Viewer

java.lang.Object
- org.jmol.api.JmolViewer
- - org.jmol.viewer.Viewer

All Implemented Interfaces:: javajs.api.JSInterface, javajs.api.PlatformViewer, AtomDataServer

public class Viewer
extends JmolViewer
implements AtomDataServer, javajs.api.PlatformViewer

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Viewer.ACCESS

Nested Classes
Modifier and Type	Class and Description
`static class`	`Viewer.ACCESS`

Field Summary

Fields
Modifier and Type	Field and Description
`private Viewer.ACCESS`	`access`
`(package private) ActionManager`	`actionManager`
`(package private) javajs.util.List<java.lang.String>`	`actionStates`
`(package private) javajs.util.List<java.lang.String>`	`actionStatesRedo`
`boolean`	`allowArrayDotNotation`
`private boolean`	`allowScripting`
`(package private) AnimationManager`	`am`
`private boolean`	`antialiasDisplay`
`(package private) JmolAppConsoleInterface`	`appConsole`
`(package private) java.lang.Object`	`applet`
`static java.lang.String`	`appletCodeBase`
`static java.lang.String`	`appletDocumentBase`
`static java.lang.String`	`appletIdiomaBase`
`java.lang.String`	`appletName`
`boolean`	`autoExit`
`private boolean`	`axesAreTainted`
`(package private) BS`	`bsFrameOffsets`
`private BS`	`bsRotateBranch`
`(package private) BS`	`bsUserVdws`
`java.util.Map<java.lang.String,java.lang.Object>`	`captureParams`
`javajs.util.List<java.lang.String>`	`chainList`
`java.util.Map<java.lang.Object,java.lang.Object>`	`chainMap`
`(package private) ColorManager`	`cm`
`private CommandHistory`	`commandHistory`
`private java.lang.String`	`commandOptions`
`java.lang.Object`	`compiler`
`boolean`	`creatingImage`
`private int`	`currentCursor`
`private int`	`currentShapeID`
`private java.lang.String`	`currentShapeState`
`(package private) VDW`	`defaultVdw`
`java.util.Map<java.lang.String,java.lang.Object>`	`definedAtomSets`
`(package private) javajs.awt.Dimension`	`dimScreen`
`private java.lang.Object`	`display`
`boolean`	`displayLoadErrors`
`(package private) JmolDataManager`	`dm`
`private java.lang.String`	`errorMessage`
`private java.lang.String`	`errorMessageUntranslated`
`JmolScriptEvaluator`	`eval`
`private java.lang.Object`	`executor`
`FileManager`	`fm`
`(package private) javajs.util.P3[]`	`frameOffsets`
`private boolean`	`frankOn`
`java.lang.String`	`fullName`
`GlobalSettings`	`g`
`(package private) GData`	`gdata`
`private java.lang.Object`	`gRight` A graphics from a "slave" stereo display that has been synchronized with this this applet.
`boolean`	`haveDisplay`
`private boolean`	`haveJDX`
`private java.util.Map<java.lang.String,java.lang.Object>`	`headlessImageParams`
`(package private) int`	`hoverAtomIndex`
`boolean`	`hoverEnabled`
`(package private) java.lang.String`	`hoverText`
`java.lang.String`	`htmlName`
`(package private) java.util.Map<java.lang.String,java.lang.String[][]>`	`htPdbBondInfo`
`private float`	`imageFontScaling`
`private boolean`	`inMotion`
`private java.lang.String`	`insertedCommand`
`private boolean`	`isApplet`
`private boolean`	`isJNLP`
`boolean`	`isJS`
`(package private) boolean`	`isKiosk`
`(package private) boolean`	`isParallel`
`private boolean`	`isPreviewOnly`
`private boolean`	`isPrintOnly`
`private boolean`	`isSignedApplet`
`private boolean`	`isSignedAppletLocal`
`private boolean`	`isSilent`
`boolean`	`isSingleThreaded`
`private boolean`	`isStereoSlave` A flag to indicate that THIS is the right-side panel of a pair of synced applets running a left-right stereo display (that would be piped into a dual-image polarized projector system such as GeoWall).
`boolean`	`isSyntaxAndFileCheck`
`boolean`	`isSyntaxCheck`
`(package private) boolean`	`isTainted`
`boolean`	`isWebGL`
`(package private) javajs.api.GenericMenuInterface`	`jmolpopup`
`(package private) JmolStateCreator`	`jsc`
`static java.lang.String`	`jsDocumentBase`
`private JmolRendererInterface`	`jsExporter3D`
`private java.util.Map<java.lang.String,java.lang.Object>`	`jsParams`
`private JmolJSpecView`	`jsv`
`private java.lang.String`	`language`
`(package private) java.util.Map<java.lang.String,java.lang.Object>`	`ligandModels`
`(package private) java.util.Map<java.lang.String,java.lang.Boolean>`	`ligandModelSet`
`boolean`	`listCommands`
`(package private) java.util.Map<java.lang.String,JmolScriptFunction>`	`localFunctions`
`(package private) java.lang.String`	`logFileName`
`private java.lang.String`	`logFilePath`
`private int`	`maximumSize`
`private MinimizerInterface`	`minimizer`
`private ModelManager`	`mm`
`private JmolAdapter`	`modelAdapter`
`private javajs.api.GenericMenuInterface`	`modelkitPopup`
`private int`	`motionEventNumber`
`private javajs.api.GenericMouseInterface`	`mouse` either org.jmol.awt.Mouse or org.jmol.awtjs2d.Mouse
`private boolean`	`mouseEnabled`
`private boolean`	`movingSelected`
`ModelSet`	`ms`
`private boolean`	`multiTouch`
`(package private) boolean`	`mustRender`
`(package private) JmolNMRInterface`	`nmrCalculation`
`private boolean`	`noGraphicsAllowed`
`private boolean`	`noneSelected`
`static int`	`nProcessors`
`private OutputManager`	`outputManager`
`(package private) JmolPropertyManager`	`pm`
`(package private) int`	`prevFrame`
`private float`	`prevMorphModel`
`private double`	`privateKey`
`boolean`	`queueOnHold`
`private RadiusData`	`rd`
`private boolean`	`refreshing`
`(package private) JmolRepaintManager`	`rm`
`private int`	`rotateBondIndex`
`private int`	`rotatePrev1`
`private int`	`rotatePrev2`
`private JmolScriptManager`	`scm`
`(package private) JmolScriptEditorInterface`	`scriptEditor`
`boolean`	`scriptEditorVisible`
`(package private) ShapeManager`	`shm`
`private boolean`	`showSelected`
`(package private) SelectionManager`	`slm`
`StatusManager`	`sm`
`private SmilesMatcherInterface`	`smilesMatcher`
`int`	`stateScriptVersionInt`
`(package private) static java.util.Map<java.lang.String,JmolScriptFunction>`	`staticFunctions`
`private StateManager`	`stm`
`static java.lang.String`	`strJavaVendor`
`static java.lang.String`	`strJavaVersion`
`static java.lang.String`	`strOSName`
`static java.lang.String`	`SYNC_GRAPHICS_MESSAGE`
`static java.lang.String`	`SYNC_NO_GRAPHICS_MESSAGE`
`(package private) java.lang.String`	`syncId`
`private TempArray`	`tempArray`
`(package private) java.util.Map<java.lang.String,java.lang.Object>`	`timeouts`
`(package private) TransformManager`	`tm`
`private boolean`	`useCommandThread`
`(package private) int[]`	`userVdwMars`
`(package private) float[]`	`userVdws`
`private static java.lang.String`	`version_date`
`private java.util.Map<java.lang.String,java.lang.Object>`	`vwrOptions`

Fields inherited from class org.jmol.api.JmolViewer
apiPlatform, menuStructure

Constructor Summary

Constructors
Constructor and Description

Viewer(java.util.Map<java.lang.String,java.lang.Object> info)
new way...

Constructors
Constructor and Description
`Viewer(java.util.Map<java.lang.String,java.lang.Object> info)` new way...

