Uses of Class
org.jmol.viewer.Viewer
Packages that use Viewer
Package
Description
Provides a software implementation of complete 3D graphics engine
for rendering molecules and associated shapes.
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Uses of Viewer in org.jmol.adapter.readers.cif
Methods in org.jmol.adapter.readers.cif with parameters of type Viewer -
Uses of Viewer in org.jmol.adapter.readers.pdb
Methods in org.jmol.adapter.readers.pdb with parameters of type ViewerModifier and TypeMethodDescriptionString[]JmolDataReader.getJmolDataFrameScripts(Viewer vwr, int tok, int modelIndex, int modelCount, String type, String qFrame, String[] props, boolean isSpinPointGroup) JmolDataReader.getPlotSpinSet(Viewer vwr, BS bs, int modelIndex, P3 minXYZ, P3 maxXYZ) remove non-spin atoms and atoms with duplicated spin and set min/max XYZ for the plot -
Uses of Viewer in org.jmol.adapter.readers.quantum
Methods in org.jmol.adapter.readers.quantum with parameters of type Viewer -
Uses of Viewer in org.jmol.adapter.smarter
Fields in org.jmol.adapter.smarter declared as ViewerMethods in org.jmol.adapter.smarter with parameters of type Viewer -
Uses of Viewer in org.jmol.adapter.writers
Fields in org.jmol.adapter.writers declared as ViewerMethods in org.jmol.adapter.writers with parameters of type ViewerModifier and TypeMethodDescriptionstatic StringCDXMLWriter.fromString(Viewer vwr, String type, String mol) voidvoidvoidvoidvoidvoidvoid -
Uses of Viewer in org.jmol.api
Methods in org.jmol.api with parameters of type ViewerModifier and TypeMethodDescriptionvoidSymmetryInterface.calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms) JmolAnnotationParser.calculateDSSRStructure(Viewer vwr, BS bsAtoms) JmolAnnotationParser.catalogStructureUnits(Viewer vwr, SV svMap, int[] modelAtomIndices, Map<String, int[]> resMap, Object object, Map<String, Integer> modelMap) JmolAnnotationParser.catalogValidations(Viewer vwr, SV validation, int[] modelAtomIndices, Map<String, int[]> valResMap, Map<String, Integer> map, Map<String, Integer> modelMap) JmolMovieCreatorInterface.createMovie(Viewer vwr, String[] files, int width, int height, int fps, String fileName) create a movie from a set of image filesJmolAnnotationParser.getAnnotationInfo(Viewer vwr, SV a, String match, int type, int modelIndex) JmolAnnotationParser.getAtomBits(Viewer vwr, String key, Object dssr, Map<String, Object> cache, int type, int modelIndex, BS bsModel) JmolAnnotationParser.getAtomValidation(Viewer vwr, String type, Atom atom) voidJmolAnnotationParser.getBasePairs(Viewer vwr, int modelIndex) JmolDialogInterface.getFileNameFromDialog(Viewer vwr, String dialogType, String inputFileName) JmolDialogInterface.getImageFileNameFromDialog(Viewer vwr, String fileName, String type, String[] imageChoices, String[] imageExtensions, int qualityJPG, int qualityPNG) static ObjectInterface.getInterface(String name, Viewer vwr, String state) SymmetryInterface.getIterator(Viewer vwr, Atom atom, BS bstoms, float radius) JmolDialogInterface.getOpenFileNameFromDialog(Map<String, Object> vwrOptions, Viewer vwr, String fileName, JmolAppAPI historyFile, String windowName, boolean allowAppend) static ObjectNote! 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)JmolDialogInterface.getSaveFileNameFromDialog(Viewer vwr, String data, String type) static SymmetryInterfaceInterface.getSymmetry(Viewer vwr, String state) static ObjectJmolRendererInterface.initializeExporter(Viewer vwr, double privateKey, GData gdata, Map<String, Object> params) booleanJmolRendererInterface.initializeOutput(Viewer vwr, double privateKey, Map<String, Object> params) voidJmolParallelProcessor.runAllProcesses(Viewer vwr) voidJmolFilesReaderInterface.set(FileManager fileManager, Viewer vwr, String[] fullPathNames, String[] namesAsGiven, String[] fileTypes, DataReader[] readers, Map<String, Object> htParams, boolean isAppend) voidJmolNavigatorInterface.set(TransformManager transformManager, Viewer vwr) voidJmolRepaintManager.set(Viewer vwr, ShapeManager shapeManager) voidSymmetryInterface.setPointGroup(Viewer vwr, SymmetryInterface pointGroupPrevious, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) voidfor Viewer.getSymStatic onlyvoid -
