All Classes
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All Classes Interface Summary Class Summary Enum Summary Exception Summary Class Description AbinitReader AboutDialog AbstractButton AbstractTableModel ActionManager ActionManagerMT AdfReader TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.AFLOWReader A reader for various AFLOW file types.AimsReader 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).AlchemyReader TRIPOS simple Alchemy reader.AlphaMonomer AlphaPolymer AlphaPolymer.Code AminoMonomer AminoPolymer AmpacReader A reader for AMPAC output.AnimationManager AnimationThread Annotation AnnotationParser A parser for output from 3DNA web service.ApbsReader AppConsole AppletConsole AppletConsole An interface to Jmol.Console.AppletWrapper Using Applet only because originally there was the possibility of non-Swing versions of the JRE being used.ArrayListTransferHandler ASimpleJvxlWriter Atom Atom AtomCollection AtomData AtomDataReader AtomDataServer AtomIndexIterator note: YOU MUST RELEASE THE ITERATORAtomIterator AtomIteratorWithinModel AtomIteratorWithinModelSet AtomPropertyMapper maps property dataAtomSetChooser A JFrame that allows for choosing an Atomset to view.AtomSetChooser.AtomSet Objects in the AtomSetChooser treeAtomSetCollection AtomSetCollectionReader AtomSetObject AtomShape AtomType AviCreator AwtClipboard This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.AwtColor AwtFile a subclass of File allowing extension to JavaScript private to org.jmol.awtAwtFont methods required by Jmol that access java.awt.Font private to org.jmol.awtAwtG2D generic 2D drawing methods -- AWT versionAwtJmolPopup AwtModelKitPopup AwtPopupHelper all popup-related awt/swing class references are in this file.AwtSwingComponent A javax.swing implementation of SwingComponent that mirrors org.jmol.awtjs.swing for compatibility with compilation with java2script.Axes AxesRenderer Backbone BackboneRenderer Balls BallsRenderer BannerFrame A simple class that throws up a white rectangle that has a single centered label.BasePair BasisFunctionReader Bbcage BbcageRenderer BCifDensityReader Binary CIF density reader.BilbaoReader 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.BinaryDcdReader DCD binary trajectory file reader.Binding BioExt BioMeshRenderer BioModel BioModelSet BioPolymer 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.BioResolver a class used by ModelLoader to handle all loading of operations specific to PDB/mmCIF files.BioShape BioShapeCollection 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.BioShapeRenderer Bond Bond BondCollection BondIterator BondIterator BondIteratorSelected BondSet BorderLayout BoxInfo The BoxInfo class holds critical information about boundboxes.Bridge A class for cataloging ladder bridges in a DSSP calculationBspf A Binary Space Partitioning ForestBspt a Binary Space Partitioning TreeBSUtil ButtonGroup BZone class to represent and produce Brillouin zone polyhedra and Wigner-Seitz cells based on https://chemapps.stolaf.edu/jmol/jsmol/spt/ext/xtal/bz.sptC Note: Color table is now in javajs/util/CU.javaCageRenderer Calculation Calculations CalculationsMMFF CalculationsUFF CarbohydrateMonomer CarbohydratePolymer Cartoon CartoonRenderer CastepDensityReader CastepReader 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.CBK Cell CgdReader A reader for TOPOS systre file Crystal Graph Data format.CGO CGOMesh CGORenderer Something like a PyMOL Compiled Graphical Object, but more interesting!Chain A Model is a collection of Chains of Groups of Atoms.ChimeMessenger A legacy Chime-compatible messenger.Cif2DataParser 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_apiCif2Reader Preliminary Cif2 reader.CifDensityReader CIF density reader.CifReader A true line-free CIF file reader for CIF files.CIPChirality A fully validated relatively efficient implementation of Cahn-Ingold-Prelog rules for assigning R/S, M/P, and E/Z stereochemical descriptors.CIPData A helper class to handle application-specific analysis and store information needed by CIPChirality and CIPDataSmiles.CIPDataSmiles A subclass that allows Jmol processing of SMILES using "...smiles...".find("SMILES","chirality")CIPDataTracker An optional class to track digraph paths to decisions.CircleRenderer Implements flat circle drawing/filling routines.ClassPreloader