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`(package private) void`	`actionRotateBond(int deltaX, int deltaY, int x, int y)`
`void`	`addCommand(java.lang.String command)` Adds one or more commands to the command history
`void`	`addFunction(JmolScriptFunction function)`
`BS`	`addHydrogens(BS bsAtoms, boolean is2DLoad, boolean isSilent)`
`BS`	`addHydrogensInline(BS bsAtoms, javajs.util.List<Atom> vConnections, javajs.util.P3[] pts)`
`void`	`addSelectionListener(JmolSelectionListener listener)`
`StateScript`	`addStateScript(java.lang.String script, boolean addFrameNumber, boolean postDefinitions)`
`StateScript`	`addStateScriptRet(java.lang.String script1, BS bsBonds, BS bsAtoms1, BS bsAtoms2, java.lang.String script2, boolean addFrameNumber, boolean postDefinitions)`
`void`	`addUnitCellOffset(javajs.util.P3 pt)`
`protected static JmolViewer`	`allocateViewer(java.lang.Object display, JmolAdapter modelAdapter, java.lang.String fullName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions, JmolStatusListener statusListener, javajs.api.GenericPlatform implementedPlatform)` old way...
`STR[]`	`allocTempEnum(int size)`
`javajs.util.P3[]`	`allocTempPoints(int size)`
`javajs.util.P3i[]`	`allocTempScreens(int size)`
`boolean`	`allowCapture()`
`boolean`	`allowEmbeddedScripts()`
`boolean`	`allowSpecAtom()`
`boolean`	`areAxesTainted()`
`void`	`assignAromaticBonds()`
`void`	`autoCalculate(int tokProperty)`
`int`	`autoHbond(BS bsFrom, BS bsTo, boolean onlyIfHaveCalculated)`
`private void`	`beginRendering(boolean isDouble, boolean isImageWrite)`
`void`	`bindAction(java.lang.String desc, java.lang.String name)`
`void`	`cacheClear()`
`int`	`cacheFileByName(java.lang.String fileName, boolean isAdd)` used in JSmolApplet.js for drag-drop behavior.
`java.lang.Object`	`cacheGet(java.lang.String key)`
`java.util.Map<java.lang.String,java.lang.Integer>`	`cacheList()`
`boolean`	`cachePngFiles()`
`void`	`cachePut(java.lang.String key, java.lang.Object data)` JmolViewer interface -- allows saving files in memory for later retrieval
`void`	`calcAtomsMinMax(BS bs, BoxInfo boxInfo)`
`void`	`calcBoundBoxDimensions(BS bs, float scale)`
`float`	`calcRotationRadius(javajs.util.P3 center)`
`float`	`calcRotationRadiusBs(BS bs)`
`void`	`calcSelectedGroupsCount()`
`void`	`calcSelectedMoleculesCount()`
`void`	`calcSelectedMonomersCount()`
`int`	`calculateFormalCharges(BS bs)`
`javajs.util.V3`	`calculateMolecularDipole()`
`void`	`calculatePartialCharges(BS bsSelected)`
`java.lang.String`	`calculatePointGroup()`
`void`	`calculateStraightness()`
`java.lang.String`	`calculateStructures(BS bsAtoms, boolean asDSSP, boolean setStructure)`
`int`	`calculateStruts(BS bs1, BS bs2)`
`javajs.util.P3[]`	`calculateSurface(BS bsSelected, float envelopeRadius)`
`java.lang.String`	`cd(java.lang.String dir)`
`void`	`checkCoordinatesChanged()`
`private static float`	`checkFloatRange(float value, float min, float max)`
`boolean`	`checkHalt(java.lang.String str, boolean isInsert)`
`void`	`checkInheritedShapes()`
`void`	`checkInMotion(int state)`
`private static int`	`checkIntRange(int value, int min, int max)`
`private void`	`checkMinimization()`
`boolean`	`checkMotionRendering(int tok)` check motion for rendering during mouse movement, spin, vibration, and animation
`(package private) java.util.Map<java.lang.String,java.lang.Object>`	`checkObjectClicked(int x, int y, int modifiers)`
`(package private) void`	`checkObjectDragged(int prevX, int prevY, int x, int y, int action)`
`boolean`	`checkObjectHovered(int x, int y)`
`private boolean`	`checkOption2(java.lang.String key1, java.lang.String key2)`
`boolean`	`checkPrivateKey(double privateKey)` Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet.
`boolean`	`checkPropertyParameter(java.lang.String name)`
`void`	`clearAllMeasurements()`
`private void`	`clearAtomSets()`
`void`	`clearBfactorRange()`
`(package private) void`	`clearClickCount()`
`void`	`clearConsole()`
`void`	`clearFunctions()`
`void`	`clearMeasurements()`
`(package private) void`	`clearMinimization()`
`void`	`clearModelDependentObjects()`
`private void`	`clearRepaintManager(int iShape)`
`void`	`clearScriptQueue()`
`void`	`clearSelection()`
`void`	`clearShapeRenderers()`
`void`	`clearThreads()`
`void`	`clearTimeout(java.lang.String name)`
`void`	`clearTimeouts()`
`java.lang.String`	`clipImageOrPasteText(java.lang.String text)`
`void`	`connect(float[][] connections)`
`void`	`createModels(int n)`
`private java.lang.String`	`createModelSetAndReturnError(java.lang.Object atomSetCollection, boolean isAppend, javajs.util.SB loadScript, java.util.Map<java.lang.String,java.lang.Object> htParams)` finally(!) we are ready to create the "model set" from the "atom set collection" - does NOT repaint
`java.lang.String`	`createZip(java.lang.String fileName, java.lang.String type, java.lang.Object data)`
`void`	`defineAtomSets(java.util.Map<java.lang.String,java.lang.Object> info)`
`int`	`deleteAtoms(BS bs, boolean fullModels)`
`void`	`deleteBonds(BS bsDeleted)`
`void`	`deleteMeasurement(int i)`
`void`	`deleteModelAtoms(int modelIndex, int firstAtomIndex, int nAtoms, BS bsDeleted)`
`void`	`deleteSaved(java.lang.String name)`
`void`	`deleteShapeAtoms(java.lang.Object[] value, BS bs)`
`(package private) void`	`depthByPixels(int pixels)`
`void`	`depthToPercent(int percentDepth)`
`(package private) java.lang.String`	`dialogAsk(java.lang.String type, java.lang.String fileName)`
`void`	`displayAtoms(BS bs, boolean isDisplay, boolean isGroup, int addRemove, boolean isQuiet)`
`void`	`displayBonds(BondSet bs, boolean isDisplay)`
`void`	`dispose()` end of life for this viewer
`private boolean`	`doHaveJDX()`
`(package private) void`	`echoMessage(java.lang.String msg)`
`java.lang.String`	`evalFile(java.lang.String strFilename)`
`float`	`evalFunctionFloat(java.lang.Object func, java.lang.Object params, float[] values)`
`boolean`	`evalParallel(ScriptContext context, ShapeManager shapeManager)`
`java.lang.String`	`evalString(java.lang.String strScript)`
`java.lang.String`	`evalStringQuiet(java.lang.String strScript)`
`java.lang.String`	`evalStringQuietSync(java.lang.String strScript, boolean isQuiet, boolean allowSyncScript)`
`java.lang.Object`	`evalStringWaitStatusQueued(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)`
`java.lang.Object`	`evaluateExpression(java.lang.Object stringOrTokens)`
`SV`	`evaluateExpressionAsVariable(java.lang.Object stringOrTokens)`
`private java.lang.Object`	`evalWait(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList)`
`BS`	`excludeAtoms(BS bs, boolean ignoreSubset)`
`void`	`exitJmol()`
`java.lang.String`	`extractMolData(java.lang.String what)`
`java.lang.Object`	`extractProperty(java.lang.Object property, SV[] args, int pt)`
`void`	`fillAtomData(AtomData atomData, int mode)`
`protected void`	`finalize()`
`void`	`finalizeTransformParameters()`
`(package private) BS`	`findAtomsInRectangle(Rectangle rect)`
`int`	`findNearestAtomIndex(int x, int y)`
`int`	`findNearestAtomIndexMovable(int x, int y, boolean mustBeMovable)`
`static java.lang.String`	`fixInlineString(java.lang.String strModel, char newLine)`
`java.lang.String`	`formatText(java.lang.String text0)`
`boolean`	`frankClicked(int x, int y)`
`boolean`	`frankClickedModelKit(int x, int y)`
`void`	`freeTempEnum(STR[] temp)`
`void`	`freeTempPoints(javajs.util.P3[] tempPoints)`
`void`	`freeTempScreens(javajs.util.P3i[] tempScreens)`
`float[][]`	`functionXY(java.lang.String functionName, int nX, int nY)` fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.
`float[][][]`	`functionXYZ(java.lang.String functionName, int nX, int nY, int nZ)`
`java.lang.String`	`generateOutputForExport(java.util.Map<java.lang.String,java.lang.Object> params)` for POV-Ray
`ActionManager`	`getActionManager()`
`javajs.util.P3[]`	`getAdditionalHydrogens(BS bsAtoms, boolean doAll, boolean justCarbon, javajs.util.List<Atom> vConnections)`
`BS`	`getAllAtoms()`
`java.lang.String`	`getAllSettings(java.lang.String prefix)`
`java.lang.String`	`getAltLocListInModel(int modelIndex)`
`(package private) int`	`getAnimationDirection()`
`ANIM`	`getAnimationReplayMode()`
`java.lang.Object`	`getApplet()`
`int`	`getArgbMinMax(float val, float min, float max)`
`int`	`getAtomArgb(int i)`
`BS`	`getAtomBits(int tokType, java.lang.Object specInfo)`
`BS`	`getAtomBitSet(java.lang.Object atomExpression)`
`(package private) BS`	`getAtomBitSetEval(JmolScriptEvaluator eval, java.lang.Object atomExpression)`
`(package private) javajs.util.List<java.lang.Integer>`	`getAtomBitSetVector(java.lang.Object atomExpression)`
`int`	`getAtomCount()`
`int`	`getAtomCountInModel(int modelIndex)`
`java.lang.String`	`getAtomDefs(java.util.Map<java.lang.String,java.lang.Object> names)`
`javajs.util.Quat[]`	`getAtomGroupQuaternions(BS bsAtoms, int nMax)`
`float[]`	`getAtomicCharges()`
`(package private) void`	`getAtomicPropertyState(javajs.util.SB commands, byte type, BS bs, java.lang.String name, float[] data)`
`void`	`getAtomIdentityInfo(int atomIndex, java.util.Map<java.lang.String,java.lang.Object> info)`
`int`	`getAtomIndexFromAtomNumber(int atomNumber)`
`int[]`	`getAtomIndices(BS bs)`
`java.lang.String`	`getAtomInfo(int atomOrPointIndex)`
`java.lang.String`	`getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)`
`int`	`getAtomModelIndex(int i)`
`java.lang.String`	`getAtomName(int i)`
`int`	`getAtomNumber(int i)`
`javajs.util.P3`	`getAtomPoint3f(int i)`
`javajs.util.List<javajs.util.P3>`	`getAtomPointVector(BS bs)`
`javajs.util.Quat`	`getAtomQuaternion(int i)`
`float`	`getAtomRadius(int i)`
`javajs.util.P3`	`getAtomSetCenter(BS bs)`
`java.lang.String`	`getAtomShapeSetState(Shape shape, AtomShape[] shapes)`
`java.lang.String`	`getAtomShapeState(AtomShape shape)`
`float`	`getAtomShapeValue(int tok, Group group, int atomIndex)`
`BS`	`getAtomsNearPlane(float distance, javajs.util.P4 plane)`
`BS`	`getAtomsNearPt(float distance, javajs.util.P3 coord)`
`BS`	`getAtomsNearPts(float distance, javajs.util.P3[] points, BS bsInclude)`
`BS`	`getAtomsWithinRadius(float distance, BS bs, boolean withinAllModels, RadiusData rd)`
`(package private) javajs.util.P3`	`getAverageAtomPoint()`
`AXES`	`getAxesMode()`
`void`	`getAxisAngle(javajs.util.A4 axisAngle)`
`javajs.util.P3[]`	`getAxisPoints()`
`int`	`getBackgroundArgb()`
`BS`	`getBaseModelBitSet()`
`int`	`getBfactor100Hi()`
`java.lang.String`	`getBindingInfo(java.lang.String qualifiers)`
`BS`	`getBitSetTrajectories()`
`int`	`getBondArgb1(int i)`
`int`	`getBondArgb2(int i)`
`int`	`getBondCount()` For use in setting a for() construct max value
`int`	`getBondCountInModel(int modelIndex)` from JmolPopup.udateModelSetComputedMenu
`int`	`getBondModelIndex(int i)`
`int`	`getBondOrder(int i)`
`(package private) boolean`	`getBondPicking()`
`javajs.util.P3`	`getBondPoint3f1(int i)`
`javajs.util.P3`	`getBondPoint3f2(int i)`
`float`	`getBondRadius(int i)`
`BS`	`getBondsForSelectedAtoms(BS bsAtoms)`
`java.lang.String`	`getBondState(Shape shape, BS bsOrderSet, boolean reportAll)`
`boolean`	`getBoolean(int tok)`
`boolean`	`getBooleanProperty(java.lang.String key)`
`javajs.util.P3`	`getBoundBoxCenter()`
`int`	`getBoundBoxCenterX()`
`int`	`getBoundBoxCenterY()`
`java.lang.String`	`getBoundBoxCommand(boolean withOptions)`
`javajs.util.V3`	`getBoundBoxCornerVector()`
`BS`	`getBoundBoxModels()`
`javajs.util.P3[]`	`getBoundBoxVertices()`
`BoxInfo`	`getBoxInfo(BS bs, float scale)`
`BS`	`getBranchBitSet(int atomIndex, int atomIndexNot, boolean allowCyclic)`
`BS[]`	`getBsBranches(float[] dihedralList)`
`java.io.BufferedInputStream`	`getBufferedInputStream(java.lang.String fullPathName)`
`java.lang.Object`	`getBufferedReaderOrErrorMessageFromName(java.lang.String name, java.lang.String[] fullPathNameReturn, boolean isBinary)`
`javajs.util.P3`	`getCamera()`
`float`	`getCameraDepth()`
`javajs.util.P3[]`	`getCameraFactors()`
`javajs.util.P3[][]`	`getCenterAndPoints(javajs.util.List<java.lang.Object[]> atomSets, boolean addCenter)`
`int`	`getChainCount()`
`int`	`getChainCountInModel(int modelIndex)`
`int`	`getChainCountInModelWater(int modelIndex, boolean countWater)`
`int`	`getChainID(java.lang.String id)` Create a unique integer for any chain string.
`java.lang.String`	`getChainIDStr(int id)`
`java.lang.String`	`getChemicalInfo(java.lang.String smiles, T t)`
`java.lang.String`	`getChimeInfo(int tok)`
`java.util.Map<java.lang.String,java.lang.Object>`	`getCifData(int modelIndex)`
`BS`	`getClickableSet()`
`java.lang.String`	`getClipboardText()`
`(package private) short`	`getColix(java.lang.Object object)`
`short`	`getColixAtomPalette(Atom atom, byte pid)`
`short`	`getColixBackgroundContrast()`
`short`	`getColixBondPalette(Bond bond, int pid)`
`short`	`getColixForPropertyValue(float val)`
`short`	`getColixRubberband()`
`int`	`getColorArgbOrGray(short colix)`
`ColorEncoder`	`getColorEncoder(java.lang.String colorScheme)`
`javajs.util.P3`	`getColorPointForPropertyValue(float val)`
`java.lang.String`	`getColorSchemeList(java.lang.String colorScheme)`
`java.lang.String`	`getCommands(java.util.Map<java.lang.String,BS> htDefine, java.util.Map<java.lang.String,BS> htMore, java.lang.String select)`
`BS`	`getConformation(int iModel, int conformationIndex, boolean doSet)`
`ScriptContext`	`getContext(java.lang.String saveName)`
`java.util.Map<java.lang.String,SV>`	`getContextVariables()`
`java.lang.String`	`getCoordinateState(BS bsSelected)`
`int`	`getCurrentAtom()`
`float[]`	`getCurrentColorRange()`
`java.lang.String`	`getCurrentFileAsString()`
`int`	`getCurrentModelIndex()`
`float`	`getCurrentSolventProbeRadius()`
`SymmetryInterface`	`getCurrentUnitCell()`
`int`	`getCursor()`
`int`	`getCursorX()`
`int`	`getCursorY()`
`java.lang.Object[]`	`getData(java.lang.String type)`
`java.lang.String`	`getData(java.lang.String atomExpression, java.lang.String type)`
`float[]`	`getDataFloat(java.lang.String label)`
`float[][]`	`getDataFloat2D(java.lang.String label)`
`float[][][]`	`getDataFloat3D(java.lang.String label)`
`float`	`getDataFloatAt(java.lang.String label, int atomIndex)`
`private JmolDataManager`	`getDataManager()`
`(package private) java.lang.String`	`getDataSeparator()`
`(package private) java.lang.String`	`getDefaultDirectory()`
`javajs.util.P3`	`getDefaultLattice()`
`java.lang.String`	`getDefaultLoadFilter()`
`java.lang.String`	`getDefaultLoadScript()`
`java.lang.String`	`getDefaultMeasurementLabel(int nPoints)`
`java.lang.String`	`getDefaultPropertyParam(int propertyID)`
`RadiusData`	`getDefaultRadiusData()`
`java.lang.String`	`getDefaultStructure(BS bsAtoms, BS bsAllAtoms)`
`java.lang.String`	`getDefaultVdwNameOrData(int mode, VDW type, BS bs)`
`BS`	`getDefinedAtomSet(java.lang.String name)`
`int`	`getDelayMaximumMs()`
`BS`	`getDeletedAtoms()`
`int[][]`	`getDihedralMap(int[] atoms)`
`java.lang.Object`	`getDisplay()`
`int`	`getDisplayModelIndex()`
`java.lang.String`	`getDistanceUnits(java.lang.String s)`
`(package private) boolean`	`getDragSelected()`
`boolean`	`getDrawHover()`
`boolean`	`getEchoStateActive()`
`java.lang.String[]`	`getElectronDensityLoadInfo()`
`(package private) int`	`getElementNumber(int i)`
`BS`	`getElementsPresentBitSet(int modelIndex)`
`(package private) java.lang.String`	`getElementSymbol(int i)`
`java.lang.String`	`getEmbeddedFileState(java.lang.String filename)`
`java.lang.String`	`getEnergyUnits()`
`java.lang.String`	`getErrorMessage()`
`java.lang.String`	`getErrorMessageUn()`
`ScriptContext`	`getEvalContextAndHoldQueue(JmolScriptEvaluator jse)`
`java.lang.Object`	`getExecutor()`
`java.lang.String`	`getExportDriverList()`
`java.lang.Object`	`getFileAsBytes(java.lang.String pathName, javajs.util.OC out)`
`java.util.Map<java.lang.String,java.lang.Object>`	`getFileAsMap(java.lang.String name)`
`java.lang.String`	`getFileAsString(java.lang.String name, boolean checkProtected)`
`java.lang.String`	`getFileAsString4(java.lang.String name, int nBytesMax, boolean doSpecialLoad, boolean allowBinary, boolean checkProtected)`
`boolean`	`getFileAsStringBin(java.lang.String[] data, boolean allowBinary)`
`(package private) java.lang.Object`	`getFileData()`
`(package private) java.lang.String`	`getFileHeader()`
`java.lang.String[]`	`getFileInfo()`
`java.lang.String`	`getFileName()`
`java.lang.String`	`getFilePath(java.lang.String name, boolean asShortName)`
`float`	`getFloat(int tok)`
`javajs.awt.Font`	`getFont3D(java.lang.String fontFace, java.lang.String fontStyle, float fontSize)`
`java.lang.String`	`getFontLineShapeState(java.lang.String s, java.lang.String myType, TickInfo[] tickInfos)`
`java.lang.String`	`getFontState(java.lang.String myType, javajs.awt.Font font3d)`
`int`	`getFrameCount()`
`long`	`getFrameDelayMs(int i)`
`BS`	`getFrameOffsets()`
`java.lang.String`	`getFrameTitle()`
`int`	`getFrontPlane()`
`java.lang.String`	`getFullPathName(boolean orPrevious)`
`java.lang.String[]`	`getFullPathNameOrError(java.lang.String filename)`
`JmolScriptFunction`	`getFunction(java.lang.String name)`
`java.lang.String`	`getFunctionCalls(java.lang.String selectedFunction)`
`java.util.Map<java.lang.String,JmolScriptFunction>`	`getFunctions(boolean isStatic)`
`java.lang.Object`	`getGLmolView()` This method is only called by JmolGLmol applet._refresh();
`GData`	`getGraphicsData()`
`int`	`getGroupCount()`
`int`	`getGroupCountInModel(int modelIndex)`
`BS`	`getGroupsWithin(int nResidues, BS bs)`
`java.lang.Object`	`getHelixData(BS bs, int tokType)`
`void`	`getHelp(java.lang.String what)`
`int`	`getHermiteLevel()`
`java.util.Map<java.lang.String,java.lang.String>`	`getHeteroList(int modelIndex)`
`BS`	`getHiddenSet()`
`int`	`getHoverDelay()`
`java.lang.String`	`getHtmlName()`
`java.lang.String`	`getHybridizationAndAxes(int atomIndex, javajs.util.V3 z, javajs.util.V3 x, java.lang.String lcaoType)`
`private java.lang.Object`	`getImage(boolean isDouble, boolean isImageWrite)`
`byte[]`	`getImageAsBytes(java.lang.String type, int width, int height, int quality, java.lang.String[] errMsg)`
`float`	`getImageFontScaling()`
`char`	`getInlineChar()`
`boolean`	`getInMotion(boolean includeAnim)`
`java.lang.String`	`getInsertedCommand()`
`int`	`getInt(int tok)`
`int`	`getIsosurfacePropertySmoothing(boolean asPower)`
`int`	`getJDXBaseModelIndex(int modelIndex)` get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file.
`int`	`getJmolDataFrameIndex(int modelIndex, java.lang.String type)`
`int`	`getJmolDataSourceFrame(int modelIndex)`
`(package private) java.lang.String`	`getJmolFrameType(int modelIndex)`
`static java.lang.String`	`getJmolVersion()`
`java.lang.Object`	`getJspecViewProperties(java.lang.Object myParam)`
`(package private) JmolJSpecView`	`getJSV()`
`java.lang.String`	`getLanguage()`
`java.lang.Object`	`getLigandModel(java.lang.String id, java.lang.String prefix, java.lang.String suffix, java.lang.String terminator)` obtain CIF data for a ligand for purposes of adding hydrogens
`(package private) java.lang.String`	`getLoadState(java.util.Map<java.lang.String,java.lang.Object> htParams)`