Uses of Viewer in org.jmol.api.js
Methods in org.jmol.api.js with parameters of type ViewerModifier and TypeMethodDescriptionJmolToJSmolInterface.consoleGetImageDialog(Viewer vwr, String title, Map<String, GenericImageDialog> imageMap) -
Uses of Viewer in org.jmol.awt
Constructors in org.jmol.awt with parameters of type ViewerModifierConstructorDescriptionFileDropper(JmolStatusListener statusListener, Viewer vwr, JmolDropEditor dropListener) -
Uses of Viewer in org.jmol.awtjs2d
Constructors in org.jmol.awtjs2d with parameters of type Viewer -
Uses of Viewer in org.jmol.console
Fields in org.jmol.console declared as ViewerMethods in org.jmol.console with parameters of type ViewerModifier and TypeMethodDescriptionprotected voidvoidConstructors in org.jmol.console with parameters of type ViewerModifierConstructorDescriptionImageDialog(Viewer vwr, String title, Map<String, GenericImageDialog> imageMap) -
Uses of Viewer in org.jmol.consolejs
Methods in org.jmol.consolejs with parameters of type Viewer -
Uses of Viewer in org.jmol.dialog
Fields in org.jmol.dialog declared as ViewerMethods in org.jmol.dialog with parameters of type ViewerModifier and TypeMethodDescriptionDialog.getFileNameFromDialog(Viewer v, String dType, String iFileName) Dialog.getImageFileNameFromDialog(Viewer vwr, String fileName, String type, String[] imageChoices, String[] imageExtensions, int qualityJPG0, int qualityPNG0) Dialog.getOpenFileNameFromDialog(Map<String, Object> vwrOptions, Viewer vwr, String fileName, JmolAppAPI jmolApp, String windowName, boolean allowAppend) Dialog.getSaveFileNameFromDialog(Viewer vwr, String fileName, String type) Constructors in org.jmol.dialog with parameters of type ViewerModifierConstructorDescriptionFilePreview(Viewer vwr, JFileChooser fileChooser, boolean allowAppend, Map<String, Object> vwrOptions) Constructor -
Uses of Viewer in org.jmol.dssx
Methods in org.jmol.dssx with parameters of type ViewerModifier and TypeMethodDescriptionAnnotationParser.calculateDSSRStructure(Viewer vwr, BS bsAtoms) DSSR1.calculateDSSRStructure(Viewer vwr, BS bsAtoms) AnnotationParser.catalogStructureUnits(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Object object, Map<String, Integer> modelMap) AnnotationParser.catalogValidations(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String, int[]> resMap, Map<String, Integer> atomMap, Map<String, Integer> modelMap) Returns a LstAnnotationParser.getAnnotationInfo(Viewer vwr, SV a, String match, int type, int modelIndex) Get a string report of annotation dataAnnotationParser.getAtomBits(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, BS bsModel) DSSR1.getAtomBits(Viewer vwr, String key, Object dbObj, Map<String, Object> annotationCache, int type, int modelIndex, BS bsModel) AnnotationParser.getAtomValidation(Viewer vwr, String type, Atom atom) Get all validation values corresponding to a specific validation type.voidAnnotationParser.getBasePairs(Viewer vwr, int modelIndex) voidDSSR1.getBasePairs(Viewer vwr, int modelIndex) -
Uses of Viewer in org.jmol.export
Fields in org.jmol.export declared as ViewerMethods in org.jmol.export with parameters of type ViewerModifier and TypeMethodDescriptionbooleanExport3D.initializeOutput(Viewer vwr, double privateKey, Map<String, Object> params) protected boolean -
Uses of Viewer in org.jmol.g3d
Methods in org.jmol.g3d with parameters of type ViewerModifier and TypeMethodDescriptionvoidGraphics3D.initialize(Viewer vwr, GenericPlatform apiPlatform) booleanGraphics3D.initializeOutput(Viewer vwr, double privateKey, Map<String, Object> params) -
Uses of Viewer in org.jmol.i18n
Constructors in org.jmol.i18n with parameters of type Viewer -
Uses of Viewer in org.jmol.image
