- yellowLevel - Variable in class org.openscience.jmol.app.janocchio.NMRTableCellRenderer
- yellowValue - Variable in class org.openscience.jmol.app.janocchio.CoupleTable
- yellowValue - Variable in class org.openscience.jmol.app.janocchio.NoeTable
- yEndcap - Variable in class org.jmol.g3d.CylinderRenderer
- yGT - Static variable in class org.jmol.util.GData
- yIndex - Variable in class org.jmol.jvxl.readers.MapFileReader
- yLast - Variable in class org.jmol.util.GData
- yLight - Variable in class org.jmol.util.Shader
- yLT - Static variable in class org.jmol.util.GData
- yMax - Variable in class org.jmol.quantum.QuantumCalculation
- yMin - Variable in class org.jmol.quantum.QuantumCalculation
- yNav - Variable in class org.jmol.modelset.Orientation
- yNav - Variable in class org.jmol.thread.MoveToThread
- ypos - Variable in class org.jmol.render.UccageRenderer
- yTip - Variable in class org.jmol.g3d.CylinderRenderer
- yTrans - Variable in class org.jmol.modelset.Orientation
- yTrans - Variable in class org.jmol.navigate.Navigator
- yTrans - Variable in class org.jmol.thread.MoveToThread
- yTransDelta - Variable in class org.jmol.navigate.Navigator
- yTranslationFraction - Variable in class org.jmol.viewer.TransformManager
- yTransStart - Variable in class org.jmol.navigate.Navigator
- yWhenPressed - Variable in class org.jmol.awt.Mouse
- yWhenPressed - Variable in class org.jmol.awtjs2d.Mouse
- yxNext - Variable in class org.jmol.util.MeshCapper.CapVertex
-
Y-X scan queue forward link
- yzCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
- yzCount - Variable in class org.jmol.jvxl.data.VolumeData
- yzCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
- yzCount - Variable in class org.jmol.quantum.NciCalculation
- yzPlanePts - Static variable in class org.jmol.jvxl.calc.MarchingCubes
- yzPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
- yzPlanes - Variable in class org.jmol.jvxl.readers.SurfaceReader
- yzPlanesRaw - Variable in class org.jmol.jvxl.readers.VolumeFileReader
- yzPlanesRaw - Variable in class org.jmol.quantum.NciCalculation
- yzPlanesRho - Variable in class org.jmol.quantum.NciCalculation
Z
- z - Variable in class org.jmol.modelset.Text
- z - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- z - Variable in class org.jmol.quantum.SlaterData
- z - Variable in class org.jmol.render.SticksRenderer
- z - Static variable in class org.jmol.script.T
- Z - Variable in class org.jmol.quantum.QuantumCalculation
- Z - Static variable in class org.jmol.util.BoxInfo
- z1 - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- z1t - Variable in class org.jmol.g3d.LineRenderer
- z2 - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- Z2 - Variable in class org.jmol.quantum.QuantumCalculation
- z2t - Variable in class org.jmol.g3d.LineRenderer
- za - Variable in class org.jmol.quantum.NMRNoeMatrix.NOEAtom
- zA - Variable in class org.jmol.g3d.CylinderRenderer
- zA - Variable in class org.jmol.render.SticksRenderer
- zAend - Variable in class org.jmol.g3d.CylinderRenderer
- zAf - Variable in class org.jmol.g3d.CylinderRenderer
- zAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
- zap - Static variable in class org.jmol.script.T
- zap() - Method in interface org.jmol.api.JmolAppConsoleInterface
- zap() - Method in class org.jmol.console.GenericConsole
- zap() - Method in class org.jmol.viewer.ModelManager
- zap(boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
- ZAP_TITLE - Static variable in class org.jmol.viewer.JC
- zapMsg(String) - Method in class org.jmol.viewer.Viewer
- ZAPPED - Enum constant in enum org.jmol.c.FIL
- zb - Variable in class org.jmol.g3d.Pixelator
- zB - Variable in class org.jmol.render.SticksRenderer
- zBohr - Variable in class org.jmol.quantum.QuantumCalculation
- zBox - Variable in class org.jmol.render.LabelsRenderer
- zbuf - Variable in class org.jmol.g3d.Graphics3D
- zbuf - Variable in class org.jmol.g3d.SphereRenderer
- zBuffer - Variable in class org.jmol.g3d.Platform3D
- zBufferT - Variable in class org.jmol.g3d.Platform3D
- zbufT - Variable in class org.jmol.g3d.Graphics3D
- zdepth - Static variable in class org.jmol.script.T
- zDepth - Variable in class org.jmol.g3d.PixelatorShaded
- zDepth - Variable in class org.jmol.viewer.GlobalSettings