`java.lang.String`	`getLocalUrl(java.lang.String fileName)`
`java.lang.String`	`getLogFileName()`
`(package private) java.lang.String`	`getLogFilePath()`
`short`	`getMadBond()`
`short`	`getMarBond()`
`(package private) javajs.util.M3`	`getMatrixRotate()`
`javajs.util.M4`	`getMatrixtransform()`
`float`	`getMaxZoomPercent()`
`java.lang.String`	`getMeasureDistanceUnits()`
`int`	`getMeasurementCount()`
`int[]`	`getMeasurementCountPlusIndices(int i)`
`java.lang.String`	`getMeasurementInfoAsString()`
`java.lang.String`	`getMeasurementState(Measures measures, javajs.util.List<Measurement> mList, int measurementCount, javajs.awt.Font font3d, TickInfo ti)`
`java.lang.String`	`getMeasurementStringValue(int i)`
`java.lang.String`	`getMenu(java.lang.String type)`
`java.util.Map<java.lang.String,javajs.util.List<javajs.util.List<java.lang.Object>>>`	`getMessageQueue()`
`java.lang.String`	`getMinimizationInfo()`
`MinimizerInterface`	`getMinimizer(boolean createNew)`
`JmolAdapter`	`getModelAdapter()`
`java.lang.String`	`getModelAtomProperty(Atom atom, java.lang.String text)`
`java.util.Map<java.lang.String,java.lang.Object>`	`getModelAuxiliaryInfo(int modelIndex)`
`java.lang.Object`	`getModelAuxiliaryInfoValue(int modelIndex, java.lang.String keyName)` changed in Jmol 13.1.5 to remove ambiguity in JavaScript
`BS`	`getModelBitSet(BS atomList, boolean allTrajectories)`
`java.lang.String`	`getModelCml(BS bs, int nAtomsMax, boolean addBonds)`
`int`	`getModelCount()`
`javajs.util.V3`	`getModelDipole()`
`java.lang.String`	`getModelExtract(java.lang.Object atomExpression, boolean doTransform, boolean isModelKit, java.lang.String type)`
`java.lang.String`	`getModelFileInfo()`
`java.lang.String`	`getModelFileInfoAll()`
`java.lang.String`	`getModelFileName(int modelIndex)`
`int`	`getModelFileNumber(int modelIndex)`
`int`	`getModelIndexFromId(java.lang.String id)`
`java.lang.String`	`getModelInfoAsString()`
`(package private) BS`	`getModelKitStateBitSet(BS bs, BS bsDeleted)`
`java.lang.String`	`getModelName(int modelIndex)`
`int`	`getModelNumber(int modelIndex)`
`java.lang.String`	`getModelNumberDotted(int modelIndex)`
`int`	`getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)`
`java.util.Properties`	`getModelProperties(int modelIndex)`
`java.lang.String`	`getModelProperty(int modelIndex, java.lang.String propertyName)`
`ModelSet`	`getModelSet()`
`java.util.Map<java.lang.String,java.lang.Object>`	`getModelSetAuxiliaryInfo()`
`java.lang.Object`	`getModelSetAuxiliaryInfoValue(java.lang.String strKey)`
`java.lang.String`	`getModelSetFileName()`
`java.lang.String`	`getModelSetName()`
`java.lang.String`	`getModelSetPathName()`
`java.util.Properties`	`getModelSetProperties()`
`java.lang.String`	`getModelSetProperty(java.lang.String strProp)`
`java.lang.String`	`getModelSetTypeName()`
`private java.lang.String`	`getModelTitle(int modelIndex)`
`BS`	`getModelUndeletedAtomsBitSet(int modelIndex)`
`BS`	`getModelUndeletedAtomsBitSetBs(BS bsModels)`
`SymmetryInterface`	`getModelUnitCell(int modelIndex)`
`byte`	`getModeMultipleBond()`
`javajs.util.List<java.lang.Object>`	`getModulationList(BS bs, java.lang.String type, javajs.util.P3 t456)`
`java.lang.String`	`getMoInfo(int modelIndex)`
`BS`	`getMoleculeBitSet(int atomIndex)`
`int`	`getMotionEventNumber()`
`BS`	`getMotionFixedAtoms()`
`boolean`	`getMouseEnabled()`
`java.lang.String`	`getMoveToText(float timespan)`
`javajs.util.P3`	`getNavigationCenter()`
`float`	`getNavigationDepthPercent()`
`javajs.util.P3`	`getNavigationOffset()`
`float`	`getNavigationOffsetPercent(char XorY)`
`boolean`	`getNavOn()`
`JmolNMRInterface`	`getNMRCalculation()`
`java.lang.String`	`getNMRPredict(boolean openURL)`
`java.lang.Boolean`	`getNoneSelected()`
`(package private) int`	`getObjectArgb(int objId)`
`short`	`getObjectColix(int objId)`
`int`	`getObjectMad(int objId)`
`void`	`getObjectMap(java.util.Map<java.lang.String,?> map, char c)` used in autocompletion in console using TAB
`Orientation`	`getOrientation()`
`(package private) java.util.Map<java.lang.String,java.lang.Object>`	`getOrientationInfo()`
`java.lang.String`	`getOrientationText(int type, java.lang.String name)`
`SV`	`getOrSetNewVariable(java.lang.String key, boolean doSet)`
`javajs.util.OC`	`getOutputChannel(java.lang.String localName, java.lang.String[] fullPath)`
`private OutputManager`	`getOutputManager()`
`java.lang.Object`	`getParameter(java.lang.String key)`
`java.lang.Object`	`getParameterEscaped(java.lang.String key)`
`float[]`	`getPartialCharges()`
`java.lang.String`	`getPathForAllFiles()`
`java.lang.String`	`getPdbAtomData(BS bs, javajs.util.OC sb)`
`java.lang.String[][]`	`getPdbBondInfo(java.lang.String group3)`
`java.lang.String`	`getPdbData(int modelIndex, java.lang.String type, java.lang.Object[] parameters)`
`java.lang.String`	`getPDBHeader()`
`(package private) MeasurementPending`	`getPendingMeasurement()`
`boolean`	`getPerspectiveDepth()`
`int`	`getPickingMode()`
`javajs.util.List<java.lang.Object>`	`getPlaneIntersection(int type, javajs.util.P4 plane, float scale, int flags)`
`java.lang.String`	`getPointGroupAsString(boolean asDraw, java.lang.String type, int index, float scale)`
`java.util.Map<java.lang.String,java.lang.Object>`	`getPointGroupInfo(java.lang.Object atomExpression)`
`int`	`getPolymerCount()`
`int`	`getPolymerCountInModel(int modelIndex)`
`javajs.util.P3[]`	`getPolymerLeadMidPoints(int modelIndex, int polymerIndex)`
`void`	`getPolymerPointsAndVectors(BS bs, javajs.util.List<javajs.util.P3[]> vList)`
`private java.lang.Object`	`getPopupMenu()`
`boolean`	`getPreserveState()` This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.
`java.lang.Object`	`getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)`
`java.lang.String`	`getPropertyColorScheme()`
`private JmolPropertyManager`	`getPropertyManager()`
`int`	`getPropertyNumber(java.lang.String name)`
`java.lang.String`	`getProteinStructureState()`
`char`	`getQuaternionFrame()`
`boolean`	`getRefreshing()`
`BS`	`getRenderableBitSet()`
`(package private) int`	`getRotateBondIndex()`
`void`	`getRotation(javajs.util.M3 matrixRotation)`
`javajs.util.P3`	`getRotationCenter()`
`javajs.util.Quat`	`getRotationQuaternion()`
`Rectangle`	`getRubberBandSelection()`
`java.lang.String`	`getSavedCoordinates(java.lang.String saveName)`
`java.lang.String`	`getSavedState(java.lang.String saveName)`
`java.lang.String`	`getSavedStructure(java.lang.String saveName)`
`float`	`getScalePixelsPerAngstrom(boolean asAntialiased)`
`java.lang.String[]`	`getSceneList()`
`int`	`getScreenDim()`
`int`	`getScreenHeight()`
`java.lang.Object`	`getScreenImageBuffer(java.lang.Object graphic, boolean isImageWrite)` Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo
`int`	`getScreenWidth()`
`ScriptContext`	`getScriptContext(java.lang.String why)`
`private JmolScriptManager`	`getScriptManager()`
`java.lang.Boolean`	`getScriptQueueInfo()`
`AtomIndexIterator`	`getSelectedAtomIterator(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel)`
`BS`	`getSelectedAtoms()`
`BS`	`getSelectedAtomsNoSubset()`
`int`	`getSelectionCount()`
`boolean`	`getSelectionHaloEnabled(boolean isRenderer)`
`BS`	`getSelectionSubset()`
`BS`	`getSequenceBits(java.lang.String specInfo, BS bs)`
`java.lang.String`	`getSetHistory(int howFarBack)` Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
`java.lang.String`	`getShapeErrorState()`
`ShapeManager`	`getShapeManager()`
`java.lang.Object`	`getShapeProperty(int shapeType, java.lang.String propertyName)`
`private int`	`getShapePropertyAsInt(int shapeID, java.lang.String propertyName)`
`boolean`	`getShapePropertyData(int shapeType, java.lang.String propertyName, java.lang.Object[] data)`
`java.lang.Object`	`getShapePropertyIndex(int shapeType, java.lang.String propertyName, int index)`
`void`	`getShapeSetState(AtomShape atomShape, Shape shape, int monomerCount, Group[] monomers, BS bsSizeDefault, java.util.Map<java.lang.String,BS> temp, java.util.Map<java.lang.String,BS> temp2)`
`java.lang.String`	`getShapeState(Shape shape)`
`boolean`	`getShowAxes()`
`boolean`	`getShowBbcage()`
`boolean`	`getShowFrank()`
`boolean`	`getShowNavigationPoint()`
`boolean`	`getShowUnitCell()`
`boolean`	`getSlabEnabled()`
`BS`	`getSmartsMatch(java.lang.String smarts, BS bsSelected)`
`java.lang.String`	`getSmiles(BS bs)`
`SmilesMatcherInterface`	`getSmilesMatcher()`
`java.lang.String`	`getSmilesOpt(BS bsSelected, int index1, int index2, boolean explicitH, boolean isBioSmiles, boolean bioAllowUnmatchedRings, boolean bioAddCrossLinks, boolean bioAddComment)` returns the SMILES string for a sequence or atom set does not include attached protons on groups
`java.util.Map<java.lang.String,java.lang.Object>`	`getSpaceGroupInfo(java.lang.String spaceGroup)`
`java.lang.String`	`getSpecularState()`
`boolean`	`getSpinOn()`
`java.lang.String`	`getSpinState()`
`java.lang.String`	`getStandardLabelFormat(int type)`
`JmolStateCreator`	`getStateCreator()`
`java.lang.String`	`getStateInfo()`
`java.lang.String`	`getStateInfo3(java.lang.String type, int width, int height)`
`javajs.util.List<javajs.util.List<javajs.util.List<java.lang.Object>>>`	`getStatusChanged(java.lang.String statusNameList)`
`(package private) StatusManager`	`getStatusManager()`
`int`	`getStrandCount(int type)`
`java.util.Map<STR,float[]>`	`getStructureList()`
`java.lang.String`	`getStructureState()`
`(package private) int`	`getSurfaceDistanceMax()`
`java.lang.Object`	`getSymmetryInfo(BS bsAtoms, java.lang.String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, java.lang.String id, int type)`
`java.lang.String`	`getSymmetryInfoAsString()`
`java.lang.String`	`getSymmetryOperation(java.lang.String spaceGroup, int symop, javajs.util.P3 pt1, javajs.util.P3 pt2, boolean labelOnly)`
`BS`	`getTaintedAtoms(byte type)`
`boolean`	`getTestFlag(int i)`
`java.util.Map<java.lang.String,java.lang.Object>`	`getTimeouts()`
`java.lang.String`	`getTrajectoryState()`
`java.lang.String`	`getTransformText()`
`java.lang.String`	`getTranslationScript()`
`float`	`getTranslationXPercent()`
`float`	`getTranslationYPercent()`
`(package private) float`	`getTranslationZPercent()`
`private BS`	`getUndeletedGroupAtomBits(BS bs)`
`float`	`getUnitCellInfo(int infoType)`
`java.lang.String`	`getUnitCellInfoText()`
`javajs.util.M4`	`getUnscaledTransformMatrix()`
`int`	`getVanderwaalsMar(int i)`
`int`	`getVanderwaalsMarType(int atomicAndIsotopeNumber, VDW type)`
`java.lang.Object`	`getVariableList()`
`Vibration`	`getVibration(int atomIndex)`
`Point3fi`	`getVibrationPoint(Vibration vibration, Point3fi pt)`
`java.util.Map<java.lang.String,java.lang.Object>`	`getViewerOptions()`
`BS`	`getVisibleFramesBitSet()`
`BS`	`getVisibleSet()`
`java.lang.String`	`getWrappedStateScript()`
`java.lang.String`	`getZapName()`
`boolean`	`getZoomEnabled()`
`int`	`getZoomPercent()`
`float`	`getZoomPercentFloat()`
`float`	`getZoomSetting()`
`int`	`getZShadeStart()`
`void`	`haltScriptExecution()`
`void`	`handleError(java.lang.Error er, boolean doClear)`
`static boolean`	`hasDatabasePrefix(java.lang.String fileName)`
`boolean`	`hasDisplay()`
`boolean`	`hasFocus()`
`boolean`	`haveAccess(Viewer.ACCESS a)`
`boolean`	`haveFileSet()`
`boolean`	`haveFrame()`
`(package private) boolean`	`haveModelKit()`
`(package private) boolean`	`haveModelSet()`
`boolean`	`havePartialCharges()`
`void`	`highlight(BS bs)`
`void`	`highlightBond(int index, boolean isHover)`
`void`	`homePosition()`
`(package private) void`	`hoverOff()`
`(package private) void`	`hoverOn(int atomIndex, boolean isLabel)`
`void`	`hoverOnPt(int x, int y, java.lang.String text, java.lang.String id, javajs.util.P3 pt)`
`void`	`initialize(boolean clearUserVariables)`
`JmolRendererInterface`	`initializeExporter(java.util.Map<java.lang.String,java.lang.Object> params)`
`private void`	`initializeModel(boolean isAppend)`
`void`	`invertAtomCoordPlane(javajs.util.P4 plane, BS bs)`
`void`	`invertAtomCoordPt(javajs.util.P3 pt, BS bs)`
`void`	`invertSelected(javajs.util.P3 pt, javajs.util.P4 plane, int iAtom, BS invAtoms)`
`void`	`invertSelection()`
`(package private) boolean`	`isAnimationOn()`
`boolean`	`isAntialiased()`
`boolean`	`isApplet()`
`(package private) boolean`	`isAtomAssignable(int i)`
`boolean`	`isAtomPDB(int i)`
`boolean`	`isAtomSelected(int atomIndex)`
`boolean`	`isBound(int action, int gesture)`
`static boolean`	`isDatabaseCode(char ch)`
`boolean`	`isFunction(java.lang.String name)`
`boolean`	`isHeadless()`
`boolean`	`isInPosition(javajs.util.V3 axis, float degrees)`
`(package private) boolean`	`isInSelectionSubset(int atomIndex)`
`boolean`	`isJmolDataFrame()`
`boolean`	`isJmolDataFrameForModel(int modelIndex)`
`boolean`	`isJmolVariable(java.lang.String key)`
`(package private) boolean`	`isKiosk()`
`boolean`	`isModelPDB(int i)`
`boolean`	`isMovie()`
`boolean`	`isNavigating()`
`boolean`	`isParallel()`
`boolean`	`isPreviewOnly()`
`boolean`	`isRepaintPending()`
`boolean`	`isScriptExecuting()`
`private boolean`	`isScriptQueued()`
`boolean`	`isSelected(int atomIndex)`
`boolean`	`isSignedApplet()`
`private static boolean`	`isStaticFunction(java.lang.String name)`
`(package private) boolean`	`isStereoDouble()`
`boolean`	`isTrajectory(int modelIndex)`
`boolean`	`isVibrationOn()`
`boolean`	`isWindowCentered()`
`private void`	`jmolTest()`
`java.lang.String`	`jsEval(java.lang.String strEval)`
`java.lang.String`	`listSavedStates()`
`private java.lang.String`	`loadAtomDataAndReturnError(java.lang.Object atomSetCollection, int tokType)` or just apply the data to the current model set
`void`	`loadImage(java.lang.String pathName, java.lang.String echoName)`
`(package private) void`	`loadImageData(java.lang.Object image, java.lang.String nameOrError, java.lang.String echoName, ScriptContext sc)`
`java.lang.String`	`loadInline(java.util.List<java.lang.Object> arrayData, boolean isAppend)` External applications only; does not preserver state -- intentionally!
`java.lang.String`	`loadInline(java.lang.String strModel)` from Applet and external applications only
`java.lang.String`	`loadInline(java.lang.String[] arrayModels)` external apps only
`java.lang.String`	`loadInline(java.lang.String[] arrayModels, boolean isAppend)` external apps and applet only
`java.lang.String`	`loadInline(java.lang.String strModel, char newLine)` external apps only
`java.lang.String`	`loadInlineAppend(java.lang.String strModel, boolean isAppend)` used by applet and console
`private java.lang.String`	`loadInlineScript(java.lang.String strModel, char newLine, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams)` used by loadInline and openFileFull
`private java.lang.String`	`loadInlineScriptRepaint(java.lang.String strModel, char newLine, boolean isAppend)`
`java.lang.String`	`loadModelFromFile(java.lang.String fullPathName, java.lang.String fileName, java.lang.String[] fileNames, java.lang.Object reader, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams, javajs.util.SB loadScript, int tokType)` Used by the ScriptEvaluator LOAD command to open one or more files.
`private java.lang.String`	`loadModelFromFileRepaint(java.lang.String fullPathName, java.lang.String fileName, java.lang.String[] fileNames, java.lang.Object reader)`
`void`	`loadShape(int shapeID)`
`void`	`log(java.lang.String data)`
`int[]`	`makeConnections(float minDistance, float maxDistance, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy)`
`boolean`	`menuEnabled()`
`void`	`mergeShapes(Shape[] newShapes)`
`void`	`minimize(int steps, float crit, BS bsSelected, BS bsFixed, float rangeFixed, boolean addHydrogen, boolean isOnly, boolean isSilent, boolean isLoad2D)`
`int`	`modelGetLastVibrationIndex(int modelIndex, int tok)`
`boolean`	`modelHasVibrationVectors(int modelIndex)`
`(package private) boolean`	`modelSetHasVibrationVectors()`
`void`	`morph(float frame)`
`void`	`move(JmolScriptEvaluator eval, javajs.util.V3 dRot, float dZoom, javajs.util.V3 dTrans, float dSlab, float floatSecondsTotal, int fps)`
`void`	`moveAtoms(javajs.util.M3 mNew, javajs.util.M3 matrixRotate, javajs.util.V3 translation, javajs.util.P3 center, boolean isInternal, BS bsAtoms, boolean translationOnly)`
`protected void`	`moveAtomWithHydrogens(int atomIndex, int deltaX, int deltaY, int deltaZ, BS bsAtoms)`
`boolean`	`movePyMOL(JmolScriptEvaluator eval, float floatSecondsTotal, float[] pymolView)`
`void`	`moveSelected(int deltaX, int deltaY, int deltaZ, int x, int y, BS bsSelected, boolean isTranslation, boolean asAtoms)`
`void`	`moveTo(JmolScriptEvaluator eval, float floatSecondsTotal, javajs.util.P3 center, javajs.util.V3 rotAxis, float degrees, javajs.util.M3 rotationMatrix, float zoom, float xTrans, float yTrans, float rotationRadius, javajs.util.P3 navCenter, float xNav, float yNav, float navDepth, float cameraDepth, float cameraX, float cameraY)`
`void`	`moveUpdate(float floatSecondsTotal)`
`(package private) void`	`navigate(int keyWhere, int modifiers)`
`void`	`navigateAxis(javajs.util.V3 rotAxis, float degrees)`
`void`	`navigateList(JmolScriptEvaluator eval, javajs.util.List<java.lang.Object[]> list)`
`void`	`navigatePt(javajs.util.P3 center)`
`void`	`navTranslatePercent(float x, float y)`
`MeasurementData`	`newMeasurementData(java.lang.String id, javajs.util.List<java.lang.Object> points)`
`boolean`	`noGraphicsAllowed()`
`void`	`notifyError(java.lang.String errType, java.lang.String errMsg, java.lang.String errMsgUntranslated)`
`void`	`notifyMinimizationStatus()`
`int`	`notifyMouseClicked(int x, int y, int action, int mode)`
`void`	`notifyStatusReady(boolean isReady)`
`void`	`notifyViewerRepaintDone()`
`java.lang.String`	`openDOM(java.lang.Object DOMNode)` applet DOM method -- does not preserve state
`javajs.util.OC`	`openExportChannel(double privateKey, java.lang.String fileName, boolean asWriter)`
`java.lang.String`	`openFile(java.lang.String fileName)` for JmolSimpleViewer -- external applications only (and no-script JavaScript)
`void`	`openFileAsyncSpecial(java.lang.String fileName, int flags)` opens a file as a model, a script, or a surface via the creation of a script that is queued \t at the beginning disallows script option - used by JmolFileDropper and JmolPanel file-open actions - sets up a script to load the file
`private java.lang.Object`	`openFileFull(java.lang.String fileName, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams, javajs.util.SB loadScript)` does NOT repaint
`java.lang.String`	`openFiles(java.lang.String[] fileNames)` for JmolSimpleViewer -- external applications only
`java.lang.String`	`openReader(java.lang.String fullPathName, java.lang.String fileName, java.io.Reader reader)` Opens the file, given an already-created reader.
`java.lang.String`	`openStringInline(java.lang.String strModel)` only used by file dropper.
`java.lang.String`	`openStringInlineParamsAppend(java.lang.String strModel, java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)` Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.