Methods in org.jmol.image with parameters of type ViewerModifier and TypeMethodDescriptionAviCreator.createMovie(Viewer vwr, String[] files, int width, int height, int fps, String fileName) -
Uses of Viewer in org.jmol.inchi
Methods in org.jmol.inchi with parameters of type Viewer -
Uses of Viewer in org.jmol.io
Methods in org.jmol.io with parameters of type ViewerModifier and TypeMethodDescriptionJmolUtil.getAtomSetCollectionOrBufferedReaderFromZip(Viewer vwr, InputStream is, String fileName, String[] zipDirectory, Map<String, Object> htParams, int subFilePtr, boolean asBufferedReader) 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.voidFilesReader.set(FileManager fileManager, Viewer vwr, String[] name, String[] nameAsGiven, String[] types, DataReader[] readers, Map<String, Object> htParams, boolean isAppend) Constructors in org.jmol.io with parameters of type Viewer -
Uses of Viewer in org.jmol.jsv
Methods in org.jmol.jsv with parameters of type Viewer -
Uses of Viewer in org.jmol.minimize
Fields in org.jmol.minimize declared as ViewerMethods in org.jmol.minimize with parameters of type ViewerModifier and TypeMethodDescriptionintMinimizationThread.setManager(Object manager, Viewer vwr, Object options) -
Uses of Viewer in org.jmol.modelkit
Fields in org.jmol.modelkit declared as Viewer -
Uses of Viewer in org.jmol.modelset
Fields in org.jmol.modelset declared as ViewerMethods in org.jmol.modelset with parameters of type ViewerModifier and TypeMethodDescriptionfloatAtom.atomPropertyFloat(Viewer vwr, int tokWhat, P3 ptTemp) called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()intAtom.atomPropertyInt(Viewer vwr, int tokWhat) called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()Atom.atomPropertyString(Viewer vwr, int tokWhat) Atom.atomPropertyTuple(Viewer vwr, int tok, P3 ptTemp) shortAtom.calculateMad(Viewer vwr, RadiusData rd) static LabelToken[]Compiles a set of tokens for each primitive element of a label.static StringModelLoader.createAtomDataSet(Viewer vwr, ModelSet modelSet, int tokType, Object asc, BS bsSelected) LabelToken.formatLabel(Viewer vwr, Atom atom, String strFormat, P3 ptTemp) static StringLabelToken.formatLabelAtomArray(Viewer vwr, Atom atom, LabelToken[] tokens, char chAtom, int[] indices, P3 ptTemp) returns a formatted string based on the precompiled label tokensstatic StringLabelToken.formatLabelBond(Viewer vwr, Bond bond, LabelToken[] tokens, Map<String, Object> values, int[] indices, P3 ptTemp) static StringLabelToken.formatLabelMeasure(Viewer vwr, Measurement m, String label, float value, String units) floatAtom.getVanderwaalsRadiusFloat(Viewer vwr, VDW type) static TextText.newEcho(Viewer vwr, Font font, String target, short colix, int valign, int align, float scalePixelsPerMicron) static TextText.newLabel(Viewer vwr, Font font, String text, short colix, short bgcolix, int align, float scalePixelsPerMicron) static TextText.newMeasure(Viewer vwr, Font font, short colix) voidAtom.setMadAtom(Viewer vwr, RadiusData rd) Constructors in org.jmol.modelset with parameters of type Viewer -
Uses of Viewer in org.jmol.modelsetbio
Methods in org.jmol.modelsetbio with parameters of type Viewer -
Uses of Viewer in org.jmol.multitouch
Methods in org.jmol.multitouch with parameters of type ViewerModifier and TypeMethodDescriptionbooleanJmolMultiTouchAdapter.setMultiTouchClient(Viewer vwr, JmolMultiTouchClient client, boolean isSimulation) booleanJmolMultiTouchClientAdapter.setMultiTouchClient(Viewer vwr, JmolMultiTouchClient client, boolean isSimulation) void -
Uses of Viewer in org.jmol.multitouch.sparshui
Methods in org.jmol.multitouch.sparshui with parameters of type ViewerModifier and TypeMethodDescriptionbooleanJmolSparshClientAdapter.setMultiTouchClient(Viewer vwr, JmolMultiTouchClient client, boolean isSimulation) -
Uses of Viewer in org.jmol.popup
Fields in org.jmol.popup declared as ViewerMethods in org.jmol.popup with parameters of type ViewerModifier and TypeMethodDescriptionprotected voidJmolGenericPopup.initialize(Viewer vwr, PopupResource bundle, String title) -
