All Classes and Interfaces
Class
Description
TODO: adf-2007.out causes failure reading basis functions
A reader for ADF output.
A reader for various AFLOW file types.
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).
TRIPOS simple Alchemy reader.
A reader for AMPAC output.
A parser for output from 3DNA web service.
An interface to Jmol.Console.
note: YOU MUST RELEASE THE ITERATOR
maps property data
A JFrame that allows for choosing an Atomset to view.
Objects in the AtomSetChooser tree
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
a subclass of File allowing extension to JavaScript
private to org.jmol.awt
methods required by Jmol that access java.awt.Font
private to org.jmol.awt
generic 2D drawing methods -- AWT version
all popup-related awt/swing class references are in this file.
A javax.swing implementation of SwingComponent
that mirrors org.jmol.awtjs.swing for compatibility with
compilation with java2script.
A simple class that throws up a white rectangle that has a single centered
label.
Binary CIF density reader.
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.
DCD binary trajectory file reader.
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.
a class used by ModelLoader to handle all loading
of operations specific to PDB/mmCIF files.
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.
The BoxInfo class holds critical information about boundboxes.
A class for cataloging ladder bridges in a DSSP calculation
A Binary Space Partitioning Forest
a Binary Space Partitioning Tree
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
Note: Color table is now in javajs/util/CU.java
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.
A reader for TOPOS systre file Crystal Graph Data format.
Something like a PyMOL Compiled Graphical Object, but more interesting!
A Model is a collection of Chains of Groups of Atoms.
A legacy Chime-compatible messenger.
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
Preliminary Cif2 reader.
CIF density reader.
A true line-free CIF file reader for CIF files.
Allows checking specific blocks
e.g.
An XCrysDen XSF writer
see http://www.xcrysden.org/doc/XSF.html
A fully validated relatively efficient implementation of Cahn-Ingold-Prelog
rules for assigning R/S, M/P, and E/Z stereochemical descriptors.
A helper class to handle application-specific analysis and store
information needed by CIPChirality and CIPDataSmiles.
A subclass that allows Jmol processing of SMILES using
"...smiles...".find("SMILES","chirality")
An optional class to track digraph paths to decisions.
Implements flat circle drawing/filling routines.
An XCrysDen XSF writer
see http://www.xcrysden.org/doc/XSF.html
Implements a queue for a bash-like command history.
A reader of OUT and OUTP files for CRYSTAL
http://www.crystal.unito.it/
CSF file reader based on CIF idea -- fluid property fields.
Iterator used for finding all points within a box or a hemi-box
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.
Draws shaded cylinders in 3D.
change QS.MAX_TYPE_SUPPORTED if you implement this
adds spherical H orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds spherical I orbital contributions
adds 7 spherical F orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds 9 spherical G orbital contributions
adds 10 cartesian F orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds 15 cartesian G orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds 21 cartesian H orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds 28 cartesian I orbital contributions
Default implementation of the logger.
A reader for Dgrid BASISFILE data.
methods required by Jmol that access java.awt.Component
private to org.jmol.awt
methods required by Jmol that access java.awt.Component
private to org.jmol.awt
The original non-JSON parser for output from 3DNA web service.
A parser for output from 3DNA web service.
sort from smallest to largest absolute
the internal tree is made up of elements ...
FoldingAtHome json reader.
JFileChooser with possibility to fix size and location
A simple Dropping class to allow files to be dragged onto a target.
File previsualisation before opening
open a set of models residing in different files
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.
Provides font support using a int fid
(Font ID) as an index into font table.
A generic interface for font queries.
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
Reader for Gaussian fchk files
for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot)
also allows appended freq data
Reader for Gaussian 94/98/03/09 output files.
Reader for Gaussian Wfn files -- not implemented yet
A collection of all methods necessary for initialization of and communication with the applet.
The overall parent of all popup classes in Jmol and JSmol.
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
J2SRequireImport is needed because we use ArrayUtil in a static method
Reads Ghemical (
http://www.uku.fi/~thassine/ghemical)
molecular mechanics (*.mm1gp) files.
Provides high-level graphics primitives for 3D visualization for the software
renderers.
The essential container for every atom.
The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12
implementing translations in JavaScript
Problems identified (Bob Hanson) --
-- Coordinates for the asymmetric unit are conventional.
Enum for hydrogen bonding donor/acceptor type
Implementation of hermite curves for drawing smoothed curves
that pass through specified points.
The history file contains data from previous uses of Jmol.