`private java.lang.String`	`openStringsInlineParamsAppend(java.lang.String[] arrayModels, java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)` opens multiple files inline; does NOT repaint
`java.lang.String`	`outputToFile(java.util.Map<java.lang.String,java.lang.Object> params)`
`void`	`pauseScriptExecution()`
`void`	`popHoldRepaint(java.lang.String why)`
`(package private) void`	`popupMenu(int x, int y, char type)`
`boolean`	`processMouseEvent(int id, int x, int y, int modifiers, long time)`
`void`	`processMultitouchEvent(int groupID, int eventType, int touchID, int iData, javajs.util.P3 pt, long time)`
`void`	`processTwoPointGesture(float[][][] touches)`
`java.lang.String`	`processWriteOrCapture(java.util.Map<java.lang.String,java.lang.Object> params)` from eval write command only includes option to write set of files
`java.lang.String`	`prompt(java.lang.String label, java.lang.String data, java.lang.String[] list, boolean asButtons)`
`void`	`pushHoldRepaint()`
`void`	`pushHoldRepaintWhy(java.lang.String why)`
`void`	`rebond()`
`void`	`rebondState(boolean isStateScript)`
`void`	`refresh(int mode, java.lang.String strWhy)` initiate a repaint/update sequence if it has not already been requested.
`void`	`refreshMeasures(boolean andStopMinimization)`
`void`	`releaseScreenImage()`
`java.lang.String`	`removeCommand()` Removes one command from the command history
`void`	`removeFunction(java.lang.String name)`
`void`	`removeSelectionListener(JmolSelectionListener listener)`
`void`	`removeUserVariable(java.lang.String key)`
`private void`	`render()`
`private void`	`render1(java.lang.Object graphic, java.lang.Object img, int x, int y)`
`void`	`renderScreenImage(java.lang.Object g, int width, int height)`
`void`	`renderScreenImageStereo(java.lang.Object gLeft, boolean checkStereoSlave, int width, int height)`
`(package private) void`	`reportSelection(java.lang.String msg)`
`void`	`requestRepaintAndWait(java.lang.String why)`
`void`	`reset(boolean includingSpin)`
`void`	`resetAromatic()`
`void`	`resetBioshapes(BS bsAllAtoms)`
`void`	`resetError()`
`void`	`resetShapes(boolean andCreateNew)`
`(package private) void`	`resizeImage(int width, int height, boolean isImageWrite, boolean isExport, boolean isReset)`
`javajs.awt.Dimension`	`resizeInnerPanel(int width, int height)`
`(package private) java.lang.String`	`resolveDatabaseFormat(java.lang.String fileName)`
`boolean`	`restoreBonds(java.lang.String saveName)`
`(package private) void`	`restoreModelOrientation(int modelIndex)`
`(package private) void`	`restoreModelRotation(int modelIndex)`
`boolean`	`restoreOrientation(java.lang.String saveName, float timeSeconds)`
`void`	`restoreRotation(java.lang.String saveName, float timeSeconds)`
`void`	`restoreScene(java.lang.String saveName, float timeSeconds)`
`boolean`	`restoreSelection(java.lang.String saveName)`
`boolean`	`rotateAboutPointsInternal(JmolScriptEvaluator eval, javajs.util.P3 point1, javajs.util.P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected, javajs.util.V3 translation, javajs.util.List<javajs.util.P3> finalPoints, float[] dihedralList)`
`(package private) void`	`rotateArcBall(int x, int y, float factor)`
`boolean`	`rotateAxisAngleAtCenter(JmolScriptEvaluator eval, javajs.util.P3 rotCenter, javajs.util.V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected)`
`void`	`rotateFront()`
`void`	`rotatePoint(javajs.util.P3 pt, javajs.util.P3 ptRot)`
`(package private) void`	`rotateSelected(float deltaX, float deltaY, BS bsSelected)`
`void`	`rotateX(float angleRadians)`
`void`	`rotateXDeg(int angleDegrees)`
`(package private) void`	`rotateXYBy(float xDelta, float yDelta)`
`void`	`rotateY(float angleRadians)`
`void`	`rotateYDeg(int angleDegrees)`
`void`	`rotateZ(float angleRadians)`
`void`	`rotateZBy(int zDelta, int x, int y)`
`java.lang.String`	`runScript(java.lang.String script)` run a script immediately and return output buffer string Jmol 13.1.15
`void`	`saveBonds(java.lang.String saveName)`
`ScriptContext`	`saveContext(java.lang.String saveName)`
`void`	`saveCoordinates(java.lang.String saveName, BS bsSelected)`
`(package private) void`	`saveModelOrientation()`
`void`	`saveOrientation(java.lang.String saveName, float[] pymolView)`
`void`	`saveScene(java.lang.String saveName, java.util.Map<java.lang.String,java.lang.Object> scene)`
`void`	`saveSelection(java.lang.String saveName)`
`void`	`saveState(java.lang.String saveName)`
`void`	`saveStructure(java.lang.String saveName)`
`float`	`scaleToPerspective(int z, float sizeAngstroms)`
`float`	`scaleToScreen(int z, int milliAngstroms)`
`java.lang.String`	`script(java.lang.String strScript)`
`java.lang.Object`	`scriptCheck(java.lang.String strScript)`
`private java.lang.Object`	`scriptCheckRet(java.lang.String strScript, boolean returnContext)`
`void`	`scriptEcho(java.lang.String strEcho)`
`void`	`scriptStatus(java.lang.String strStatus)`
`void`	`scriptStatusMsg(java.lang.String strStatus, java.lang.String statusMessage)`
`java.lang.String`	`scriptWait(java.lang.String strScript)`
`java.lang.Object`	`scriptWaitStatus(java.lang.String strScript, java.lang.String statusList)`
`void`	`select(BS bs, boolean isGroup, int addRemove, boolean isQuiet)`
`void`	`selectAll()`
`void`	`selectBonds(BS bs)`
`void`	`setAnimation(int tok)`
`void`	`setAnimationDirection(int direction)`
`void`	`setAnimationFps(int fps)`
`private void`	`setAnimationMode(java.lang.String mode)`
`void`	`setAnimationOn(boolean animationOn)`
`void`	`setAnimationRange(int modelIndex1, int modelIndex2)`
`void`	`setAnimationReplayMode(ANIM replayMode, float firstFrameDelay, float lastFrameDelay)`
`void`	`setAnimDisplay(BS bs)`
`void`	`setAnimMorphCount(int n)`
`private void`	`setAntialias(int tok, boolean TF)`
`void`	`setAppendNew(boolean value)`
`(package private) void`	`setApplySymmetryToBonds(boolean TF)`
`void`	`setAtomCoord(int atomIndex, float x, float y, float z)`
`void`	`setAtomCoordRelative(int atomIndex, float x, float y, float z)`
`void`	`setAtomCoords(BS bs, int tokType, java.lang.Object xyzValues)`
`void`	`setAtomCoordsRelative(javajs.util.T3 offset, BS bs)`
`void`	`setAtomData(int type, java.lang.String name, java.lang.String coordinateData, boolean isDefault)`
`void`	`setAtomLabel(java.lang.String value, int i)`
`private void`	`setAtomPickingOption(java.lang.String option)`
`void`	`setAtomProperty(BS bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)`
`void`	`setAutoBond(boolean TF)`
`private void`	`setAxesModeMolecular(boolean TF)`
`(package private) void`	`setAxesModeUnitCell(boolean TF)`
`void`	`setAxesOrientationRasmol(boolean TF)`
`(package private) void`	`setAxesScale(float scale)`
`void`	`setBackgroundImage(java.lang.String fileName, java.lang.Object image)`
`void`	`setBackgroundModelIndex(int modelIndex)`
`private void`	`setBondPickingOption(java.lang.String option)`
`void`	`setBondTolerance(float bondTolerance)`
`void`	`setBooleanProperty(java.lang.String key, boolean value)`
`private void`	`setBooleanPropertyTok(java.lang.String key, int tok, boolean value)`
`void`	`setBoundBox(javajs.util.P3 pt1, javajs.util.P3 pt2, boolean byCorner, float scale)`
`void`	`setCenterAt(int relativeTo, javajs.util.P3 pt)`
`void`	`setCenterBitSet(BS bsCenter, boolean doScale)`
`void`	`setCenterSelected()`
`void`	`setCentroid(BS bs, int[] minmax)`
`void`	`setCGO(javajs.util.List<java.lang.Object> info)`
`void`	`setColorBackground(java.lang.String colorName)`
`BS`	`setConformation()`
`void`	`setCurrentAtom(int iAtom)`
`void`	`setCurrentCage(java.lang.String isosurfaceId)`
`void`	`setCurrentCagePts(javajs.util.P3[] points)`
`void`	`setCurrentColorRange(float min, float max)`
`void`	`setCurrentColorRange(java.lang.String label)`
`void`	`setCurrentColorRangeData(float[] data, BS bs)`
`void`	`setCurrentModelID(java.lang.String id)`
`void`	`setCurrentModelIndex(int modelIndex)`
`void`	`setCurrentModelIndexClear(int modelIndex, boolean clearBackground)`
`void`	`setCurrentUnitCellOffset(javajs.util.P3 pt, int ijk)`
`void`	`setCursor(int cursor)`
`void`	`setData(java.lang.String type, java.lang.Object[] data, int arrayCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)`
`void`	`setDebugScript(boolean debugScript)`
`private void`	`setDefaultColors(boolean isRasmol)`
`void`	`setDefaultLattice(javajs.util.P3 p)`
`private void`	`setDefaultsType(java.lang.String type)`
`void`	`setDihedrals(float[] dihedralList, BS[] bsBranches, float rate)`
`void`	`setDisplay(java.lang.Object canvas)`
`void`	`setEchoStateActive(boolean TF)`
`void`	`setElementArgb(int elementNumber, int argb)`
`java.lang.String`	`setErrorMessage(java.lang.String errMsg, java.lang.String errMsgUntranslated)`
`void`	`setFileInfo(java.lang.String[] fileInfo)`
`private void`	`setFileLoadStatus(FIL ptLoad, java.lang.String fullPathName, java.lang.String fileName, java.lang.String modelName, java.lang.String strError, java.lang.Boolean isAsync)`
`void`	`setFloatProperty(java.lang.String key, float value)`
`private void`	`setFloatPropertyTok(java.lang.String key, int tok, float value)`
`void`	`setFocus()`
`void`	`setFormalCharges(int formalCharge)`
`void`	`setFrame(int i)`
`void`	`setFrameDelayMs(long millis)`
`(package private) void`	`setFrameOffset(int modelIndex)`
`void`	`setFrameOffsets(BS bsAtoms)`
`void`	`setFrameTitle(int modelIndex, java.lang.String title)`
`void`	`setFrameTitleObj(java.lang.Object title)`
`(package private) void`	`setFrameVariables()`
`void`	`setFrankOn(boolean TF)`
`void`	`setHoverLabel(java.lang.String strLabel)`
`void`	`setInMotion(boolean inMotion)`
`void`	`setInsertedCommand(java.lang.String strScript)`
`void`	`setIntProperty(java.lang.String key, int value)`
`private void`	`setIntPropertyTok(java.lang.String key, int tok, int value)`
`void`	`setIteratorForAtom(AtomIndexIterator iterator, int atomIndex, float distance)`
`void`	`setIteratorForPoint(AtomIndexIterator iterator, int modelIndex, javajs.util.P3 pt, float distance)`
`void`	`setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)`
`void`	`setJmolDataFrame(java.lang.String type, int modelIndex, int dataIndex)`
`void`	`setJmolDefaults()`
`void`	`setJmolStatusListener(JmolStatusListener jmolStatusListener)`
`void`	`setLigandModel(java.lang.String key, java.lang.String data)`
`java.lang.Object`	`setLoadFormat(java.lang.String name, char type, boolean withPrefix)` Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first.
`private java.util.Map<java.lang.String,java.lang.Object>`	`setLoadParameters(java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)`
`void`	`setMarBond(short marBond)`
`private void`	`setMaximumSize(int x)`
`void`	`setMenu(java.lang.String fileOrText, boolean isFile)`
`void`	`setMeshCreator(java.lang.Object meshCreator)` an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
`void`	`setMinBondDistance(float minBondDistance)`
`private void`	`setModelKitMode(boolean value)`
`void`	`setModelSet(ModelSet modelSet)`
`void`	`setModelVisibility()`
`void`	`setModulation(BS bs, boolean isOn, javajs.util.P3 t1, boolean isQ)`
`void`	`setMotionFixedAtoms(BS bs)`
`void`	`setMouseEnabled(boolean TF)`
`private BS`	`setMovableBitSet(BS bsSelected, boolean checkMolecule)`
`void`	`setMovie(java.util.Map<java.lang.String,java.lang.Object> info)`
`void`	`setNavigationDepthPercent(float percent)`
`void`	`setNavigationMode(boolean TF)`
`void`	`setNavOn(boolean navOn)`
`void`	`setNavXYZ(float x, float y, float z)`
`void`	`setNewRotationCenter(javajs.util.P3 center)`
`void`	`setNoneSelected(boolean noneSelected)`
`void`	`setObjectArgb(java.lang.String name, int argb)`
`(package private) void`	`setObjectColor(java.lang.String name, java.lang.String colorName)`
`void`	`setObjectMad(int iShape, java.lang.String name, int mad)`
`java.lang.String`	`setObjectProp(java.lang.String id, int tokCommand)`
`void`	`setObjectVisibility(java.lang.String name, boolean b)`
`private void`	`setOptions(java.util.Map<java.lang.String,java.lang.Object> info)`
`boolean`	`setParallel(boolean TF)`
`void`	`setPdbConectBonding(boolean isAuto, boolean isStateScript)`
`(package private) void`	`setPendingMeasurement(MeasurementPending mp)`
`void`	`setPercentVdwAtom(int value)`
`void`	`setPerspectiveDepth(boolean perspectiveDepth)`
`void`	`setPicked(int iAtom)`
`(package private) void`	`setPickingMode(java.lang.String strMode, int pickingMode)`
`(package private) void`	`setPickingStyle(java.lang.String style, int pickingStyle)`
`void`	`setPropertyColorScheme(java.lang.String scheme, boolean isTranslucent, boolean isOverloaded)`
`void`	`setProteinType(STR type, BS bs)`
`void`	`setRasmolDefaults()`
`private void`	`setRefreshing(boolean TF)`
`void`	`setRotateBondIndex(int index)`
`void`	`setRotationMatrix(javajs.util.M3 rotationMatrix)`
`void`	`setRotationRadius(float angstroms, boolean doAll)`
`void`	`setRubberbandArgb(int argb)`
`void`	`setScreenDimension(int width, int height)`
`private void`	`setScriptQueue(boolean TF)`
`void`	`setScriptStatus(java.lang.String strStatus, java.lang.String statusMessage, int msWalltime, java.lang.String strErrorMessageUntranslated)`
`void`	`setSelectedAtom(int atomIndex, boolean TF)`
`void`	`setSelectionHalos(boolean TF)`
`void`	`setSelectionSet(BS set)`
`void`	`setSelectionSubset(BS subset)`
`void`	`setShapeErrorState(int shapeID, java.lang.String state)`
`void`	`setShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object value)`
`void`	`setShapeSize(int shapeID, int mad, BS bsSelected)`
`void`	`setShapeSizeRD(int shapeID, RadiusData rd, BS bsAtoms)`
`void`	`setShowAxes(boolean value)`
`void`	`setShowBbcage(boolean value)`
`void`	`setShowHydrogens(boolean TF)`
`void`	`setShowMeasurements(boolean TF)`
`void`	`setShowUnitCell(boolean value)`
`void`	`setSlabDepthInternal(boolean isDepth)`
`void`	`setSmilesString(java.lang.String s)`
`void`	`setSpin(java.lang.String key, int value)`
`void`	`setSpinOn(boolean spinOn)`
`private void`	`setStartupBooleans()`
`void`	`setStatusAtomHovered(int atomIndex, java.lang.String info)`
`void`	`setStatusAtomPicked(int atomIndex, java.lang.String info, java.util.Map<java.lang.String,java.lang.Object> map)`
`(package private) void`	`setStatusFrameChanged(boolean isVib, boolean doNotify)`
`void`	`setStatusMeasuring(java.lang.String status, int intInfo, java.lang.String strMeasure, float value)`
`void`	`setStatusObjectHovered(java.lang.String id, java.lang.String info, javajs.util.P3 pt)`
`void`	`setStatusResized(int width, int height)`
`void`	`setStereo(boolean isStereoSlave, java.lang.Object gRight)`
`void`	`setStereoMode(int[] twoColors, STER stereoMode, float degrees)`
`private void`	`setStrandCount(int type, int value)`
`void`	`setStringProperty(java.lang.String key, java.lang.String value)`
`private void`	`setStringPropertyTok(java.lang.String key, int tok, java.lang.String value)`
`void`	`setStructureList(float[] list, STR type)`
`private void`	`setSync()`
`void`	`setSyncDriver(int mode)`
`private void`	`setSyncTarget(int mode, boolean TF)`
`void`	`setTainted(boolean TF)`
`void`	`setTaintedAtoms(BS bs, byte type)`
`void`	`setTimeout(java.lang.String name, int mSec, java.lang.String script)`
`(package private) void`	`setTrajectory(int modelIndex)`
`void`	`setTrajectoryBs(BS bsModels)`
`private void`	`setTransformManagerDefaults()`
`void`	`setUnits(java.lang.String units, boolean isDistance)`
`void`	`setUserScale(int[] scale)`
`SV`	`setUserVariable(java.lang.String name, SV value)`
`(package private) void`	`setUserVdw(VDW mode)`
`(package private) void`	`setVdwStr(java.lang.String name)`
`void`	`setVectorScale(float scale)`
`void`	`setVibrationOff()`
`void`	`setVibrationPeriod(float period)`
`void`	`setVibrationScale(float scale)`
`void`	`setZslabPoint(javajs.util.P3 pt)`
`void`	`show2D(java.lang.String smiles)`
`void`	`showConsole(boolean showConsole)`
`void`	`showEditor(java.lang.String[] file_text)`
`void`	`showMessage(java.lang.String s)`
`void`	`showParameter(java.lang.String key, boolean ifNotSet, int nMax)`
`void`	`showString(java.lang.String str, boolean isPrint)`
`java.lang.String`	`showTimeout(java.lang.String name)`
`void`	`showUrl(java.lang.String urlString)`
`(package private) void`	`slabByPixels(int pixels)`
`(package private) void`	`slabDepthByPixels(int pixels)`
`void`	`slabInternal(javajs.util.P4 plane, boolean isDepth)`
`void`	`slabReset()`
`void`	`slabToPercent(int percentSlab)`
`void`	`spinXYBy(int xDelta, int yDelta, float speed)`
`void`	`startHoverWatcher(boolean tf)`
`void`	`startSpinningAxis(javajs.util.P3 pt1, javajs.util.P3 pt2, boolean isClockwise)`
`(package private) void`	`stopMinimization()`
`void`	`stopMotion()`
`void`	`syncScript(java.lang.String script, java.lang.String applet, int port)`
`void`	`toCartesian(javajs.util.P3 pt, boolean asAbsolute)` absolute or relative to origin of UNITCELL {x y z}
`void`	`toFractional(javajs.util.P3 pt, boolean asAbsolute)` absolute or relative to origin of UNITCELL {x y z}
`void`	`togglePickingLabel(BS bs)`
`void`	`toUnitCell(javajs.util.P3 pt, javajs.util.P3 offset)` relative to origin without regard to UNITCELL {x y z}
`void`	`transformPoints(int count, javajs.util.P3[] pointsAngstroms, javajs.util.P3i[] pointsScreens)`
`javajs.util.P3i`	`transformPt(javajs.util.P3 pointAngstroms)`
`void`	`transformPt3f(javajs.util.P3 pointAngstroms, javajs.util.P3 pointScreen)`
`void`	`transformPtNoClip(javajs.util.P3 pointAngstroms, javajs.util.P3 pt)`
`void`	`transformPtScr(javajs.util.P3 pointAngstroms, javajs.util.P3i pointScreen)`
`javajs.util.P3i`	`transformPtVib(javajs.util.P3 pointAngstroms, Vibration vibrationVector)`
`void`	`transformVector(javajs.util.V3 vectorAngstroms, javajs.util.V3 vectorTransformed)`
`void`	`translate(char xyz, float x, char type, BS bsAtoms)`
`void`	`translateXYBy(int xDelta, int yDelta)`
`void`	`triggerTimeout(java.lang.String name)`
`void`	`unBindAction(java.lang.String desc, java.lang.String name)`
`(package private) void`	`undoClear()`
`void`	`undoMoveAction(int action, int n)`
`(package private) void`	`undoMoveActionClear(int taintedAtom, int type, boolean clearRedo)`
`float`	`unscaleToScreen(float z, float screenDistance)`
`void`	`unsetProperty(java.lang.String key)`
`void`	`unTransformPoint(javajs.util.P3 pointScreen, javajs.util.P3 pointAngstroms)`
`void`	`updateJS(int width, int height)` for JavaScript only
`private void`	`updateJSView(int imodel, int iatom)` File has been loaded or model has been changed or atom picked.
`private boolean`	`updateWindow(int width, int height)`
`boolean`	`useMinimizationThread()`
`java.lang.String`	`writeFileData(java.lang.String fileName, java.lang.String type, int modelIndex, java.lang.Object[] parameters)`
`void`	`writeTextFile(java.lang.String fileName, java.lang.String data)`
`void`	`zap(boolean notify, boolean resetUndo, boolean zapModelKit)`
`private void`	`zapMsg(java.lang.String msg)`
`(package private) void`	`zoomBy(int pixels)`
`(package private) void`	`zoomByFactor(float factor, int x, int y)`
`int`	`zValueFromPercent(int zPercent)`