- zDepthPercentSetting - Variable in class org.jmol.viewer.TransformManager
- zDepthToPercent(int) - Method in class org.jmol.viewer.TransformManager
- zDepthValue - Variable in class org.jmol.viewer.TransformManager
- zEndcap - Variable in class org.jmol.g3d.CylinderRenderer
- zero - Variable in class org.jmol.viewer.TransformManager4D
- ZERO - Static variable in class org.jmol.adapter.readers.cif.TopoCifParser
- zeroBase - Variable in class org.jmol.modelset.AtomIteratorWithinModel
- zerobasedxyzrasmol - Static variable in class org.jmol.script.T
- zeroBasedXyzRasmol - Variable in class org.jmol.viewer.GlobalSettings
- zeroFontId - Variable in class org.jmol.shape.Labels
- zeroPad - Variable in class org.jmol.modelset.LabelToken
- zeta - Variable in class org.jmol.quantum.SlaterData
- zeta1 - Static variable in class org.jmol.quantum.NciCalculation
- zeta2 - Static variable in class org.jmol.quantum.NciCalculation
- zeta3 - Static variable in class org.jmol.quantum.NciCalculation
- zGT - Static variable in class org.jmol.util.GData
- zIndex - Variable in class org.jmol.awtjs.swing.JDialog
- zIndex - Variable in class org.jmol.jvxl.readers.MapFileReader
- zipFileName - Variable in class org.jmol.console.ScriptEditor
- zLight - Variable in class org.jmol.util.Shader
- zLT - Static variable in class org.jmol.util.GData
- zMargin - Variable in class org.jmol.g3d.Graphics3D
- zMax - Variable in class org.jmol.quantum.QuantumCalculation
- zMin - Variable in class org.jmol.quantum.QuantumCalculation
- zmPct - Variable in class org.jmol.viewer.TransformManager
-
zoom percent zmPct is the current displayed zoom value, AFTER rendering; may not be the same as zmPctSet, particularly if zoom is not enabled
- zmPctSet - Variable in class org.jmol.viewer.TransformManager
-
zoom percent setting the current setting of zoom; may not be the same as zmPct, particularly if zoom is not enabled
- znuc - Variable in class org.jmol.quantum.QMAtom
- znucl - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
- zOffset - Variable in class org.jmol.viewer.TransformManager4D
- zoneIndex - Variable in class org.jmol.util.BZone
- zoom - Variable in class org.jmol.modelset.Orientation
- zoom - Static variable in class org.jmol.script.T
- zoom - Variable in class org.jmol.thread.MoveToThread
- ZOOM_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
- ZOOM_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
- zoomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
- zoomBy(int) - Method in class org.jmol.viewer.TransformManager
-
standard response to user mouse vertical shift-drag
- zoomBy(int) - Method in class org.jmol.viewer.Viewer
- zoomByFactor(float, int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
- zoomByFactor(float, int, int) - Method in class org.jmol.navigate.Navigator
- zoomByFactor(float, int, int) - Method in class org.jmol.viewer.TransformManager
- zoomByFactor(float, int, int) - Method in class org.jmol.viewer.Viewer
- zoomByFactor(int, int, int) - Method in class org.jmol.viewer.ActionManager
- zoomByPercent(float) - Method in class org.jmol.viewer.TransformManager
- zoomenabled - Static variable in class org.jmol.script.T
- zoomEnabled - Variable in class org.jmol.viewer.TransformManager
- zoomFactor - Variable in class org.jmol.viewer.TransformManager
- zoomheight - Static variable in class org.jmol.script.T
- zoomHeight - Variable in class org.jmol.viewer.GlobalSettings
- zoomHeight - Variable in class org.jmol.viewer.TransformManager
- zoomlarge - Static variable in class org.jmol.script.T
- zoomLarge - Variable in class org.jmol.viewer.GlobalSettings
- zoomPercent0 - Variable in class org.jmol.thread.MoveToThread
- zoomRatio - Variable in class org.jmol.viewer.TransformManager
- zoomTo - Static variable in class org.jmol.script.T
- zoomTo(int) - Method in class org.jmol.viewer.ActionManager
- zoomToPercent(float) - Method in class org.jmol.viewer.TransformManager
- zoomTrigger - Variable in class org.jmol.viewer.ActionManager
- zroot - Variable in class org.jmol.g3d.SphereRenderer
- zshade - Static variable in class org.jmol.script.T
- zShadeEnabled - Variable in class org.jmol.viewer.TransformManager
- zshadepower - Static variable in class org.jmol.script.T
- zShadePower - Variable in class org.jmol.g3d.PixelatorShaded