CmdExt Color ColorEncoder ColorManager ColumnSelectionModel CommandHistory Implements a queue for a bash-like command history.CommandWatcherThread Component Connection Connections ConsoleTextArea Constraint Contact ContactPair ContactRenderer Container ContextToken CoupleColourSelectionPanel CoupleParameterSelectionPanel CoupleTable CreditsDialog CrystalReader A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/CsfReader CSF file reader based on CIF idea -- fluid property fields.CubeIterator Iterator used for finding all points within a box or a hemi-boxCubeReader 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 CylinderRenderer Draws shaded cylinders in 3D.DataAdder DataAdder11H change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical H orbital contributionsDataAdder13I change QS.MAX_TYPE_SUPPORTED if you implement this adds spherical I orbital contributionsDataAdder7F adds 7 spherical F orbital contributionsDataAdder9G change QS.MAX_TYPE_SUPPORTED if you implement this adds 9 spherical G orbital contributionsDataAdderF adds 10 cartesian F orbital contributionsDataAdderG change QS.MAX_TYPE_SUPPORTED if you implement this adds 15 cartesian G orbital contributionsDataAdderH change QS.MAX_TYPE_SUPPORTED if you implement this adds 21 cartesian H orbital contributionsDataAdderI change QS.MAX_TYPE_SUPPORTED if you implement this adds 28 cartesian I orbital contributionsDataManager DefaultLogger Default implementation of the logger.DelPhiBinaryReader DgridReader A reader for Dgrid BASISFILE data.Dialog Dialog.TypeFilter Dimension Dipole Dipoles DipolesRenderer Display methods required by Jmol that access java.awt.Component private to org.jmol.awtDisplay methods required by Jmol that access java.awt.Component private to org.jmol.awtDisplayPanel DmolReader Document DOMReader Dots DotsRenderer DragBinding Draw Draw.EnumDrawType DrawMesh DrawRenderer Dsn6BinaryReader DSSP DSSR0 The original non-JSON parser for output from 3DNA web service.DSSR1 A parser for output from 3DNA web service.Echo EchoRenderer Edge Edge.EnumBondOrder EfvetReader EigenSort sort from smallest to largest absoluteElement the internal tree is made up of elements ...Elements Ellipsoid Ellipsoids EllipsoidsRenderer EnterListener EnvelopeCalculation Escape EspressoReader Event EventManager Export3D FAHReader FoldingAtHome json reader.FFParam FIL FileChooser JFileChooser with possibility to fix size and locationFileDropper A simple Dropping class to allow files to be dragged onto a target.FileLoadThread FileManager FilePreview File previsualisation before openingFilePreview.FPPanel FileReader FileReader FilesReader open a set of models residing in different filesFlowLayout FoldingXyzReader 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.Font Provides font support using a byte fid (Font ID) as an index into font table.FontLineShape FontLineShapeRenderer FontManager A generic interface for font queries.ForceField ForceFieldMMFF 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 calculationForceFieldReader ForceFieldUFF FrameCounter FrameDeltaDisplay Frank FrankRenderer G3DRenderer GamessReader GamessUKReader GamessUSReader GaussianDialog GaussianFchkReader Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq dataGaussianReader Reader for Gaussian 94/98/03/09 output files.GaussianWfnReader Reader for Gaussian Wfn files -- not implemented yetGData GenericApplet A collection of all methods necessary for initialization of and communication with the applet, whether it be JavaScript or Java.GenericConsole GenericConsoleTextArea GenericFileInterface GenericGraphics GenericImageDialog GenericMenuInterface GenericMouseInterface GenericPlatform GenericPopup The overall parent of all popup classes in Jmol and JSmol.GenericTextArea GenNBOReader 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 structureGeodesic J2SRequireImport is needed because we use ArrayUtil in a static methodGeoSurface GeoSurfaceRenderer Gesture GhemicalMMReader Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.GlobalSettings Graphics3D Provides high-level graphics primitives for 3D visualization for the software renderers.Grid GridBagConstraints GridBagLayout GromacsReader Group The essential container for every atom.GT The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12 implementing translations in