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.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 String
CDXMLWriter.fromString
(Viewer vwr, String type, String mol) void
void
void
void
void
void
void
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Uses of Viewer in org.jmol.api
Methods in org.jmol.api with parameters of type ViewerModifier and TypeMethodDescriptionvoid
SymmetryInterface.calculateCIPChiralityForAtoms
(Viewer vwr, BS bsAtoms) String[]
SymmetryInterface.calculateCIPChiralityForSmiles
(Viewer vwr, String smiles) 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 filesSymmetryInterface.findSpaceGroup
(Viewer vwr, BS atoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) JmolAnnotationParser.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) void
JmolAnnotationParser.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 Object
Interface.getInterface
(String name, Viewer vwr, String state) SymmetryInterface.getITASettingValue
(Viewer vwr, String itaIndex, String key) 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 Object
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)JmolDialogInterface.getSaveFileNameFromDialog
(Viewer vwr, String data, String type) SymmetryInterface.getSpaceGroupJSON
(Viewer vwr, String name, String data, int index) SymmetryInterface.getSubgroupJSON
(Viewer vwr, int ita1, int ita2, int index1, int index2) static SymmetryInterface
Interface.getSymmetry
(Viewer vwr, String state) static Object
SymmetryInterface.getWyckoffPosition
(Viewer vwr, P3 pt, String letter) JmolRendererInterface.initializeExporter
(Viewer vwr, double privateKey, GData gdata, Map<String, Object> params) boolean
JmolRendererInterface.initializeOutput
(Viewer vwr, double privateKey, Map<String, Object> params) void
JmolParallelProcessor.runAllProcesses
(Viewer vwr) void
JmolFilesReaderInterface.set
(FileManager fileManager, Viewer vwr, String[] fullPathNames, String[] namesAsGiven, String[] fileTypes, DataReader[] readers, Map<String, Object> htParams, boolean isAppend) void
JmolNavigatorInterface.set
(TransformManager transformManager, Viewer vwr) void
JmolRepaintManager.set
(Viewer vwr, ShapeManager shapeManager) void
SymmetryInterface.setPointGroup
(Viewer vwr, SymmetryInterface pointGroupPrevious, T3 center, T3[] atomset, BS bsAtoms, boolean haveVibration, float distanceTolerance, float linearTolerance, int maxAtoms, boolean localEnvOnly) void
void
for Viewer.getSymStatic onlyvoid
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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 void
void
Constructors 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.void
AnnotationParser.getBasePairs
(Viewer vwr, int modelIndex) void
DSSR1.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 TypeMethodDescriptionboolean
Export3D.initializeOutput
(Viewer vwr, double privateKey, Map<String, Object> params) protected boolean
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Uses of Viewer in org.jmol.g3d
Methods in org.jmol.g3d with parameters of type ViewerModifier and TypeMethodDescriptionvoid
Graphics3D.initialize
(Viewer vwr, GenericPlatform apiPlatform) boolean
Graphics3D.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.void
FilesReader.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 TypeMethodDescriptionint
MinimizationThread.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 TypeMethodDescriptionfloat
Atom.atomPropertyFloat
(Viewer vwr, int tokWhat, P3 ptTemp) 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) short
Atom.calculateMad
(Viewer vwr, RadiusData rd) static LabelToken[]
Compiles a set of tokens for each primitive element of a label.static String
ModelLoader.createAtomDataSet
(Viewer vwr, ModelSet modelSet, int tokType, Object asc, BS bsSelected) LabelToken.formatLabel
(Viewer vwr, Atom atom, String strFormat, P3 ptTemp) static String
LabelToken.formatLabelAtomArray
(Viewer vwr, Atom atom, LabelToken[] tokens, char chAtom, int[] indices, P3 ptTemp) returns a formatted string based on the precompiled label tokensstatic String
LabelToken.formatLabelBond
(Viewer vwr, Bond bond, LabelToken[] tokens, Map<String, Object> values, int[] indices, P3 ptTemp) static String
LabelToken.formatLabelMeasure
(Viewer vwr, Measurement m, String label, float value, String units) float
Atom.getVanderwaalsRadiusFloat
(Viewer vwr, VDW type) static Text
Text.newEcho
(Viewer vwr, Font font, String target, short colix, int valign, int align, float scalePixelsPerMicron) static Text
Text.newLabel
(Viewer vwr, Font font, String text, short colix, short bgcolix, int align, float scalePixelsPerMicron) static Text
Text.newMeasure
(Viewer vwr, Font font, short colix) void
Atom.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 TypeMethodDescriptionboolean
JmolMultiTouchAdapter.setMultiTouchClient
(Viewer vwr, JmolMultiTouchClient client, boolean isSimulation) boolean
JmolMultiTouchClientAdapter.setMultiTouchClient
(Viewer vwr, JmolMultiTouchClient client, boolean isSimulation) void