Methods inherited from class org.jmol.api.JmolViewer
allocateViewer, allocateViewer, checkOption, getJmolValueAsString, getJsObjectInfo, mouseEvent, openFileAsync, renderScreenImage, setConsole

Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

autoExit
```
public boolean autoExit
```

haveDisplay
```
public boolean haveDisplay
```

isJS
```
public boolean isJS
```

isWebGL
```
public boolean isWebGL
```

isSingleThreaded
```
public boolean isSingleThreaded
```

queueOnHold
```
public boolean queueOnHold
```

fullName
```
public java.lang.String fullName
```

appletDocumentBase

public static java.lang.String appletDocumentBase

appletCodeBase

public static java.lang.String appletCodeBase

appletIdiomaBase

public static java.lang.String appletIdiomaBase

jsDocumentBase

public static java.lang.String jsDocumentBase

compiler
```
public java.lang.Object compiler
```

definedAtomSets

public java.util.Map<java.lang.String,java.lang.Object> definedAtomSets

ms
```
public ModelSet ms
```

fm
```
public FileManager fm
```

isApplet
```
private boolean isApplet
```

isJNLP
```
private boolean isJNLP
```

isSyntaxAndFileCheck
```
public boolean isSyntaxAndFileCheck
```

isSyntaxCheck
```
public boolean isSyntaxCheck
```

listCommands
```
public boolean listCommands
```

mustRender
```
boolean mustRender
```

htmlName
```
public java.lang.String htmlName
```

appletName
```
public java.lang.String appletName
```

insertedCommand

private java.lang.String insertedCommand

gdata
```
GData gdata
```

applet
```
java.lang.Object applet
```

actionManager
```
ActionManager actionManager
```

am
```
AnimationManager am
```

cm
```
ColorManager cm
```

dm
```
JmolDataManager dm
```

shm
```
ShapeManager shm
```

slm
```
SelectionManager slm
```

rm
```
JmolRepaintManager rm
```

g
```
public GlobalSettings g
```

sm
```
public StatusManager sm
```

tm
```
TransformManager tm
```

strJavaVendor

public static final java.lang.String strJavaVendor

strOSName

public static final java.lang.String strOSName

strJavaVersion

public static final java.lang.String strJavaVersion

syncId
```
java.lang.String syncId
```

logFilePath
```
private java.lang.String logFilePath
```

allowScripting
```
private boolean allowScripting
```

isPrintOnly
```
private boolean isPrintOnly
```

isSignedApplet
```
private boolean isSignedApplet
```

isSignedAppletLocal
```
private boolean isSignedAppletLocal
```

isSilent
```
private boolean isSilent
```

multiTouch
```
private boolean multiTouch
```

noGraphicsAllowed
```
private boolean noGraphicsAllowed
```

useCommandThread
```
private boolean useCommandThread
```

commandOptions

private java.lang.String commandOptions

vwrOptions

private java.util.Map<java.lang.String,java.lang.Object> vwrOptions

display
```
private java.lang.Object display
```

modelAdapter
```
private JmolAdapter modelAdapter
```

access
```
private Viewer.ACCESS access
```

commandHistory
```
private CommandHistory commandHistory
```

mm
```
private ModelManager mm
```

stm
```
private StateManager stm
```

scm
```
private JmolScriptManager scm
```

eval
```
public JmolScriptEvaluator eval
```

tempArray
```
private TempArray tempArray
```

allowArrayDotNotation
```
public boolean allowArrayDotNotation
```

version_date

private static java.lang.String version_date

isPreviewOnly
```
private boolean isPreviewOnly
```

mouseEnabled
```
private boolean mouseEnabled
```

noneSelected
```
private boolean noneSelected
```

mouse
```
private javajs.api.GenericMouseInterface mouse
```
either org.jmol.awt.Mouse or org.jmol.awtjs2d.Mouse

ligandModels

java.util.Map<java.lang.String,java.lang.Object> ligandModels

ligandModelSet

java.util.Map<java.lang.String,java.lang.Boolean> ligandModelSet

minimizer
```
private MinimizerInterface minimizer
```

smilesMatcher

private SmilesMatcherInterface smilesMatcher

jsc
```
JmolStateCreator jsc
```

bsFrameOffsets
```
BS bsFrameOffsets
```

frameOffsets
```
javajs.util.P3[] frameOffsets
```

motionEventNumber
```
private int motionEventNumber
```

inMotion
```
private boolean inMotion
```

refreshing
```
private boolean refreshing
```

axesAreTainted
```
private boolean axesAreTainted
```

dimScreen
```
final javajs.awt.Dimension dimScreen
```

maximumSize
```
private int maximumSize
```

imageFontScaling
```
private float imageFontScaling
```

gRight
```
private java.lang.Object gRight
```
A graphics from a "slave" stereo display that has been synchronized with this this applet.

isStereoSlave
```
private boolean isStereoSlave
```
A flag to indicate that THIS is the right-side panel of a pair of synced applets running a left-right stereo display (that would be piped into a dual-image polarized projector system such as GeoWall).

captureParams

public java.util.Map<java.lang.String,java.lang.Object> captureParams

jsParams

private java.util.Map<java.lang.String,java.lang.Object> jsParams

antialiasDisplay
```
private boolean antialiasDisplay
```

hoverAtomIndex
```
int hoverAtomIndex
```

hoverText
```
java.lang.String hoverText
```

hoverEnabled
```
public boolean hoverEnabled
```

currentCursor
```
private int currentCursor
```

prevFrame
```
int prevFrame
```

prevMorphModel
```
private float prevMorphModel
```

haveJDX
```
private boolean haveJDX
```

jsv
```
private JmolJSpecView jsv
```

language
```
private java.lang.String language
```

rd
```
private RadiusData rd
```

frankOn
```
private boolean frankOn
```

scriptEditorVisible
```
public boolean scriptEditorVisible
```

appConsole
```
JmolAppConsoleInterface appConsole
```

scriptEditor
```
JmolScriptEditorInterface scriptEditor
```

jmolpopup

javajs.api.GenericMenuInterface jmolpopup

modelkitPopup

private javajs.api.GenericMenuInterface modelkitPopup

headlessImageParams

private java.util.Map<java.lang.String,java.lang.Object> headlessImageParams

pm
```
JmolPropertyManager pm
```

isTainted
```
boolean isTainted
```

movingSelected
```
private boolean movingSelected
```

showSelected
```
private boolean showSelected
```

rotateBondIndex
```
private int rotateBondIndex
```

rotatePrev1
```
private int rotatePrev1
```

rotatePrev2
```
private int rotatePrev2
```

bsRotateBranch
```
private BS bsRotateBranch
```

creatingImage
```
public boolean creatingImage
```

outputManager
```
private OutputManager outputManager
```

SYNC_GRAPHICS_MESSAGE

public static final java.lang.String SYNC_GRAPHICS_MESSAGE

See Also:: Constant Field Values

SYNC_NO_GRAPHICS_MESSAGE

public static final java.lang.String SYNC_NO_GRAPHICS_MESSAGE

See Also:: Constant Field Values

bsUserVdws
```
BS bsUserVdws
```

userVdws
```
float[] userVdws
```

userVdwMars
```
int[] userVdwMars
```

defaultVdw
```
VDW defaultVdw
```

errorMessage
```
private java.lang.String errorMessage
```

errorMessageUntranslated

private java.lang.String errorMessageUntranslated

currentShapeID
```
private int currentShapeID
```

currentShapeState

private java.lang.String currentShapeState

staticFunctions

static final java.util.Map<java.lang.String,JmolScriptFunction> staticFunctions

localFunctions

java.util.Map<java.lang.String,JmolScriptFunction> localFunctions

privateKey
```
private double privateKey
```

isKiosk
```
boolean isKiosk
```

executor
```
private java.lang.Object executor
```

nProcessors
```
public static int nProcessors
```

displayLoadErrors
```
public boolean displayLoadErrors
```

isParallel
```
boolean isParallel
```

actionStates

final javajs.util.List<java.lang.String> actionStates

actionStatesRedo

final javajs.util.List<java.lang.String> actionStatesRedo

stateScriptVersionInt
```
public int stateScriptVersionInt
```

jsExporter3D

private JmolRendererInterface jsExporter3D

htPdbBondInfo

java.util.Map<java.lang.String,java.lang.String[][]> htPdbBondInfo

timeouts

java.util.Map<java.lang.String,java.lang.Object> timeouts

chainMap

public java.util.Map<java.lang.Object,java.lang.Object> chainMap

chainList

public javajs.util.List<java.lang.String> chainList

nmrCalculation
```
JmolNMRInterface nmrCalculation
```

logFileName
```
java.lang.String logFileName
```

Constructor Detail
- Viewer
```
public Viewer(java.util.Map<java.lang.String,java.lang.Object> info)
```
  new way...
  
  Parameters:
  
  info - "display" "adapter" "statusListener" "platform" "options" "fullName" "documentBase" "codeBase" "multiTouch" [options] "noGraphics" "printOnly" "previewOnly" "debug" "applet" "signedApplet" "appletProxy" "useCommandThread" "platform" [option] "backgroundTransparent" "exit" "listCommands" "check" "checkLoad" "silent" "access:READSPT" "access:NONE" "menuFile" "headlessMaxTimeMs" "headlessImage" "isDataOnly"

Method Detail

finalize
```
protected void finalize()
                 throws java.lang.Throwable
```
Overrides:

finalize in class java.lang.Object

Throws:

java.lang.Throwable

hasDisplay
```
public boolean hasDisplay()
```

isApplet
```
public boolean isApplet()
```
Specified by:

isApplet in class JmolViewer

setInsertedCommand

public void setInsertedCommand(java.lang.String strScript)

getActionManager

public ActionManager getActionManager()

getLogFilePath
```
java.lang.String getLogFilePath()
```

isSignedApplet
```
public boolean isSignedApplet()
```

getJmolVersion

public static java.lang.String getJmolVersion()

allocateViewer

protected static JmolViewer allocateViewer(java.lang.Object display,
                                           JmolAdapter modelAdapter,
                                           java.lang.String fullName,
                                           java.net.URL documentBase,
                                           java.net.URL codeBase,
                                           java.lang.String commandOptions,
                                           JmolStatusListener statusListener,
                                           javajs.api.GenericPlatform implementedPlatform)

old way...