JavaScriptGuiMap GulpReader Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.HallInfo HallRotation HallRotationTerm HallTranslation Halos HalosRenderer HB Enum for hydrogen bonding donor/acceptor typeHBond Helix HelpDialog HermiteRenderer Implementation of hermite curves for drawing smoothed curves that pass through specified points.HistoryFile The history file contains data from previous uses of Jmol.Hover HoverRenderer HoverWatcherThread HTMLElement HTMLWindowEvent The window.Event in HTML5 See SwingController.HyperChemReader Support for .hin, HyperChem's native file format.Image methods required by Jmol that access java.awt.Image private to org.jmol.awtImage methods required by Jmol that access java.awt.Image private to org.jmol.awtImageDialog InputReader InputScannerThread Insets Int2IntHash Int2IntHashEntry Interface InvalidSmilesException Exception thrown for invalid SMILES StringIsoExt IsoFxyReader IsoFxyzReader IsoIntersectAtomReader IsoIntersectGridReader A class to read a linear combination of cube file data.IsoIntersectReader IsoMepReader IsoMlpReader IsoMOReader IsoPlaneReader IsoShapeReader IsoSolventReader Isosurface IsosurfaceMesh IsosurfaceRenderer JaguarReader Jaguar reader tested for the two samples files in CVS.JaguarReader JanaReader A reader for Jana M50+M40 file pairs.JButton JC JcampdxReader A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS= <Models> <ModelData id="acetophenone" type="MOL"> acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ...JCheckBox JCheckBoxMenuItem JComboBox<T> JComponent JComponentImp implementation of a JComponentJContentPane JDialog There is really no need here for awt.Dialog.JDXMOLParser Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.JEditorPane A simple implementation of a Swing JTextPane.JLabel JMenu JMenuItem JmeReader Jmol Jmol Java2Script rendition of Jmol using HTML5-only or WebGL-based graphicsJmol JmolAbstractButton JmolAdapter The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.JmolAdapterAtomIterator JmolAdapterBondIterator JmolAdapterStructureIterator JmolAnnotationParser JmolApp JmolAppAPI JmolAppConsoleInterface JmolApplet JmolAppletInterface This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.JmolAsyncException JmolAudio JmolAudioPlayer JmolBinding JmolButton JmolCallbackListener JmolChimeMessenger JmolConsole JmolData JmolDataManager JmolDataReader JmolData file reader, for a modified PDB formatJmolDialogInterface JmolDomReaderInterface JmolDropEditor JmolEnvCalc JmolFilesReaderInterface JmolFrame JmolGenericPopup An abstract popup class that is instantiated for a given platform and context as one of:JmolGestureServerInterface JmolGraphicsInterface JmolInstance JmolJDXMOLParser JmolJDXMOLReader JmolJniClientAdapter JmolJSpecView JmolLabel JmolMeasurementClient JmolModulationSet JmolMolecule an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES stringsJmolMovieCreatorInterface JmolMultiTouchAdapter JmolMultiTouchClient JmolMultiTouchClientAdapter JmolNavigatorInterface JmolNMRInterface JmolObject a class to store rendering information prior to finishing file loading, specifically designed for reading PyMOL PSE files.JmolPanel JmolPanel.ActionChangedListener JmolParallelProcessor JmolPatternMatcher JmolPdfCreatorInterface JmolPlugin JmolPopup An abstract popup class that is instantiated for a given platform and context as one of:JmolPropertyManager JmolRendererInterface JmolRepaintManager JmolResourceHandler Provides access to resources (for example, strings and images).JmolSceneGenerator JmolScriptEditorInterface JmolScriptEvaluator JmolScriptFunction JmolScriptManager JmolSelectionListener listen to atom selections in a Jmol ViewerJmolSparshClientAdapter JmolStateCreator JmolStatusListener JmolSyncInterface JmolThread JmolToggleButton JmolToJSmolInterface methods in JSmol JavaScript accessed in JmolJmolTouchSimulatorInterface JmolUtil JmolViewer JmolViewer is the main API for the Viewer class.JmolZipUtilities JPanel JPopupMenu JRadioButtonMenuItem JSConsole JSConsole JScrollPane JSExporter A class to output WebGL graphics.JSFile A class that mimics java.io.FileJSFont methods required by Jmol that access java.awt.Font private to org.jmol.awtjs2dJsG2D generic 2D drawing methods -- JavaScript versionJSJmolPopup JSModelKitPopup JSmolAppletObject JsonNioClient a client of a JsonNioService -- just needs notices of the service shutting down or indicating that a banner needs to be changed.JsonNioClient.TouchHandler JsonNioServer JsonNioService A class for interacting with Jmol over local sockets.JSONReader JSONWriter JSpecView JSplitPane JSPopupHelper For menus, popup-related awt/swing class references are in this file.JSVInterface and interface for JSpecView for the Jmol applicationJTable JTextField JTextPane A simple implementation of a Swing JTextPane.Jvxl JvxlCoder JvxlData JvxlReader JvxlWrite JvxlXmlReader KeyJCheckBox KeyJCheckBoxMenuItem KeyJMenu KeyJMenuItem KeyJRadioButtonMenuItem KinemageReader KioskFrame 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.orgLabels LabelSetter LabelsRenderer LabelToken Language LayoutManager LcaoCartoon LcaoCartoonRenderer Leaf A leaf of Point3f objects in the bsp treeLineRenderer ListSelectionModel LoadMeasureThread LoadMeasureThreadJSON Logger Logger mechanism.LoggerInterface Interface used for the logging mechanism.LogPanel LoopedStreams MagresReader MainPopupResourceBundle MapFileReader MarchingCubes MarchingSquares MathExt MdCrdReader Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD commandMdTopReader A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" fileMeasure MeasureCouple MeasureDist Calculates the difference between calculated and experimental values for coloring tableMeasurement MeasurementData MeasurementPending MeasurementTable MeasureNoe Measures MeasuresRenderer MepCalculation Mesh MeshCapper 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.MeshCollection MeshData Class to generate mesh data (faces, vertices, and normals) for several kinds of generic meshes.MeshData MeshDataServer MeshRenderer an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and IsosurfaceRendererMeshRibbon MeshRibbonRenderer MeshSlicer MeshSurface MinAngle MinAtom MinBond MinimizationThread Minimizer MinObject MinPosition not implemented -- would be a force toward a given position in spaceMinTorsion MlpCalculation MMCifReader mmCIF files are recognized prior to class creation.MMCifValidationParser MMConstraint MMFFAngleCalc MMFFDistanceCalc MMFFESCalc MMFFOOPCalc MMFFSBCalc MMFFTorsionCalc MMFFVDWCalc MMTFReader 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.MOCalculation Model ModelKitPopup An abstract popup class that is instantiated for a given platform and context as one of:ModelKitPopupResourceBundle ModelLoader ModelManager ModelSet Modulation A class to allow for more complex vibrations and associated phenomena, such as modulated crystals, including Fourier series, Crenel functions, and sawtooth functionsModulationSet 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 occupancyMol2Reader A minimal multi-file reader for TRIPOS SYBYL mol2 files.Mol3DReader 3D onlyMoldenReader A molecular structure and orbital reader for MolDen files.MolecularOrbital MolecularOrbitalRenderer Molecules MolReader A reader for MDLI mol and sdf files.MolWriter MonitorInputStream Monomer A class to maintain information about biomolecule groups that are (potentially) part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.MopacArchiveReader 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 cellMopacGraphfReader Reads Mopac 2007 GRAPHF output filesMopacReader Reads Mopac 93, 6, 7, 2002, or 2009 output filesMopacSlaterReader MOReader General methods for reading molecular orbital data, including embedded output from the NBO program.MotionPoint Mouse formerly org.jmol.viewer.MouseManager14 methods required by Jmol that access java.awt.event private to org.jmol.awtMouse JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now)MouseState MoveToThread MrcBinaryReader MSCifParser MSInterface Modulated Structure Reader InterfaceMsmsReader MSRdr 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_1MyFileFilter NamfisReader NamfisSaver Navigator Navigator is a user input mechanism that utilizes the keypad to drive through the model.NBO NBOParser NBORenderer NciCalculation NffReader Nmr NMR_DisplayPanel NMR_JmolPanel NMR_Viewer Implements some lost interfaces.NmrApplet NMRCalculation NmrGuiMap NmrMolecule NMRNoeMatrix Class for calculating NOE intensities by full matrix relaxation approach.NMRNoeMatrix.NOEAtom NMRNoeMatrix.NOEParams NmrPlugin NmrReader NmrReaderThread NmrResourceHandler Provides access to resources (for example, strings and images).NmrSaver NMRTableCellRenderer Node Nodes of the bspt.Node NoeColourSelectionPanel NoeParameterSelectionPanel NoeTable Normix Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookupNucleicMonomer NucleicPolymer NucleicRenderer extends CartoonRenderer for nucleicsNWChemReader A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.ObjReader OdysseyReader Orbitals Orientation OutputManager OutputManagerAwt OutputManagerJS P2nReader P2N file reader.PAL Enum for animation mode.Parameters Parser PatternMatcher PdbReader PDB file reader.PeriodicVolumeFileReader PfaatBinding PhosphorusMonomer PhosphorusPolymer PickleReader generic Python Pickle file reader only utilizing records needed for PyMOL.Pixelator PixelatorScreened A class to create a "screened" translucent effect by discarding pixels in a checkerboard fashion.PixelatorShaded A class to do Z Shading of pixels.PixelatorT Handle pixels in Pass 2 - TranslucencyPlatform Platform WebGL interfacePlatform JavaScript 2D canvas version requires Ajax-based URL stream processing.Platform3D 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.PlatformViewer Plot3D Plot3DRenderer PltFormattedReader Pmesh Pmesh4Reader PmeshReader PMESH format created for Jmol.PmeshRenderer PMeshWriter A class called by reflection from IsosurfaceMesh from the Jmol command WRITE xxxx.pmesh (ascii) or WRITE xxxx.pmb (binary)PO Just a marker for resourceClass.getClass().getResource(resourceName); Jmol now reads the PO files directly for its translations.Point3fi 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)PointGroup PointIterator PolygonFileReader Polyhedra PolyhedraRenderer Polyhedron PolyhedronStereoSorter PopInJmol PopulationDisplay PopupHelper PopupResource PovrayDialog A dialog for controling the creation of a povray input file from a Chemframe and a display.PqrReader PQR file reader.PrecisionRenderer 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.PreferencesDialog PropertyManager The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().ProteinStructure PsiReader Reader for Psi3 output files.PyMOL PyMOL settings and constants.PymolAtomReader PyMOLGroup PyMOLMeshReader PyMOL surface/mesh reader.PyMOLReader PyMOL PSE (binary Python session) file reader.PyMOLScene A class to allow manipulation of scenes dissociated from file loading.QchemReader A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.QCJSONReader A molecular structure and orbital reader for MolDen files.QCJSONWriter A very experimental class for writing QCJSON files.QMAtom QS Constants and static methods for quantum shells.QuantumCalculation QuantumPlaneCalculation Allows modification of the planes prior to isosurface creation Used by Noncovalent Interaction Calculation for progressive readersRadiusData RadiusData.EnumType Ras3DReader RasmolBinding RecentFilesDialog Manages a list of recently opened files.Rectangle RepaintManager Resolver Resource Rgb16 Ribbons RibbonsRenderer RocketRenderer Rockets RocketsRenderer SC 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.Scene ScriptButtons ScriptCompiler ScriptContext ScriptDelayThread ScriptEditor ScriptError Error handling for ScriptEvaluator, ScriptProcess, and ScriptParamsScriptEval ScriptException ScriptExpr The ScriptExpr class holds the main functions for processing mathematical and atom selection expressions.ScriptExt ScriptFlowContext ScriptFunction ScriptInterruption ScriptManager ScriptMathProcessor 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 2/16/2007ScriptParallelProcessor ScriptParam The ScriptParam class holds methods used to parse parameters in Jmol scripts.ScriptProcess the idea here is that the process { ...ScriptProcessRunnable ScriptQueueThread ScriptTokenParser SelectionManager Shader All functions.