- zShadePower - Variable in class org.jmol.viewer.GlobalSettings
- zslab - Static variable in class org.jmol.script.T
- zSlab - Variable in class org.jmol.g3d.PixelatorShaded
- zSlab - Variable in class org.jmol.modelset.Text
- zSlab - Variable in class org.jmol.render.LabelsRenderer
- zSlab - Variable in class org.jmol.viewer.GlobalSettings
- zSlabPercentSetting - Variable in class org.jmol.viewer.TransformManager
- zSlabPoint - Variable in class org.jmol.viewer.TransformManager
- zSlabToPercent(int) - Method in class org.jmol.viewer.TransformManager
- zSlabValue - Variable in class org.jmol.viewer.TransformManager
- zTip - Variable in class org.jmol.g3d.CylinderRenderer
- zValueFromPercent(int) - Method in class org.jmol.viewer.TransformManager
_
- __ - Static variable in class org.jmol.script.T
- ___Exporter - Class in org.jmol.export
- ___Exporter() - Constructor for class org.jmol.export.___Exporter
- __CartesianExporter - Class in org.jmol.export
- __CartesianExporter() - Constructor for class org.jmol.export.__CartesianExporter
- __RayTracerExporter - Class in org.jmol.export
- __RayTracerExporter() - Constructor for class org.jmol.export.__RayTracerExporter
- _1_4pi - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
- _8PI2_ - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
- _activeLevels - Static variable in class org.jmol.util.Logger
- _AM1_C - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
-
Data from MOPAC F90 source parameters_for_xxx_C.F90 for use in GamessReader.
- _args - Static variable in class org.jmol.script.T
- _args - Variable in class org.jmol.viewer.StatusManager
- _atomPickedCallback(int, int) - Method in interface org.jmol.api.js.JSmolAppletObject
- _birth - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
- _id1 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _id2 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _IdtfExporter - Class in org.jmol.export
- _IdtfExporter() - Constructor for class org.jmol.export._IdtfExporter
- _logger - Static variable in class org.jmol.util.Logger
- _logLevel - Static variable in class org.jmol.util.Logger
- _MayaExporter - Class in org.jmol.export
- _MayaExporter() - Constructor for class org.jmol.export._MayaExporter
- _MNDO_C - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- _myId - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
- _myType - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _nCurrent - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
- _nMoves - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
- _nTraces - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _ObjExporter - Class in org.jmol.export
-
Class to export Wavefront OBJ files.
- _ObjExporter() - Constructor for class org.jmol.export._ObjExporter
- _offset - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _offsetCentroid - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _PM3_C - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- _PM6_C - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- _PM7_C - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- _PovrayExporter - Class in org.jmol.export
- _PovrayExporter() - Constructor for class org.jmol.export._PovrayExporter
- _refresh() - Method in interface org.jmol.api.js.JSmolAppletObject
- _RM1_C - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
- _rotation - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _scale - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _StlExporter - Class in org.jmol.export
-
STereoLithography file format exporter for 3D printing.
- _StlExporter() - Constructor for class org.jmol.export._StlExporter
- _TachyonExporter - Class in org.jmol.export
- _TachyonExporter() - Constructor for class org.jmol.export._TachyonExporter
- _traces1 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _traces2 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
- _visible - Variable in class org.jmol.awtjs.swing.Component
- _VrmlExporter - Class in org.jmol.export
-
A basic VRML generator.
- _VrmlExporter() - Constructor for class org.jmol.export._VrmlExporter
- _X3dExporter - Class in org.jmol.export
- _X3dExporter() - Constructor for class org.jmol.export._X3dExporter
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