Parameters:: display -; modelAdapter -; fullName -; documentBase -; codeBase -; commandOptions -; statusListener -; implementedPlatform -
Returns:: JmolViewer object

getStatusManager
```
StatusManager getStatusManager()
```

haveAccess

public boolean haveAccess(Viewer.ACCESS a)

getModelAdapter
```
public JmolAdapter getModelAdapter()
```
Specified by:

getModelAdapter in class JmolViewer

getSymmetryInfo

public java.lang.Object getSymmetryInfo(BS bsAtoms,
                                        java.lang.String xyz,
                                        int op,
                                        javajs.util.P3 pt,
                                        javajs.util.P3 pt2,
                                        java.lang.String id,
                                        int type)

getSmartsMatch

public BS getSmartsMatch(java.lang.String smarts,
                         BS bsSelected)
                  throws java.lang.Exception

Specified by:: getSmartsMatch in class JmolViewer
Throws:: java.lang.Exception

getViewerOptions

public java.util.Map<java.lang.String,java.lang.Object> getViewerOptions()

setOptions

private void setOptions(java.util.Map<java.lang.String,java.lang.Object> info)

setDisplay

public void setDisplay(java.lang.Object canvas)

newMeasurementData

public MeasurementData newMeasurementData(java.lang.String id,
                                          javajs.util.List<java.lang.Object> points)

getDataManager

private JmolDataManager getDataManager()

getScriptManager

private JmolScriptManager getScriptManager()

checkOption2

private boolean checkOption2(java.lang.String key1,
                             java.lang.String key2)

isPreviewOnly
```
public boolean isPreviewOnly()
```

isHeadless
```
public boolean isHeadless()
```

setStartupBooleans
```
private void setStartupBooleans()
```

noGraphicsAllowed
```
public boolean noGraphicsAllowed()
```

getExportDriverList

public java.lang.String getExportDriverList()

getHtmlName
```
public java.lang.String getHtmlName()
```

getDisplay
```
public java.lang.Object getDisplay()
```
Specified by:

getDisplay in class JmolViewer

dispose
```
public void dispose()
```
end of life for this viewer

Overrides:

dispose in class JmolViewer

reset

public void reset(boolean includingSpin)

homePosition
```
public void homePosition()
```
Specified by:

homePosition in class JmolViewer

initialize

public void initialize(boolean clearUserVariables)

listSavedStates

public java.lang.String listSavedStates()

saveOrientation

public void saveOrientation(java.lang.String saveName,
                            float[] pymolView)

saveScene

public void saveScene(java.lang.String saveName,
                      java.util.Map<java.lang.String,java.lang.Object> scene)

restoreScene

public void restoreScene(java.lang.String saveName,
                         float timeSeconds)

restoreOrientation

public boolean restoreOrientation(java.lang.String saveName,
                                  float timeSeconds)

restoreRotation

public void restoreRotation(java.lang.String saveName,
                            float timeSeconds)

saveModelOrientation
```
void saveModelOrientation()
```

getOrientation
```
public Orientation getOrientation()
```

restoreModelOrientation

void restoreModelOrientation(int modelIndex)

restoreModelRotation

void restoreModelRotation(int modelIndex)

saveBonds

public void saveBonds(java.lang.String saveName)

saveContext

public ScriptContext saveContext(java.lang.String saveName)

getContext

public ScriptContext getContext(java.lang.String saveName)

restoreBonds

public boolean restoreBonds(java.lang.String saveName)

saveState

public void saveState(java.lang.String saveName)

deleteSaved

public void deleteSaved(java.lang.String name)

getSavedState

public java.lang.String getSavedState(java.lang.String saveName)

saveStructure

public void saveStructure(java.lang.String saveName)

getSavedStructure

public java.lang.String getSavedStructure(java.lang.String saveName)

saveCoordinates

public void saveCoordinates(java.lang.String saveName,
                            BS bsSelected)

getSavedCoordinates

public java.lang.String getSavedCoordinates(java.lang.String saveName)

saveSelection

public void saveSelection(java.lang.String saveName)

restoreSelection

public boolean restoreSelection(java.lang.String saveName)

getMatrixtransform

public javajs.util.M4 getMatrixtransform()

getRotationQuaternion

public javajs.util.Quat getRotationQuaternion()

getGLmolView
```
public java.lang.Object getGLmolView()
```
This method is only called by JmolGLmol applet._refresh();

Returns:

enough data to update a WebGL view

setRotationRadius

public void setRotationRadius(float angstroms,
                              boolean doAll)

getRotationCenter

public javajs.util.P3 getRotationCenter()

setCenterAt

public void setCenterAt(int relativeTo,
                        javajs.util.P3 pt)

setCenterBitSet

public void setCenterBitSet(BS bsCenter,
                            boolean doScale)

setNewRotationCenter

public void setNewRotationCenter(javajs.util.P3 center)

getNavigationCenter

public javajs.util.P3 getNavigationCenter()

getNavigationDepthPercent

public float getNavigationDepthPercent()

navigate

void navigate(int keyWhere,
              int modifiers)

getNavigationOffset

public javajs.util.P3 getNavigationOffset()

getNavigationOffsetPercent

public float getNavigationOffsetPercent(char XorY)

isNavigating
```
public boolean isNavigating()
```

isInPosition

public boolean isInPosition(javajs.util.V3 axis,
                            float degrees)

move

public void move(JmolScriptEvaluator eval,
                 javajs.util.V3 dRot,
                 float dZoom,
                 javajs.util.V3 dTrans,
                 float dSlab,
                 float floatSecondsTotal,
                 int fps)

stopMotion
```
public void stopMotion()
```

setRotationMatrix

public void setRotationMatrix(javajs.util.M3 rotationMatrix)

moveTo

public void moveTo(JmolScriptEvaluator eval,
                   float floatSecondsTotal,
                   javajs.util.P3 center,
                   javajs.util.V3 rotAxis,
                   float degrees,
                   javajs.util.M3 rotationMatrix,
                   float zoom,
                   float xTrans,
                   float yTrans,
                   float rotationRadius,
                   javajs.util.P3 navCenter,
                   float xNav,
                   float yNav,
                   float navDepth,
                   float cameraDepth,
                   float cameraX,
                   float cameraY)

moveUpdate

public void moveUpdate(float floatSecondsTotal)

getMoveToText

public java.lang.String getMoveToText(float timespan)

navigateList

public void navigateList(JmolScriptEvaluator eval,
                         javajs.util.List<java.lang.Object[]> list)

navigatePt

public void navigatePt(javajs.util.P3 center)

navigateAxis

public void navigateAxis(javajs.util.V3 rotAxis,
                         float degrees)

navTranslatePercent

public void navTranslatePercent(float x,
                                float y)

setMouseEnabled

public void setMouseEnabled(boolean TF)

processMultitouchEvent

public void processMultitouchEvent(int groupID,
                                   int eventType,
                                   int touchID,
                                   int iData,
                                   javajs.util.P3 pt,
                                   long time)

Specified by:: processMultitouchEvent in class JmolViewer

zoomBy
```
void zoomBy(int pixels)
```

zoomByFactor

void zoomByFactor(float factor,
                  int x,
                  int y)

rotateXYBy

void rotateXYBy(float xDelta,
                float yDelta)

spinXYBy

public void spinXYBy(int xDelta,
                     int yDelta,
                     float speed)

rotateZBy

public void rotateZBy(int zDelta,
                      int x,
                      int y)

rotateSelected

void rotateSelected(float deltaX,
                    float deltaY,
                    BS bsSelected)

setMovableBitSet

private BS setMovableBitSet(BS bsSelected,
                            boolean checkMolecule)

translateXYBy

public void translateXYBy(int xDelta,
                          int yDelta)

rotateFront
```
public void rotateFront()
```
Specified by:

rotateFront in class JmolViewer

rotateX
```
public void rotateX(float angleRadians)
```
Specified by:

rotateX in class JmolViewer

rotateY
```
public void rotateY(float angleRadians)
```
Specified by:

rotateY in class JmolViewer

rotateZ
```
public void rotateZ(float angleRadians)
```
Specified by:

rotateZ in class JmolViewer

rotateXDeg
```
public void rotateXDeg(int angleDegrees)
```
Specified by:

rotateXDeg in class JmolViewer

rotateYDeg
```
public void rotateYDeg(int angleDegrees)
```
Specified by:

rotateYDeg in class JmolViewer

translate

public void translate(char xyz,
                      float x,
                      char type,
                      BS bsAtoms)

getTranslationXPercent
```
public float getTranslationXPercent()
```

getTranslationYPercent
```
public float getTranslationYPercent()
```

getTranslationZPercent
```
float getTranslationZPercent()
```

getTranslationScript

public java.lang.String getTranslationScript()

getZShadeStart
```
public int getZShadeStart()
```

isWindowCentered
```
public boolean isWindowCentered()
```

getZoomPercent
```
public int getZoomPercent()
```
Specified by:

getZoomPercent in class JmolViewer

getZoomSetting
```
public float getZoomSetting()
```

getZoomPercentFloat
```
public float getZoomPercentFloat()
```
Specified by:

getZoomPercentFloat in class JmolViewer

getMaxZoomPercent
```
public float getMaxZoomPercent()
```

slabReset
```
public void slabReset()
```

getZoomEnabled
```
public boolean getZoomEnabled()
```

getSlabEnabled
```
public boolean getSlabEnabled()
```

slabByPixels
```
void slabByPixels(int pixels)
```

depthByPixels
```
void depthByPixels(int pixels)
```

slabDepthByPixels
```
void slabDepthByPixels(int pixels)
```

slabInternal

public void slabInternal(javajs.util.P4 plane,
                         boolean isDepth)

slabToPercent

public void slabToPercent(int percentSlab)

depthToPercent

public void depthToPercent(int percentDepth)

setSlabDepthInternal

public void setSlabDepthInternal(boolean isDepth)

zValueFromPercent

public int zValueFromPercent(int zPercent)

getUnscaledTransformMatrix
```
public javajs.util.M4 getUnscaledTransformMatrix()
```
Specified by:

getUnscaledTransformMatrix in class JmolViewer

finalizeTransformParameters

public void finalizeTransformParameters()

rotatePoint

public void rotatePoint(javajs.util.P3 pt,
                        javajs.util.P3 ptRot)

transformPt

public javajs.util.P3i transformPt(javajs.util.P3 pointAngstroms)

transformPtVib

public javajs.util.P3i transformPtVib(javajs.util.P3 pointAngstroms,
                                      Vibration vibrationVector)

transformPtScr

public void transformPtScr(javajs.util.P3 pointAngstroms,
                           javajs.util.P3i pointScreen)

transformPtNoClip

public void transformPtNoClip(javajs.util.P3 pointAngstroms,
                              javajs.util.P3 pt)

transformPt3f

public void transformPt3f(javajs.util.P3 pointAngstroms,
                          javajs.util.P3 pointScreen)

transformPoints

public void transformPoints(int count,
                            javajs.util.P3[] pointsAngstroms,
                            javajs.util.P3i[] pointsScreens)

transformVector

public void transformVector(javajs.util.V3 vectorAngstroms,
                            javajs.util.V3 vectorTransformed)

unTransformPoint

public void unTransformPoint(javajs.util.P3 pointScreen,
                             javajs.util.P3 pointAngstroms)

getScalePixelsPerAngstrom

public float getScalePixelsPerAngstrom(boolean asAntialiased)

scaleToScreen

public float scaleToScreen(int z,
                           int milliAngstroms)

unscaleToScreen

public float unscaleToScreen(float z,
                             float screenDistance)

scaleToPerspective

public float scaleToPerspective(int z,
                                float sizeAngstroms)

setSpin

public void setSpin(java.lang.String key,
                    int value)

getSpinState

public java.lang.String getSpinState()

setSpinOn

public void setSpinOn(boolean spinOn)

getSpinOn
```
public boolean getSpinOn()
```

setNavOn
```
public void setNavOn(boolean navOn)
```

getNavOn
```
public boolean getNavOn()
```

setNavXYZ

public void setNavXYZ(float x,
                      float y,
                      float z)

getOrientationText

public java.lang.String getOrientationText(int type,
                                           java.lang.String name)

getOrientationInfo

java.util.Map<java.lang.String,java.lang.Object> getOrientationInfo()

getMatrixRotate
```
javajs.util.M3 getMatrixRotate()
```

getAxisAngle

public void getAxisAngle(javajs.util.A4 axisAngle)

getTransformText

public java.lang.String getTransformText()

getRotation

public void getRotation(javajs.util.M3 matrixRotation)

getCurrentColorRange
```
public float[] getCurrentColorRange()
```

setDefaultColors

private void setDefaultColors(boolean isRasmol)

getColorArgbOrGray

public int getColorArgbOrGray(short colix)

setRubberbandArgb

public void setRubberbandArgb(int argb)

getColixRubberband
```
public short getColixRubberband()
```

setElementArgb

public void setElementArgb(int elementNumber,
                           int argb)

setVectorScale
```
public void setVectorScale(float scale)
```
Specified by:

setVectorScale in class JmolViewer

isVibrationOn
```
public boolean isVibrationOn()
```

setVibrationScale
```
public void setVibrationScale(float scale)
```
Specified by:

setVibrationScale in class JmolViewer

setVibrationOff
```
public void setVibrationOff()
```

setVibrationPeriod
```
public void setVibrationPeriod(float period)
```
Specified by:

setVibrationPeriod in class JmolViewer

setObjectColor

void setObjectColor(java.lang.String name,
                    java.lang.String colorName)

setObjectVisibility

public void setObjectVisibility(java.lang.String name,
                                boolean b)

setObjectArgb

public void setObjectArgb(java.lang.String name,
                          int argb)

setBackgroundImage

public void setBackgroundImage(java.lang.String fileName,
                               java.lang.Object image)

getObjectArgb
```
int getObjectArgb(int objId)
```

getObjectColix

public short getObjectColix(int objId)

getFontState

public java.lang.String getFontState(java.lang.String myType,
                                     javajs.awt.Font font3d)

setColorBackground
```
public void setColorBackground(java.lang.String colorName)
```
Specified by:

setColorBackground in class JmolViewer

getBackgroundArgb
```
public int getBackgroundArgb()
```
Specified by:

getBackgroundArgb in class JmolViewer

setObjectMad

public void setObjectMad(int iShape,
                         java.lang.String name,
                         int mad)

getObjectMad
```
public int getObjectMad(int objId)
```

setPropertyColorScheme

public void setPropertyColorScheme(java.lang.String scheme,
                                   boolean isTranslucent,
                                   boolean isOverloaded)

getPropertyColorScheme

public java.lang.String getPropertyColorScheme()

getColixBackgroundContrast

public short getColixBackgroundContrast()

getSpecularState

public java.lang.String getSpecularState()

getColixAtomPalette

public short getColixAtomPalette(Atom atom,
                                 byte pid)

getColixBondPalette

public short getColixBondPalette(Bond bond,
                                 int pid)

getColorSchemeList

public java.lang.String getColorSchemeList(java.lang.String colorScheme)

setUserScale

public void setUserScale(int[] scale)

getColixForPropertyValue

public short getColixForPropertyValue(float val)

getColorPointForPropertyValue

public javajs.util.P3 getColorPointForPropertyValue(float val)

select

public void select(BS bs,
                   boolean isGroup,
                   int addRemove,
                   boolean isQuiet)

setSelectionSet
```
public void setSelectionSet(BS set)
```
Specified by:

setSelectionSet in class JmolViewer

selectBonds
```
public void selectBonds(BS bs)
```

displayAtoms

public void displayAtoms(BS bs,
                         boolean isDisplay,
                         boolean isGroup,
                         int addRemove,
                         boolean isQuiet)

getUndeletedGroupAtomBits

private BS getUndeletedGroupAtomBits(BS bs)

getHiddenSet
```
public BS getHiddenSet()
```

isSelected

public boolean isSelected(int atomIndex)

isInSelectionSubset

boolean isInSelectionSubset(int atomIndex)

reportSelection

void reportSelection(java.lang.String msg)

getAtomSetCenter

public javajs.util.P3 getAtomSetCenter(BS bs)

clearAtomSets
```
private void clearAtomSets()
```

getDefinedAtomSet

public BS getDefinedAtomSet(java.lang.String name)

selectAll
```
public void selectAll()
```
Specified by:

selectAll in class JmolViewer

setNoneSelected

public void setNoneSelected(boolean noneSelected)

getNoneSelected

public java.lang.Boolean getNoneSelected()

clearSelection
```
public void clearSelection()
```
Specified by:

clearSelection in class JmolViewer

setSelectionSubset

public void setSelectionSubset(BS subset)

getSelectionSubset
```
public BS getSelectionSubset()
```

invertSelection
```
public void invertSelection()
```

getSelectedAtoms
```
public BS getSelectedAtoms()
```
Specified by:

getSelectedAtoms in class JmolViewer

getSelectedAtomsNoSubset
```
public BS getSelectedAtomsNoSubset()
```

setSelectedAtom

public void setSelectedAtom(int atomIndex,
                            boolean TF)

isAtomSelected

public boolean isAtomSelected(int atomIndex)

getSelectionCount
```
public int getSelectionCount()
```
Specified by:

getSelectionCount in class JmolViewer

setFormalCharges

public void setFormalCharges(int formalCharge)

addSelectionListener
```
public void addSelectionListener(JmolSelectionListener listener)
```
Specified by:

addSelectionListener in class JmolViewer

removeSelectionListener
```
public void removeSelectionListener(JmolSelectionListener listener)
```
Specified by:

removeSelectionListener in class JmolViewer

getAtomBitSetEval

BS getAtomBitSetEval(JmolScriptEvaluator eval,
                     java.lang.Object atomExpression)

processTwoPointGesture
```
public void processTwoPointGesture(float[][][] touches)
```
Specified by:

processTwoPointGesture in interface javajs.api.JSInterface

processMouseEvent

public boolean processMouseEvent(int id,
                                 int x,
                                 int y,
                                 int modifiers,
                                 long time)

Specified by:: processMouseEvent in interface javajs.api.JSInterface
Specified by:: processMouseEvent in class JmolViewer

getRubberBandSelection

public Rectangle getRubberBandSelection()

isBound

public boolean isBound(int action,
                       int gesture)

getCursorX
```
public int getCursorX()
```

getCursorY
```
public int getCursorY()
```

getDefaultDirectory
```
java.lang.String getDefaultDirectory()
```

getLocalUrl

public java.lang.String getLocalUrl(java.lang.String fileName)

getBufferedInputStream

public java.io.BufferedInputStream getBufferedInputStream(java.lang.String fullPathName)

Specified by:: getBufferedInputStream in interface AtomDataServer

getBufferedReaderOrErrorMessageFromName

public java.lang.Object getBufferedReaderOrErrorMessageFromName(java.lang.String name,
                                                                java.lang.String[] fullPathNameReturn,
                                                                boolean isBinary)

setLoadParameters

private java.util.Map<java.lang.String,java.lang.Object> setLoadParameters(java.util.Map<java.lang.String,java.lang.Object> htParams,
                                                                           boolean isAppend)

openFileAsyncSpecial
```
public void openFileAsyncSpecial(java.lang.String fileName,
                                 int flags)
```
opens a file as a model, a script, or a surface via the creation of a script that is queued \t at the beginning disallows script option - used by JmolFileDropper and JmolPanel file-open actions - sets up a script to load the file

Specified by:

openFileAsyncSpecial in interface javajs.api.JSInterface

Specified by:

openFileAsyncSpecial in class JmolViewer

Parameters:

fileName -

flags - 1 = check PDBcartoons

openFile
```
public java.lang.String openFile(java.lang.String fileName)
```
for JmolSimpleViewer -- external applications only (and no-script JavaScript)

Specified by:

openFile in class JmolViewer

Parameters:

fileName -

Returns:

null or error

openFiles
```
public java.lang.String openFiles(java.lang.String[] fileNames)
```
for JmolSimpleViewer -- external applications only

Specified by:

openFiles in class JmolViewer

Parameters:

fileNames -

Returns:

null or error

openReader

public java.lang.String openReader(java.lang.String fullPathName,
                                   java.lang.String fileName,
                                   java.io.Reader reader)

Opens the file, given an already-created reader.