The window.Event in HTML5
See SwingController.
Support for .hin, HyperChem's native file format.
methods required by Jmol that access java.awt.Image
private to org.jmol.awt
methods required by Jmol that access java.awt.Image
private to org.jmol.awt
This class adapts Richard Apodaca's 2020 molfile-to-inchi LLVM-derived Web Assembly
implementation of IUPAC InChI v.
Exception thrown for invalid SMILES String
A class to read a linear combination of cube file data.
Jaguar reader tested for the two samples files in CVS.
A reader for Jana M50+M40 file pairs.
A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS=
records
Designed by Robert Lancashire and Bob Hanson
specifications (by example here):
##$MODELS= acetophenone
DSViewer 3D 0
17 17 0 0 0 0 0 0 0 0999 V2000 ...
implementation of a JComponent
There is really no need here for awt.Dialog.
Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.
A simple implementation of a Swing JTextPane.
Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
The JmolAdapter interface defines the API used by the JmolViewer to
read external files and fetch atom properties necessary for rendering.
This is the API of methods that are available to JavaScript
via LiveConnect to the Jmol applet.
JmolData file reader, for a modified PDB format
An abstract popup class that is
instantiated for a given platform and
context as one of:
an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom
for use in finding molecules in models and SMILES strings
a class to store rendering information prior to finishing file loading,
specifically designed for reading PyMOL PSE files.
An abstract popup class that is
instantiated for a given platform and
context as one of:
Provides access to resources (for example, strings and images).
listen to atom selections in a Jmol Viewer
methods in JSmol JavaScript accessed in Jmol
JmolViewer is the main API for the Viewer class.
A class to output WebGL graphics.
A class that mimics java.io.File
methods required by Jmol that access java.awt.Font
private to org.jmol.awtjs2d
generic 2D drawing methods -- JavaScript version
a client of a JsonNioService -- just needs notices of the service shutting
down or indicating that a banner needs to be changed.
A class for interacting with Jmol over local sockets.
For menus, popup-related awt/swing class references are in this file.
and interface for JSpecView for the Jmol application
A simple implementation of a Swing JTextPane.
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
A leaf of Point3f objects in the bsp tree
Logger mechanism.
Interface used for the logging mechanism.
Amber Coordinate File Reader
not a stand-alone reader -- must be after COORD keyword in LOAD command
A reader for Amber Molecular Dynamics topology files --
requires subsequent COORD "xxxx.mdcrd" file
Calculates the difference between calculated and experimental values for coloring table
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.
Class to generate mesh data (faces, vertices, and normals) for several kinds
of generic meshes.
an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
not implemented -- would be a force toward a given position in space
mmCIF files are recognized prior to class creation.
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.
An abstract popup class that is instantiated for a given platform and context
as one of:
An abstract popup class that is instantiated for a given platform and context
as one of:
A class to allow for more complex vibrations and associated phenomena, such
as modulated crystals, including Fourier series, Crenel functions, and
sawtooth functions
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
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
3D only
A molecular structure and orbital reader for MolDen files.
A reader for MDLI mol and sdf files.
A class to maintain information about biomolecule groups that are (potentially)
part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.
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
Reads Mopac 2007 GRAPHF output files
Reads Mopac 93, 6, 7, 2002, or 2009 output files
General methods for reading molecular orbital data, including embedded output
from the NBO program.
formerly org.jmol.viewer.MouseManager14
methods required by Jmol that access java.awt.event
private to org.jmol.awt
JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now)
Modulated Structure Reader Interface
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
Navigator is a user input mechanism that utilizes the keypad to drive through
the model.
Implements some lost interfaces.
Class for calculating NOE intensities by full matrix relaxation approach.
Provides access to resources (for example, strings and images).
Nodes of the bspt.
Provides quantization of normalized vectors so that shading for
lighting calculations can be handled by a simple index lookup
extends CartoonRenderer for nucleics
A reader for NWChem 4.6
NWChem is a quantum chemistry program developed at
Pacific Northwest National Laboratory.
A (preliminary) reader for OPTIMADE resources.
Reads ORCA input and output files
Reads ORCA input and output files
P2N file reader.
Enum for animation mode.
PDB file reader.
An XCrysDen XSF writer
see http://www.xcrysden.org/doc/XSF.html
generic Python Pickle file reader
only utilizing records needed for PyMOL.
A class to create a "screened" translucent effect by
discarding pixels in a checkerboard fashion.
A class to do Z Shading of pixels.