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, HoverShapeManager ShapeRenderer Sheet ShelxReader A reader for SHELX output (RES) files.SiestaReader SIESTA http://www.icmab.es/siesta/SimpleEdge minimal bond interface for SMILES and CIPSimpleMarchingCubes SimpleMarchingCubesOld SimpleNode Just the bare minimum for CIP, and non-BioSMILESSimpleUnitCell 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) periodicitySinglePointGesture SINGLE_POINT_GESTURE only passes single-touch gestures.SlaterData SlaterReader Slice SmarterJmolAdapter SmilesAromatic SmilesAtom This class represents an atom in aSmilesMolecule.SmilesBond Bond in a SmilesMoleculeSmilesExt SmilesGenerator Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal.SmilesMatcher 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 methodsSmilesMatcherInterface SmilesMeasure SmilesParser Parses a SMILES string or SMARTS pattern to create aSmilesSearch.SmilesRing Ring of (tentatively) aromatic nodes and edgesSmilesRingSet a list of fused ringsSmilesSearch A class to build and carry out a SMILES or SMARTS matchSmilesStereo This class relates to stereochemical issuesSpaceGroup SpartanArchive SpartanInputReader SpartanReader SpartanSmolReader SpartanUtil A class to isolate Spartan file reading methods from the rest of Jmol.SphereRenderer Implements high performance rendering of shaded spheres.SpinThread Splash SplashInterface Stars StarsRenderer StateCreator 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 JavaScriptStateManager StateScript StatusBar StatusListener StatusManager 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.STER Sticks SticksRenderer STR Strands StrandsRenderer Structure Structure StructureIterator Subsystem SurfaceFileReader PolygonFileReader or VolumeFileReaderSurfaceGenerator SurfaceReader SurfaceStatus Class that holds the surface status information that the surface tool needs.SurfaceTool SurfaceToolGUI GUI for the Jmol surfaceToolSV ScriptVariable classSwingConstants SwingController SwingController is an interface that org.jmol.awtjs.swing classes will need.Symmetry SymmetryDesc A class to handle requests for information about space groups and symmetry operations.SymmetryInfo SymmetryInterface SymmetryOperation T Script token class.TableCellRenderer TableColumn TableSorter TableSorter.Arrow TableSorter.Directive TempArray Tensor Test Text TextRenderer implementation for text renderingTextRenderer TextShape TextString TickerThread TickInfo TimeoutThread TinkerReader simple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.eduTlsDataOnlyReader Trace TraceRenderer Trajectory TransformManager TransformManager4D Translator TriangleData An adaptation of Marching Cubes that allows for indicating edges on triangles.TriangleRenderer renders trianglesTriangulator Turn TwoPointGesture TWO_POINT_GESTURE This gesture requires two points of contact, but its type is not initially defined.Txt Uccage UccageRenderer UFFAngleCalc UFFDistanceCalc UFFOOPCalc UFFTorsionCalc UFFVDWCalc UhbdReader UHBD readerUnitCell 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.UnitCellIterator UseTable Util V3000Rdr A reader for Accelrys V3000 files.VaspChgcarReader http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.VaspChgcarReader VaspOutcarReader http://cms.mpi.univie.ac.at/vasp/VaspPoscarReader adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/VDW Vectors VectorsRenderer VertexDataServer Vibration A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.VibrationThread Viewer Viewer.ACCESS VolumeData VolumeDataReader VolumeFileReader VoxelDataCreator VTemp WebExport WebMOReader A molecular orbital reader for WebMO files.WebPanel WhatsNewDialog Widgets Wien2kReader A reader for Wein2k DFT files.WrappedApplet WrappedAppletLoader XcrysdenReader XmlArgusReader A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.XmlChem3dReader An chem3d c3xml readerXmlCmlReader 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.XmlHandler a SAX handler -- Java onlyXmlMagResReader XmlMolproReader A Molpro 2005 readerXmlMOReader An abstract class accessing MOReader -- currently just for XmlMolproReader only.XmlOdysseyReader An Odyssey xodydata readerXmlQEReader QuantumEspresso XML readerXmlReader A generic XML reader template -- by itself, does nothing.XmlReader XmlVaspReader Vasp vasprun.xml readerXmlXsdReader An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09XplorReader XsfReader XtalSymmetry A class used by AtomSetCollection for building the symmetry of a model and generating new atoms based on that symmetry.XyzReader 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___Exporter __CartesianExporter __RayTracerExporter _IdtfExporter _MayaExporter _ObjExporter Class to export Wavefront OBJ files._PovrayExporter _StlExporter STereoLithography file format exporter for 3D printing._TachyonExporter _VrmlExporter A basic VRML generator._X3dExporter