Specified by:: openReader in class JmolViewer
Parameters:: fullPathName -; fileName -; reader -
Returns:: null or error message

openDOM
```
public java.lang.String openDOM(java.lang.Object DOMNode)
```
applet DOM method -- does not preserve state

Specified by:

openDOM in class JmolViewer

Parameters:

DOMNode -

Returns:

null or error

loadModelFromFileRepaint

private java.lang.String loadModelFromFileRepaint(java.lang.String fullPathName,
                                                  java.lang.String fileName,
                                                  java.lang.String[] fileNames,
                                                  java.lang.Object reader)

loadModelFromFile

public java.lang.String loadModelFromFile(java.lang.String fullPathName,
                                          java.lang.String fileName,
                                          java.lang.String[] fileNames,
                                          java.lang.Object reader,
                                          boolean isAppend,
                                          java.util.Map<java.lang.String,java.lang.Object> htParams,
                                          javajs.util.SB loadScript,
                                          int tokType)

Used by the ScriptEvaluator LOAD command to open one or more files. Now necessary for EVERY load of a file, as loadScript must be passed to the ModelLoader.

Parameters:: fullPathName - TODO; fileName -; fileNames -; reader - TODO; isAppend -; htParams -; loadScript -; tokType -
Returns:: null or error

setLigandModel

public void setLigandModel(java.lang.String key,
                           java.lang.String data)

getLigandModel

public java.lang.Object getLigandModel(java.lang.String id,
                                       java.lang.String prefix,
                                       java.lang.String suffix,
                                       java.lang.String terminator)

obtain CIF data for a ligand for purposes of adding hydrogens

Parameters:: id - if null, clear "bad" entries from the set.; prefix -; suffix -; terminator - Only save to this if not null
Returns:: a ligand model or a string if just file data or null

openFileFull

private java.lang.Object openFileFull(java.lang.String fileName,
                                      boolean isAppend,
                                      java.util.Map<java.lang.String,java.lang.Object> htParams,
                                      javajs.util.SB loadScript)

does NOT repaint

Parameters:: fileName -; isAppend -; htParams -; loadScript - only necessary for string reading
Returns:: an AtomSetCollection or a String (error)

openStringInline
```
public java.lang.String openStringInline(java.lang.String strModel)
```
only used by file dropper.

Specified by:

openStringInline in class JmolViewer

loadInline
```
public java.lang.String loadInline(java.lang.String strModel)
```
from Applet and external applications only

Specified by:

loadInline in class JmolViewer

loadInline

public java.lang.String loadInline(java.lang.String strModel,
                                   char newLine)

external apps only

Specified by:: loadInline in class JmolViewer

loadInlineAppend

public java.lang.String loadInlineAppend(java.lang.String strModel,
                                         boolean isAppend)

used by applet and console

Specified by:: loadInlineAppend in class JmolViewer

loadInlineScriptRepaint

private java.lang.String loadInlineScriptRepaint(java.lang.String strModel,
                                                 char newLine,
                                                 boolean isAppend)

loadInline

public java.lang.String loadInline(java.lang.String[] arrayModels)

external apps only

Specified by:: loadInline in class JmolViewer

loadInline
```
public java.lang.String loadInline(java.lang.String[] arrayModels,
                                   boolean isAppend)
```
external apps and applet only

Specified by:

loadInline in class JmolViewer

Parameters:

arrayModels - and array of models, each of which is a String

Returns:

null or error message

loadInline
```
public java.lang.String loadInline(java.util.List<java.lang.Object> arrayData,
                                   boolean isAppend)
```
External applications only; does not preserver state -- intentionally!

Specified by:

loadInline in class JmolViewer

Parameters:

arrayData -

isAppend -

Returns:

null or error string

loadInlineScript

private java.lang.String loadInlineScript(java.lang.String strModel,
                                          char newLine,
                                          boolean isAppend,
                                          java.util.Map<java.lang.String,java.lang.Object> htParams)

used by loadInline and openFileFull

Parameters:: strModel -; newLine -; isAppend -; htParams -
Returns:: null or error message

fixInlineString

public static java.lang.String fixInlineString(java.lang.String strModel,
                                               char newLine)

openStringInlineParamsAppend

public java.lang.String openStringInlineParamsAppend(java.lang.String strModel,
                                                     java.util.Map<java.lang.String,java.lang.Object> htParams,
                                                     boolean isAppend)

Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.

Parameters:: strModel -; htParams -; isAppend -
Returns:: null or error string

openStringsInlineParamsAppend

private java.lang.String openStringsInlineParamsAppend(java.lang.String[] arrayModels,
                                                       java.util.Map<java.lang.String,java.lang.Object> htParams,
                                                       boolean isAppend)

opens multiple files inline; does NOT repaint

Parameters:: arrayModels -; htParams -; isAppend -
Returns:: null or error message

getInlineChar
```
public char getInlineChar()
```

getDataSeparator
```
java.lang.String getDataSeparator()
```

createModelSetAndReturnError

private java.lang.String createModelSetAndReturnError(java.lang.Object atomSetCollection,
                                                      boolean isAppend,
                                                      javajs.util.SB loadScript,
                                                      java.util.Map<java.lang.String,java.lang.Object> htParams)

finally(!) we are ready to create the "model set" from the "atom set collection" - does NOT repaint

Parameters:: atomSetCollection -; isAppend -; loadScript - if null, then some special method like DOM; turn of preserveState; htParams -
Returns:: errMsg

loadAtomDataAndReturnError

private java.lang.String loadAtomDataAndReturnError(java.lang.Object atomSetCollection,
                                                    int tokType)

or just apply the data to the current model set

Parameters:: atomSetCollection -; tokType -
Returns:: error or null

getEmbeddedFileState

public java.lang.String getEmbeddedFileState(java.lang.String filename)

Specified by:: getEmbeddedFileState in class JmolViewer

getFileAsBytes

public java.lang.Object getFileAsBytes(java.lang.String pathName,
                                       javajs.util.OC out)

Specified by:: getFileAsBytes in class JmolViewer

getCurrentFileAsString

public java.lang.String getCurrentFileAsString()

getFullPathName

public java.lang.String getFullPathName(boolean orPrevious)

getFileName
```
public java.lang.String getFileName()
```

getFullPathNameOrError
```
public java.lang.String[] getFullPathNameOrError(java.lang.String filename)
```
Parameters:

filename -

Returns:

String[2] where [0] is fullpathname and [1] is error message or null

getFileAsString

public java.lang.String getFileAsString(java.lang.String name,
                                        boolean checkProtected)

Specified by:: getFileAsString in class JmolViewer

getFileAsMap

public java.util.Map<java.lang.String,java.lang.Object> getFileAsMap(java.lang.String name)

getFileAsString4

public java.lang.String getFileAsString4(java.lang.String name,
                                         int nBytesMax,
                                         boolean doSpecialLoad,
                                         boolean allowBinary,
                                         boolean checkProtected)

getFileAsStringBin

public boolean getFileAsStringBin(java.lang.String[] data,
                                  boolean allowBinary)

getFilePath

public java.lang.String getFilePath(java.lang.String name,
                                    boolean asShortName)

getFileInfo

public java.lang.String[] getFileInfo()

setFileInfo

public void setFileInfo(java.lang.String[] fileInfo)

autoCalculate

public void autoCalculate(int tokProperty)

getSurfaceDistanceMax
```
int getSurfaceDistanceMax()
```

calculateStraightness
```
public void calculateStraightness()
```

calculateSurface

public javajs.util.P3[] calculateSurface(BS bsSelected,
                                         float envelopeRadius)

getStructureList

public java.util.Map<STR,float[]> getStructureList()

setStructureList

public void setStructureList(float[] list,
                             STR type)

getDefaultStructure

public java.lang.String getDefaultStructure(BS bsAtoms,
                                            BS bsAllAtoms)

calculateStructures

public java.lang.String calculateStructures(BS bsAtoms,
                                            boolean asDSSP,
                                            boolean setStructure)

getSelectedAtomIterator

public AtomIndexIterator getSelectedAtomIterator(BS bsSelected,
                                                 boolean isGreaterOnly,
                                                 boolean modelZeroBased,
                                                 boolean isMultiModel)

Specified by:: getSelectedAtomIterator in interface AtomDataServer

setIteratorForAtom

public void setIteratorForAtom(AtomIndexIterator iterator,
                               int atomIndex,
                               float distance)

Specified by:: setIteratorForAtom in interface AtomDataServer

setIteratorForPoint

public void setIteratorForPoint(AtomIndexIterator iterator,
                                int modelIndex,
                                javajs.util.P3 pt,
                                float distance)

Specified by:: setIteratorForPoint in interface AtomDataServer

fillAtomData

public void fillAtomData(AtomData atomData,
                         int mode)

Specified by:: fillAtomData in interface AtomDataServer

addStateScript

public StateScript addStateScript(java.lang.String script,
                                  boolean addFrameNumber,
                                  boolean postDefinitions)

addStateScriptRet

public StateScript addStateScriptRet(java.lang.String script1,
                                     BS bsBonds,
                                     BS bsAtoms1,
                                     BS bsAtoms2,
                                     java.lang.String script2,
                                     boolean addFrameNumber,
                                     boolean postDefinitions)

getEchoStateActive
```
public boolean getEchoStateActive()
```

setEchoStateActive

public void setEchoStateActive(boolean TF)

getMinimizer

public MinimizerInterface getMinimizer(boolean createNew)

getSmilesMatcher

public SmilesMatcherInterface getSmilesMatcher()

clearModelDependentObjects

public void clearModelDependentObjects()

zap

public void zap(boolean notify,
                boolean resetUndo,
                boolean zapModelKit)

zapMsg

private void zapMsg(java.lang.String msg)

echoMessage

void echoMessage(java.lang.String msg)

initializeModel

private void initializeModel(boolean isAppend)

startHoverWatcher
```
public void startHoverWatcher(boolean tf)
```
Specified by:

startHoverWatcher in interface javajs.api.JSInterface

getModelSetName
```
public java.lang.String getModelSetName()
```
Specified by:

getModelSetName in class JmolViewer

getModelSetFileName
```
public java.lang.String getModelSetFileName()
```
Specified by:

getModelSetFileName in class JmolViewer

getUnitCellInfoText

public java.lang.String getUnitCellInfoText()

getUnitCellInfo

public float getUnitCellInfo(int infoType)

getSpaceGroupInfo

public java.util.Map<java.lang.String,java.lang.Object> getSpaceGroupInfo(java.lang.String spaceGroup)

getPolymerPointsAndVectors

public void getPolymerPointsAndVectors(BS bs,
                                       javajs.util.List<javajs.util.P3[]> vList)

getModelSetProperty

public java.lang.String getModelSetProperty(java.lang.String strProp)

getModelSetAuxiliaryInfoValue

public java.lang.Object getModelSetAuxiliaryInfoValue(java.lang.String strKey)

getModelSetPathName
```
public java.lang.String getModelSetPathName()
```
Specified by:

getModelSetPathName in class JmolViewer

getModelSetTypeName

public java.lang.String getModelSetTypeName()

haveFrame
```
public boolean haveFrame()
```
Specified by:

haveFrame in class JmolViewer

haveModelSet
```
boolean haveModelSet()
```

clearBfactorRange
```
public void clearBfactorRange()
```

getHybridizationAndAxes

public java.lang.String getHybridizationAndAxes(int atomIndex,
                                                javajs.util.V3 z,
                                                javajs.util.V3 x,
                                                java.lang.String lcaoType)

getMoleculeBitSet

public BS getMoleculeBitSet(int atomIndex)

getAllAtoms
```
public BS getAllAtoms()
```

getModelUndeletedAtomsBitSet

public BS getModelUndeletedAtomsBitSet(int modelIndex)

getModelBitSet

public BS getModelBitSet(BS atomList,
                         boolean allTrajectories)

getModelUndeletedAtomsBitSetBs

public BS getModelUndeletedAtomsBitSetBs(BS bsModels)

excludeAtoms

public BS excludeAtoms(BS bs,
                       boolean ignoreSubset)

getModelSet
```
public ModelSet getModelSet()
```

getBoundBoxCommand

public java.lang.String getBoundBoxCommand(boolean withOptions)

setBoundBox

public void setBoundBox(javajs.util.P3 pt1,
                        javajs.util.P3 pt2,
                        boolean byCorner,
                        float scale)

getBoundBoxCenter
```
public javajs.util.P3 getBoundBoxCenter()
```
Specified by:

getBoundBoxCenter in class JmolViewer

getAverageAtomPoint
```
javajs.util.P3 getAverageAtomPoint()
```

calcBoundBoxDimensions

public void calcBoundBoxDimensions(BS bs,
                                   float scale)

getBoxInfo

public BoxInfo getBoxInfo(BS bs,
                          float scale)

calcRotationRadius

public float calcRotationRadius(javajs.util.P3 center)

calcRotationRadiusBs

public float calcRotationRadiusBs(BS bs)

getBoundBoxCornerVector
```
public javajs.util.V3 getBoundBoxCornerVector()
```
Specified by:

getBoundBoxCornerVector in class JmolViewer

getBoundBoxVertices

public javajs.util.P3[] getBoundBoxVertices()

getBoundBoxModels
```
public BS getBoundBoxModels()
```

getBoundBoxCenterX
```
public int getBoundBoxCenterX()
```

getBoundBoxCenterY
```
public int getBoundBoxCenterY()
```

getModelCount
```
public int getModelCount()
```
Specified by:

getModelCount in class JmolViewer

getModelInfoAsString

public java.lang.String getModelInfoAsString()

getSymmetryInfoAsString

public java.lang.String getSymmetryInfoAsString()

getSymmetryOperation

public java.lang.String getSymmetryOperation(java.lang.String spaceGroup,
                                             int symop,
                                             javajs.util.P3 pt1,
                                             javajs.util.P3 pt2,
                                             boolean labelOnly)

getModelSetProperties
```
public java.util.Properties getModelSetProperties()
```
Specified by:

getModelSetProperties in class JmolViewer

getModelSetAuxiliaryInfo

public java.util.Map<java.lang.String,java.lang.Object> getModelSetAuxiliaryInfo()

Specified by:: getModelSetAuxiliaryInfo in class JmolViewer

getModelNumber
```
public int getModelNumber(int modelIndex)
```
Specified by:

getModelNumber in class JmolViewer

getModelFileNumber

public int getModelFileNumber(int modelIndex)

getModelNumberDotted
```
public java.lang.String getModelNumberDotted(int modelIndex)
```
Specified by:

getModelNumberDotted in class JmolViewer

getModelName

public java.lang.String getModelName(int modelIndex)

Specified by:: getModelName in class JmolViewer

getModelProperties
```
public java.util.Properties getModelProperties(int modelIndex)
```
Specified by:

getModelProperties in class JmolViewer

getModelProperty

public java.lang.String getModelProperty(int modelIndex,
                                         java.lang.String propertyName)

Specified by:: getModelProperty in class JmolViewer

getModelFileInfo

public java.lang.String getModelFileInfo()

getModelFileInfoAll

public java.lang.String getModelFileInfoAll()

getModelAuxiliaryInfo

public java.util.Map<java.lang.String,java.lang.Object> getModelAuxiliaryInfo(int modelIndex)

Specified by:: getModelAuxiliaryInfo in class JmolViewer

getModelAuxiliaryInfoValue
```
public java.lang.Object getModelAuxiliaryInfoValue(int modelIndex,
                                                   java.lang.String keyName)
```
Description copied from class: JmolViewer

changed in Jmol 13.1.5 to remove ambiguity in JavaScript

Specified by:

getModelAuxiliaryInfoValue in class JmolViewer

Returns:

some Object or null

getModelNumberIndex

public int getModelNumberIndex(int modelNumber,
                               boolean useModelNumber,
                               boolean doSetTrajectory)

modelSetHasVibrationVectors
```
boolean modelSetHasVibrationVectors()
```

modelGetLastVibrationIndex

public int modelGetLastVibrationIndex(int modelIndex,
                                      int tok)