Uses of Viewer in org.jmol.quantum
Methods in org.jmol.quantum with parameters of type ViewerModifier and TypeMethodDescriptionstatic double[]NMRCalculation.calc2or3JorNOE(Viewer viewer, Atom[] atoms, String CHEquation, int mode) Calculate a 2-bond (geminal) or 3-bond (vicinal) coupling constant or an NOE;static double[]static NMRNoeMatrixNMRNoeMatrix.createMatrix(Viewer viewer, BS bsMol, String[] labelArray, NMRNoeMatrix.NOEParams params) void -
Uses of Viewer in org.jmol.render
Fields in org.jmol.render declared as ViewerMethods in org.jmol.render with parameters of type ViewerModifier and TypeMethodDescriptionvoidRepaintManager.set(Viewer vwr, ShapeManager shapeManager) final voidShapeRenderer.setViewerG3dShapeID(Viewer vwr, int shapeID) -
Uses of Viewer in org.jmol.script
Fields in org.jmol.script declared as ViewerMethods in org.jmol.script with parameters of type ViewerModifier and TypeMethodDescriptionvoidScriptParallelProcessor.runAllProcesses(Viewer vwr) static SVScriptEval.runUserAction(String functionName, Object[] params, Viewer vwr) intCommandWatcherThread.setManager(Object manager, Viewer vwr, Object params) static voidScriptManager.setStateScriptVersion(Viewer vwr, String version) static StringScriptEval.statementAsString(Viewer vwr, T[] statement, int iTok, boolean doLogMessages) Constructors in org.jmol.script with parameters of type ViewerModifierConstructorDescriptionScriptCompiler(Viewer vwr) ScriptQueueThread(ScriptManager scriptManager, Viewer vwr, boolean startedByCommandThread, int pt) -
Uses of Viewer in org.jmol.scriptext
Fields in org.jmol.scriptext declared as Viewer -
Uses of Viewer in org.jmol.shape
Fields in org.jmol.shape declared as ViewerMethods in org.jmol.shape with parameters of type Viewer -
Uses of Viewer in org.jmol.shapespecial
Constructors in org.jmol.shapespecial with parameters of type Viewer -
Uses of Viewer in org.jmol.shapesurface
Methods in org.jmol.shapesurface with parameters of type Viewer -
Uses of Viewer in org.jmol.symmetry
Methods in org.jmol.symmetry with parameters of type ViewerModifier and TypeMethodDescriptionvoidSymmetry.calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms) SpaceGroupFinder.checkSupercell(Viewer vwr, Symmetry uc, BS bsPoints, int abc, P3 scaling) Look for a supercell and adjust lattice down if necessary.Symmetry.getIterator(Viewer vwr, Atom atom, BS bsAtoms, float radius) static T3[]UnitCell.getMatrixAndUnitCell(Viewer vwr, SimpleUnitCell uc, Object def, M4 retMatrix) Actual constructor.CIPDataSmiles.setAtomsForSmiles(Viewer vwr, String smiles) Symmetry.setPointGroup(Viewer vwr, SymmetryInterface siLast, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) -
Uses of Viewer in org.jmol.thread
Fields in org.jmol.thread declared as ViewerMethods in org.jmol.thread with parameters of type ViewerModifier and TypeMethodDescriptionintAnimationThread.setManager(Object manager, Viewer vwr, Object params) intJmolThread.setManager(Object manager, Viewer vwr, Object params) intMoveToThread.setManager(Object manager, Viewer vwr, Object params) intSpinThread.setManager(Object manager, Viewer vwr, Object params) intVibrationThread.setManager(Object manager, Viewer vwr, Object options) static voidTimeoutThread.setTimeout(Viewer vwr, Map<String, Object> timeouts, String name, int mSec, String script) voidConstructors in org.jmol.thread with parameters of type ViewerModifierConstructorDescriptionHoverWatcherThread(ActionManager actionManager, MouseState current, MouseState moved, Viewer vwr) TimeoutThread(Viewer vwr, String name, int ms, String script) -
Uses of Viewer in org.jmol.util
Fields in org.jmol.util declared as ViewerModifier and TypeFieldDescriptionprotected ViewerGenericApplet.viewerprotected ViewerGData.vwrMeshSurface.vwrMethods in org.jmol.util with parameters of type ViewerModifier and TypeMethodDescriptionvoidBZone.createBZ(Viewer vwr, int n, Object[] array, boolean isK, String id, float scale, float foffset, P3 offset) Create a Brillouin zone.voidvoidGData.initialize(Viewer vwr, GenericPlatform apiPlatform) static floatstatic floatSimpleUnitCell.parseCalcFunctions(Viewer vwr, String[] functions, String s) static StringSimpleUnitCell.parseSimpleMath(Viewer vwr, String suvw) parse math such as "1/sqrt(3)" or "2sqrt(3) or "2cos(3pi/2)"voidWAV only for applicationConstructors in org.jmol.util with parameters of type Viewer -
