Package org.jmol.adapter.readers.xml
Class XmlMOReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xml.XmlReader
org.jmol.adapter.readers.xml.XmlCmlReader
org.jmol.adapter.readers.xml.XmlMOReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
XmlMolproReader
An abstract class accessing MOReader -- currently just for XmlMolproReader only.
Several assumptions here.
- Author:
- hansonr Bob Hanson hansonr@stolaf.edu
-
Field Summary
FieldsModifier and TypeFieldDescriptionprivate String[]
private javajs.util.Lst<float[]>
private String
private String[]
private String
private int
protected String
protected String
protected String
protected String
private int
private int
protected boolean
private int
private boolean
private javajs.util.Lst<javajs.util.Lst<float[]>>
private int
private int
private int
private int
private MOReader
private float
private float
private boolean
private int
Fields inherited from class org.jmol.adapter.readers.xml.XmlCmlReader
ASSOCIATION, CML, CRYSTAL, CRYSTAL_SCALAR, CRYSTAL_SYMMETRY, CRYSTAL_SYMMETRY_TRANSFORM3, htModelAtomMap, LATTICE_VECTOR, MODULE, MOLECULE, MOLECULE_ATOM, MOLECULE_ATOM_ARRAY, MOLECULE_ATOM_BUILTIN, MOLECULE_ATOM_SCALAR, MOLECULE_BOND, MOLECULE_BOND_ARRAY, MOLECULE_BOND_BUILTIN, MOLECULE_BOND_STEREO, MOLECULE_FORMULA, moleculeID, processing, START, state, SYMMETRY, tokens
Fields inherited from class org.jmol.adapter.readers.xml.XmlReader
atom, atts, bond, chars, keepChars, parent
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate void
private String[]
protected boolean
processEndMO
(String localName) protected boolean
processStartMO
(String localName) protected void
processXml
(XmlReader parent, Object saxReader) the current stateMethods inherited from class org.jmol.adapter.readers.xml.XmlCmlReader
applySymmetryAndSetTrajectory, breakOutAtomTokens, breakOutBondTokens, checkAtomArrayLength, checkBondArrayLength, endDocument, processEnd2, processEndElement, processStart2, processStartElement
Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
createDomNodeJS, finalizeSubclassReader, initCML, initializeReader, processDOM, processXml2, setKeepChars
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
-
Field Details
-
moReader
-
skipMOs
private boolean skipMOs -
htSlaterIDs
-
basisData
private javajs.util.Lst<float[]> basisData -
basisId
-
isSpherical
private boolean isSpherical -
minL
private int minL -
maxL
private int maxL -
basisIds
-
basisAtoms
-
orbOcc
private float orbOcc -
orbEnergy
private float orbEnergy -
gaussianCount
private int gaussianCount -
slaterCount
private int slaterCount -
coefCount
private int coefCount -
groupCount
private int groupCount -
lstGaussians
private javajs.util.Lst<javajs.util.Lst<float[]>> lstGaussians -
moCount
private int moCount -
calcType
-
iModelMO
private int iModelMO -
dclist
-
dslist
-
fclist
-
fslist
-
iHaveCoefMaps
protected boolean iHaveCoefMaps -
maxContraction
private int maxContraction
-
-
Constructor Details
-
XmlMOReader
public XmlMOReader()
-
-
Method Details
-
processXml
Description copied from class:XmlCmlReader
the current state- Overrides:
processXml
in classXmlCmlReader
- Throws:
Exception
-
processStartMO
-
processEndMO
-
buildSlaters
private void buildSlaters() -
getXlink
-