Handle pixels in Pass 2 - Translucency
WebGL interface
JavaScript 2D canvas version requires Ajax-based URL stream processing.
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.
PMESH format created for Jmol.
A class called by reflection from IsosurfaceMesh from the Jmol command
WRITE xxxx.pmesh (ascii)
or
WRITE xxxx.pmb (binary)
Just a marker for resourceClass.getClass().getResource(resourceName);
Jmol now reads the PO files directly for its translations.
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)
A dialog for controling the creation of a povray input file from a Chemframe
and a display.
PQR file reader.
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.
The PropertyManager handles all operations relating to delivery of properties
with the getProperty() method, or its specifically cast forms
getPropertyString() or getPropertyJSON().
Reader for Psi3 output files.
crude PWmat atom.config reader
http://pwmatus.com/manual
A writer for PWMAT atom.config files.
PyMOL settings and constants.
PyMOL surface/mesh reader.
PyMOL PSE (binary Python session) file reader.
A class to allow manipulation of scenes dissociated from file loading.
A reader for Q-Chem 2.1 and 3.2
Q-Chem is a quantum chemistry program developed
by Q-Chem, Inc.
A molecular structure and orbital reader for MolDen files.
A very experimental class for writing QCJSON files.
Constants and static methods for quantum shells.
Allows modification of the planes prior to isosurface creation
Used by Noncovalent Interaction Calculation for progressive readers
Manages a list of recently opened files.
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.
Error handling for ScriptEvaluator, ScriptProcess, and ScriptParams
The ScriptExpr class holds the main functions for
processing mathematical and atom selection expressions.
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
The ScriptParam class holds methods used to parse parameters
in Jmol scripts.
the idea here is that the process { ...
An abstract class subclassed by ScriptCompiler taking care of the second
phase of syntax checking.
All functions.
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
A reader for SHELX output (RES) files.
SIESTA http://www.icmab.es/siesta/
minimal bond interface for SMILES and CIP
Just the bare minimum for CIP, and non-BioSMILES
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
SINGLE_POINT_GESTURE
only passes single-touch gestures.
This class represents an atom in a
SmilesMolecule
.Bond in a SmilesMolecule
Double bond, allene, square planar and tetrahedral stereochemistry only
not octahedral or trigonal bipyramidal.
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
Parses a SMILES string or SMARTS pattern to create a
SmilesSearch
.Ring of (tentatively) aromatic nodes and edges
a list of fused rings
A class to build and carry out a SMILES or SMARTS match
This class relates to stereochemical issues
A relatively simple space group finder given a unit cell.
A class to isolate Spartan file reading methods from the rest of Jmol.
Implements high performance rendering of shaded spheres.
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
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.
PolygonFileReader or VolumeFileReader
Class that holds the surface status information that the surface tool needs.
GUI for the Jmol surfaceTool
ScriptVariable class
SwingController is an interface that org.jmol.awtjs.swing classes will need.
A class to handle requests for information about space groups and symmetry
operations.
Script token class.
implementation for text rendering
simple Tinker format requires Tinker:: prefix:
load Tinker::mydata.xyz
1/2014 hansonr@stolaf.edu
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.
An adaptation of Marching Cubes that allows for indicating edges on triangles.
renders triangles
TWO_POINT_GESTURE
This gesture requires two points of contact, but its type is not initially
defined.
UHBD reader
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.
A reader for Accelrys V3000 files.
http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html
very simple reader of just the header information.
http://cms.mpi.univie.ac.at/vasp/
adjusted for AFLOW options - adding element names, environment radius on atom line
http://cms.mpi.univie.ac.at/vasp/
A class to allow for more complex vibrations and associated
phenomena, such as modulated crystals.
A molecular orbital reader for WebMO files.
A reader for Wein2k DFT files.
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/
Use this reader as a template for adding new XML readers.
An chem3d c3xml reader
An chem3d c3xml reader
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.
a SAX handler -- Java only
A Molpro 2005 reader
An abstract class accessing MOReader -- currently just for XmlMolproReader only.
An Odyssey xodydata reader
QuantumEspresso XML reader
A generic XML reader template -- by itself, does nothing.
Vasp vasprun.xml reader
An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/
Bob Hanson hansonr@stolaf.edu 6/3/09
An XCrysDen XSF writer.
A class used by AtomSetCollection for building the symmetry of a model and
generating new atoms based on that symmetry.
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
Class to export Wavefront OBJ files.
STereoLithography file format exporter
for 3D printing.
A basic VRML generator.