Uses of Viewer in org.jmol.viewer
Fields in org.jmol.viewer declared as ViewerModifier and TypeFieldDescriptionprotected ViewerActionManager.vwrAnimationManager.vwrFileManager.vwrprotected ViewerOutputManager.vwrprotected ViewerOutputManager.vwrShapeManager.vwrprotected final ViewerStateManager.vwrprotected ViewerStatusManager.vwrprotected ViewerTransformManager.vwrMethods in org.jmol.viewer with parameters of type ViewerModifier and TypeMethodDescriptionstatic BufferedReaderFileManager.getBufferedReaderForResource(Viewer vwr, Class<?> resourceClass, String classPath, String resourceName) static GenericFileInterfaceFileManager.getLocalDirectory(Viewer vwr, boolean forDialog) static StringFileManager.getLocalPathForWritingFile(Viewer vwr, String file, boolean forDialog) static voidFileManager.setLocalPath(Viewer vwr, String path, boolean forDialog) 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.voidvoidConstructors in org.jmol.viewer with parameters of type Viewer -
Uses of Viewer in org.jmol.viewer.binding
Methods in org.jmol.viewer.binding with parameters of type Viewer -
Uses of Viewer in org.molecularplayground
Fields in org.molecularplayground declared as ViewerMethods in org.molecularplayground with parameters of type ViewerModifier and TypeMethodDescriptionstatic StringMPJmolApp.getJmolValueAsString(Viewer vwr, String var) -
Uses of Viewer in org.openscience.jmol.app
Fields in org.openscience.jmol.app declared as ViewerMethods in org.openscience.jmol.app with parameters of type Viewer -
Uses of Viewer in org.openscience.jmol.app.janocchio
Subclasses of Viewer in org.openscience.jmol.app.janocchioMethods in org.openscience.jmol.app.janocchio with parameters of type Viewer -
Uses of Viewer in org.openscience.jmol.app.jmolpanel
Fields in org.openscience.jmol.app.jmolpanel declared as ViewerMethods in org.openscience.jmol.app.jmolpanel with parameters of type ViewerModifier and TypeMethodDescriptionvoidvoidConstructors in org.openscience.jmol.app.jmolpanel with parameters of type ViewerModifierConstructorDescriptionAtomSetChooser(Viewer vwr, JFrame frame) GaussianDialog(JFrame f, Viewer vwr) MeasurementTable(Viewer vwr, JFrame parentFrame) ConstructorPovrayDialog(JFrame f, Viewer vwr) Creates a dialog for getting info related to output frames in povray format.PreferencesDialog(JmolPanel jmol, JFrame f, GuiMap guimap, Viewer vwr) -
Uses of Viewer in org.openscience.jmol.app.jmolpanel.console
Methods in org.openscience.jmol.app.jmolpanel.console with parameters of type Viewer -
Uses of Viewer in org.openscience.jmol.app.jsonkiosk
Methods in org.openscience.jmol.app.jsonkiosk with parameters of type ViewerModifier and TypeMethodDescriptionvoidJsonNioClient.TouchHandler.checkPaused(Viewer vwr) voidprocess touch or gesture commands driven by hardware.voidJsonNioClient.TouchHandler.pauseScript(Viewer vwr, boolean isPause) voidJsonNioServer.startService(int port, JsonNioClient client, Viewer jmolViewer, String name, int version) voidJsonNioService.startService(int port, JsonNioClient client, Viewer jmolViewer, String name, int version) voidJsonNioClient.TouchHandler.syncScript(Viewer vwr, String script) -
Uses of Viewer in org.openscience.jmol.app.status
Constructors in org.openscience.jmol.app.status with parameters of type ViewerModifierConstructorDescriptionStatusListener(Viewer vwr, JmolPanel jmolPanel, DisplayPanel display) -
Uses of Viewer in org.openscience.jmol.app.webexport
Methods in org.openscience.jmol.app.webexport with parameters of type ViewerModifier and TypeMethodDescriptionstatic WebExportWebExport.createAndShowGUI(Viewer vwr, HistoryFile historyFile, String wName)