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Uses of Viewer in org.jmol.multitouch.sparshui
Methods in org.jmol.multitouch.sparshui with parameters of type ViewerModifier and TypeMethodDescriptionboolean
JmolSparshClientAdapter.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 void
JmolGenericPopup.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 NMRNoeMatrix
NMRNoeMatrix.createMatrix
(Viewer viewer, BS bsMol, String[] labelArray, NMRNoeMatrix.NOEParams params) void
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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 TypeMethodDescriptionvoid
RepaintManager.set
(Viewer vwr, ShapeManager shapeManager) final void
ShapeRenderer.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 TypeMethodDescriptionvoid
ScriptParallelProcessor.runAllProcesses
(Viewer vwr) static SV
ScriptEval.runUserAction
(String functionName, Object[] params, Viewer vwr) int
CommandWatcherThread.setManager
(Object manager, Viewer vwr, Object params) static void
ScriptManager.setStateScriptVersion
(Viewer vwr, String version) static String
ScriptEval.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 TypeMethodDescriptionvoid
Symmetry.calculateCIPChiralityForAtoms
(Viewer vwr, BS bsAtoms) String[]
Symmetry.calculateCIPChiralityForSmiles
(Viewer vwr, String smiles) SpaceGroupFinder.checkSupercell
(Viewer vwr, Symmetry uc, BS bsPoints, int abc, P3 scaling) Look for a supercell and adjust lattice down if necessary.Symmetry.findSpaceGroup
(Viewer vwr, BS atoms, String xyzList, float[] unitCellParams, T3 origin, T3[] oabc, int flags) Symmetry.getITASettingValue
(Viewer vwr, String itaIndex, String key) Symmetry.getIterator
(Viewer vwr, Atom atom, BS bsAtoms, float radius) Symmetry.getSpaceGroupJSON
(Viewer vwr, String name, String data, int index) Symmetry.getSubgroupJSON
(Viewer vwr, int itaFrom, int itaTo, int index1, int index2) Retrieve subgroup information for a space group.Symmetry.getWyckoffPosition
(Viewer vwr, P3 p, String letter) 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) for the vwr.getSymTemp() only -
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 TypeMethodDescriptionint
AnimationThread.setManager
(Object manager, Viewer vwr, Object params) int
JmolThread.setManager
(Object manager, Viewer vwr, Object params) int
MoveToThread.setManager
(Object manager, Viewer vwr, Object params) int
SpinThread.setManager
(Object manager, Viewer vwr, Object params) int
VibrationThread.setManager
(Object manager, Viewer vwr, Object options) static void
TimeoutThread.setTimeout
(Viewer vwr, Map<String, Object> timeouts, String name, int mSec, String script) void
Constructors 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 Viewer
GenericApplet.viewer
protected Viewer
GData.vwr
MeshSurface.vwr
Methods in org.jmol.util with parameters of type ViewerModifier and TypeMethodDescriptionvoid
BZone.createBZ
(Viewer vwr, int n, Object[] array, boolean isK, String id, float scale, float foffset, P3 offset) Create a Brillouin zone.void
void
GData.initialize
(Viewer vwr, GenericPlatform apiPlatform) static float
void
WAV 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 Viewer
ActionManager.vwr
AnimationManager.vwr
FileManager.vwr
protected Viewer
OutputManager.vwr
protected Viewer
OutputManager.vwr
ShapeManager.vwr
protected final Viewer
StateManager.vwr
protected Viewer
StatusManager.vwr
protected Viewer
TransformManager.vwr
Methods in org.jmol.viewer with parameters of type ViewerModifier and TypeMethodDescriptionstatic BufferedReader
FileManager.getBufferedReaderForResource
(Viewer vwr, Class<?> resourceClass, String classPath, String resourceName) static GenericFileInterface
FileManager.getLocalDirectory
(Viewer vwr, boolean forDialog) static String
FileManager.getLocalPathForWritingFile
(Viewer vwr, String file, boolean forDialog) static void
FileManager.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.void
void
Constructors 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 String
MPJmolApp.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 TypeMethodDescriptionprotected void
void
void
Constructors 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 TypeMethodDescriptionvoid
JsonNioClient.TouchHandler.checkPaused
(Viewer vwr) void
process touch or gesture commands driven by hardware.void
JsonNioClient.TouchHandler.pauseScript
(Viewer vwr, boolean isPause) void
JsonNioServer.startService
(int port, JsonNioClient client, Viewer jmolViewer, String name, int version) void
JsonNioService.startService
(int port, JsonNioClient client, Viewer jmolViewer, String name, int version) void
JsonNioClient.TouchHandler.syncScript
(Viewer vwr, String script) -
Uses of Viewer in org.openscience.jmol.app.webexport
Methods in org.openscience.jmol.app.webexport with parameters of type ViewerModifier and TypeMethodDescriptionstatic WebExport
WebExport.createAndShowGUI
(Viewer vwr, HistoryFile historyFile, String wName)