Specified by:: modelGetLastVibrationIndex in class JmolViewer

modelHasVibrationVectors
```
public boolean modelHasVibrationVectors(int modelIndex)
```
Specified by:

modelHasVibrationVectors in class JmolViewer

getChainCount
```
public int getChainCount()
```
Specified by:

getChainCount in class JmolViewer

getChainCountInModel
```
public int getChainCountInModel(int modelIndex)
```
Specified by:

getChainCountInModel in class JmolViewer

getChainCountInModelWater

public int getChainCountInModelWater(int modelIndex,
                                     boolean countWater)

getGroupCount
```
public int getGroupCount()
```
Specified by:

getGroupCount in class JmolViewer

getGroupCountInModel
```
public int getGroupCountInModel(int modelIndex)
```
Specified by:

getGroupCountInModel in class JmolViewer

getPolymerCount
```
public int getPolymerCount()
```
Specified by:

getPolymerCount in class JmolViewer

getPolymerCountInModel
```
public int getPolymerCountInModel(int modelIndex)
```
Specified by:

getPolymerCountInModel in class JmolViewer

getAtomCount
```
public int getAtomCount()
```
Specified by:

getAtomCount in class JmolViewer

getAtomCountInModel
```
public int getAtomCountInModel(int modelIndex)
```
Specified by:

getAtomCountInModel in class JmolViewer

getBondCount
```
public int getBondCount()
```
For use in setting a for() construct max value

Specified by:

getBondCount in class JmolViewer

Returns:

used size of the bonds array;

getBondCountInModel
```
public int getBondCountInModel(int modelIndex)
```
from JmolPopup.udateModelSetComputedMenu

Specified by:

getBondCountInModel in class JmolViewer

Parameters:

modelIndex - the model of interest or -1 for all

Returns:

the actual number of connections

getBondsForSelectedAtoms

public BS getBondsForSelectedAtoms(BS bsAtoms)

frankClicked

public boolean frankClicked(int x,
                            int y)

frankClickedModelKit

public boolean frankClickedModelKit(int x,
                                    int y)

findNearestAtomIndex

public int findNearestAtomIndex(int x,
                                int y)

Specified by:: findNearestAtomIndex in class JmolViewer

findNearestAtomIndexMovable

public int findNearestAtomIndexMovable(int x,
                                       int y,
                                       boolean mustBeMovable)

findAtomsInRectangle

BS findAtomsInRectangle(Rectangle rect)

toCartesian
```
public void toCartesian(javajs.util.P3 pt,
                        boolean asAbsolute)
```
absolute or relative to origin of UNITCELL {x y z}

Parameters:

pt -

asAbsolute - TODO

toFractional

public void toFractional(javajs.util.P3 pt,
                         boolean asAbsolute)

absolute or relative to origin of UNITCELL {x y z}

Parameters:: pt -; asAbsolute - TODO

toUnitCell

public void toUnitCell(javajs.util.P3 pt,
                       javajs.util.P3 offset)

relative to origin without regard to UNITCELL {x y z}

Parameters:: pt -; offset -

setCurrentCage

public void setCurrentCage(java.lang.String isosurfaceId)

setCurrentCagePts

public void setCurrentCagePts(javajs.util.P3[] points)

setCurrentUnitCellOffset

public void setCurrentUnitCellOffset(javajs.util.P3 pt,
                                     int ijk)

addUnitCellOffset

public void addUnitCellOffset(javajs.util.P3 pt)

setAtomData

public void setAtomData(int type,
                        java.lang.String name,
                        java.lang.String coordinateData,
                        boolean isDefault)

setCenterSelected
```
public void setCenterSelected()
```
Specified by:

setCenterSelected in class JmolViewer

setApplySymmetryToBonds

void setApplySymmetryToBonds(boolean TF)

setBondTolerance
```
public void setBondTolerance(float bondTolerance)
```
Specified by:

setBondTolerance in class JmolViewer

setMinBondDistance
```
public void setMinBondDistance(float minBondDistance)
```
Specified by:

setMinBondDistance in class JmolViewer

getAtomIndices
```
public int[] getAtomIndices(BS bs)
```

getAtomBits

public BS getAtomBits(int tokType,
                      java.lang.Object specInfo)

getSequenceBits

public BS getSequenceBits(java.lang.String specInfo,
                          BS bs)

getAtomsNearPt

public BS getAtomsNearPt(float distance,
                         javajs.util.P3 coord)

getAtomsNearPts

public BS getAtomsNearPts(float distance,
                          javajs.util.P3[] points,
                          BS bsInclude)

getAtomsNearPlane

public BS getAtomsNearPlane(float distance,
                            javajs.util.P4 plane)

getAtomsWithinRadius

public BS getAtomsWithinRadius(float distance,
                               BS bs,
                               boolean withinAllModels,
                               RadiusData rd)

getBranchBitSet

public BS getBranchBitSet(int atomIndex,
                          int atomIndexNot,
                          boolean allowCyclic)

getAtomIndexFromAtomNumber

public int getAtomIndexFromAtomNumber(int atomNumber)

getElementsPresentBitSet
```
public BS getElementsPresentBitSet(int modelIndex)
```
Specified by:

getElementsPresentBitSet in class JmolViewer

getHeteroList

public java.util.Map<java.lang.String,java.lang.String> getHeteroList(int modelIndex)

Specified by:: getHeteroList in class JmolViewer

getVisibleSet
```
public BS getVisibleSet()
```

getClickableSet
```
public BS getClickableSet()
```

calcSelectedGroupsCount
```
public void calcSelectedGroupsCount()
```

calcSelectedMonomersCount

public void calcSelectedMonomersCount()

calcSelectedMoleculesCount

public void calcSelectedMoleculesCount()

getFileHeader
```
java.lang.String getFileHeader()
```

getFileData
```
java.lang.Object getFileData()
```

getCifData

public java.util.Map<java.lang.String,java.lang.Object> getCifData(int modelIndex)

getPDBHeader

public java.lang.String getPDBHeader()

getChimeInfo

public java.lang.String getChimeInfo(int tok)

getStateCreator

public JmolStateCreator getStateCreator()

getWrappedStateScript

public java.lang.String getWrappedStateScript()

getStateInfo
```
public java.lang.String getStateInfo()
```
Specified by:

getStateInfo in class JmolViewer

getStateInfo3

public java.lang.String getStateInfo3(java.lang.String type,
                                      int width,
                                      int height)

getStructureState

public java.lang.String getStructureState()

getProteinStructureState

public java.lang.String getProteinStructureState()

getCoordinateState

public java.lang.String getCoordinateState(BS bsSelected)

setCurrentColorRange

public void setCurrentColorRange(java.lang.String label)

setCurrentColorRangeData

public void setCurrentColorRangeData(float[] data,
                                     BS bs)

setCurrentColorRange

public void setCurrentColorRange(float min,
                                 float max)

getArgbMinMax

public int getArgbMinMax(float val,
                         float min,
                         float max)

setData

public void setData(java.lang.String type,
                    java.lang.Object[] data,
                    int arrayCount,
                    int matchField,
                    int matchFieldColumnCount,
                    int field,
                    int fieldColumnCount)

getData

public java.lang.Object[] getData(java.lang.String type)

getDataFloat

public float[] getDataFloat(java.lang.String label)

getDataFloat2D

public float[][] getDataFloat2D(java.lang.String label)

getDataFloat3D

public float[][][] getDataFloat3D(java.lang.String label)

getDataFloatAt

public float getDataFloatAt(java.lang.String label,
                            int atomIndex)

getAltLocListInModel
```
public java.lang.String getAltLocListInModel(int modelIndex)
```
Specified by:

getAltLocListInModel in class JmolViewer

setConformation
```
public BS setConformation()
```

getConformation

public BS getConformation(int iModel,
                          int conformationIndex,
                          boolean doSet)

autoHbond

public int autoHbond(BS bsFrom,
                     BS bsTo,
                     boolean onlyIfHaveCalculated)

havePartialCharges
```
public boolean havePartialCharges()
```
Specified by:

havePartialCharges in class JmolViewer

getCurrentUnitCell

public SymmetryInterface getCurrentUnitCell()

getModelUnitCell

public SymmetryInterface getModelUnitCell(int modelIndex)

getDefaultMeasurementLabel

public java.lang.String getDefaultMeasurementLabel(int nPoints)

getMeasurementCount
```
public int getMeasurementCount()
```
Specified by:

getMeasurementCount in class JmolViewer

getMeasurementStringValue
```
public java.lang.String getMeasurementStringValue(int i)
```
Specified by:

getMeasurementStringValue in class JmolViewer

getMeasurementInfoAsString

public java.lang.String getMeasurementInfoAsString()

getMeasurementCountPlusIndices
```
public int[] getMeasurementCountPlusIndices(int i)
```
Specified by:

getMeasurementCountPlusIndices in class JmolViewer

setPendingMeasurement

void setPendingMeasurement(MeasurementPending mp)

getPendingMeasurement

MeasurementPending getPendingMeasurement()

clearAllMeasurements
```
public void clearAllMeasurements()
```

clearMeasurements
```
public void clearMeasurements()
```
Specified by:

clearMeasurements in class JmolViewer

setAnimation
```
public void setAnimation(int tok)
```

setAnimationDirection

public void setAnimationDirection(int direction)

getAnimationDirection
```
int getAnimationDirection()
```

setAnimationFps
```
public void setAnimationFps(int fps)
```
Specified by:

setAnimationFps in class JmolViewer

setAnimationMode

private void setAnimationMode(java.lang.String mode)

setAnimationReplayMode

public void setAnimationReplayMode(ANIM replayMode,
                                   float firstFrameDelay,
                                   float lastFrameDelay)

getAnimationReplayMode
```
public ANIM getAnimationReplayMode()
```

setAnimationOn

public void setAnimationOn(boolean animationOn)

setAnimationRange

public void setAnimationRange(int modelIndex1,
                              int modelIndex2)

getVisibleFramesBitSet
```
public BS getVisibleFramesBitSet()
```
Specified by:

getVisibleFramesBitSet in class JmolViewer

isAnimationOn
```
boolean isAnimationOn()
```

setMovie

public void setMovie(java.util.Map<java.lang.String,java.lang.Object> info)

setAnimMorphCount
```
public void setAnimMorphCount(int n)
```

isMovie
```
public boolean isMovie()
```

getFrameCount
```
public int getFrameCount()
```

defineAtomSets

public void defineAtomSets(java.util.Map<java.lang.String,java.lang.Object> info)

morph
```
public void morph(float frame)
```

setAnimDisplay
```
public void setAnimDisplay(BS bs)
```

setCurrentModelIndex

public void setCurrentModelIndex(int modelIndex)

setTrajectory
```
void setTrajectory(int modelIndex)
```

setTrajectoryBs

public void setTrajectoryBs(BS bsModels)

isTrajectory

public boolean isTrajectory(int modelIndex)

getBitSetTrajectories
```
public BS getBitSetTrajectories()
```

getTrajectoryState

public java.lang.String getTrajectoryState()

setFrameOffset
```
void setFrameOffset(int modelIndex)
```

setFrameOffsets

public void setFrameOffsets(BS bsAtoms)

getFrameOffsets
```
public BS getFrameOffsets()
```

setCurrentModelIndexClear

public void setCurrentModelIndexClear(int modelIndex,
                                      boolean clearBackground)

getCurrentModelIndex
```
public int getCurrentModelIndex()
```

getDisplayModelIndex
```
public int getDisplayModelIndex()
```
Specified by:

getDisplayModelIndex in class JmolViewer

haveFileSet
```
public boolean haveFileSet()
```

setBackgroundModelIndex

public void setBackgroundModelIndex(int modelIndex)

setFrameVariables
```
void setFrameVariables()
```

getInMotion

public boolean getInMotion(boolean includeAnim)

getMotionEventNumber
```
public int getMotionEventNumber()
```
Specified by:

getMotionEventNumber in class JmolViewer

setInMotion
```
public void setInMotion(boolean inMotion)
```
Specified by:

setInMotion in class JmolViewer

setRefreshing

private void setRefreshing(boolean TF)

getRefreshing
```
public boolean getRefreshing()
```

pushHoldRepaint
```
public void pushHoldRepaint()
```
Specified by:

pushHoldRepaint in class JmolViewer

pushHoldRepaintWhy

public void pushHoldRepaintWhy(java.lang.String why)

Parameters:: why -

popHoldRepaint
```
public void popHoldRepaint(java.lang.String why)
```
Specified by:

popHoldRepaint in class JmolViewer

refresh
```
public void refresh(int mode,
                    java.lang.String strWhy)
```
initiate a repaint/update sequence if it has not already been requested. invoked whenever any operation causes changes that require new rendering. The repaint/update sequence will only be invoked if (a) no repaint is already pending and (b) there is no hold flag set in repaintManager. Sequence is as follows: 1) RepaintManager.refresh() checks flags and then calls Viewer.repaint() 2) Viewer.repaint() invokes display.repaint(), provided display is not null (headless) 3) The system responds with an invocation of Jmol.update(Graphics g), which we are routing through Jmol.paint(Graphics g). 4) Jmol.update invokes Viewer.setScreenDimension(size), which makes the necessary changes in parameters for any new window size. 5) Jmol.update invokes Viewer.renderScreenImage(g, size, rectClip) 6) Viewer.renderScreenImage checks object visibility, invokes render1 to do the actual creation of the image pixel map and send it to the screen, and then invokes repaintView() 7) Viewer.repaintView() invokes RepaintManager.repaintDone(), to clear the flags and then use notify() to release any threads holding on wait().

Specified by:

refresh in class JmolViewer

Parameters:

mode -

strWhy -

requestRepaintAndWait

public void requestRepaintAndWait(java.lang.String why)

clearShapeRenderers
```
public void clearShapeRenderers()
```

isRepaintPending
```
public boolean isRepaintPending()
```

notifyViewerRepaintDone
```
public void notifyViewerRepaintDone()
```
Specified by:

notifyViewerRepaintDone in class JmolViewer

areAxesTainted
```
public boolean areAxesTainted()
```

setMaximumSize
```
private void setMaximumSize(int x)
```

setScreenDimension
```
public void setScreenDimension(int width,
                               int height)
```
Specified by:

setScreenDimension in interface javajs.api.JSInterface

Specified by:

setScreenDimension in class JmolViewer

setStereo

public void setStereo(boolean isStereoSlave,
                      java.lang.Object gRight)

getImageFontScaling
```
public float getImageFontScaling()
```

resizeImage

void resizeImage(int width,
                 int height,
                 boolean isImageWrite,
                 boolean isExport,
                 boolean isReset)

getScreenWidth
```
public int getScreenWidth()
```
Specified by:

getScreenWidth in class JmolViewer

getScreenHeight
```
public int getScreenHeight()
```
Specified by:

getScreenHeight in class JmolViewer

getScreenDim
```
public int getScreenDim()
```

generateOutputForExport
```
public java.lang.String generateOutputForExport(java.util.Map<java.lang.String,java.lang.Object> params)
```
Description copied from class: JmolViewer

for POV-Ray

Specified by:

generateOutputForExport in class JmolViewer

Returns:

INI file

clearRepaintManager

private void clearRepaintManager(int iShape)

renderScreenImageStereo

public void renderScreenImageStereo(java.lang.Object gLeft,
                                    boolean checkStereoSlave,
                                    int width,
                                    int height)

updateJS
```
public void updateJS(int width,
                     int height)
```
for JavaScript only

Specified by:

updateJS in interface javajs.api.JSInterface

Parameters:

width -

height -

updateJSView
```
private void updateJSView(int imodel,
                          int iatom)
```
File has been loaded or model has been changed or atom picked. This is a call to Jmol.View for view sets (new in Jmol 14.1.8)

Parameters:

imodel -

iatom -

updateWindow

private boolean updateWindow(int width,
                             int height)

renderScreenImage

public void renderScreenImage(java.lang.Object g,
                              int width,
                              int height)

Specified by:: renderScreenImage in class JmolViewer

getImage
```
private java.lang.Object getImage(boolean isDouble,
                                  boolean isImageWrite)
```
Parameters:

isDouble -

isImageWrite - TODO

Returns:

a java.awt.Image in the case of standard Jmol; an int[] in the case of Jmol-Android a canvas in the case of JSmol

beginRendering

private void beginRendering(boolean isDouble,
                            boolean isImageWrite)

isAntialiased
```
public boolean isAntialiased()
```

render
```
private void render()
```

render1

private void render1(java.lang.Object graphic,
                     java.lang.Object img,
                     int x,
                     int y)

getScreenImageBuffer
```
public java.lang.Object getScreenImageBuffer(java.lang.Object graphic,
                                             boolean isImageWrite)
```
Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo

Specified by:

getScreenImageBuffer in class JmolViewer

getImageAsBytes

public byte[] getImageAsBytes(java.lang.String type,
                              int width,
                              int height,
                              int quality,
                              java.lang.String[] errMsg)

Specified by:: getImageAsBytes in class JmolViewer; errMsg - TODO
Returns:: byte[] image, or null and an error message

releaseScreenImage
```
public void releaseScreenImage()
```
Specified by:

releaseScreenImage in class JmolViewer

evalFile

public java.lang.String evalFile(java.lang.String strFilename)

Specified by:: evalFile in class JmolViewer

getInsertedCommand

public java.lang.String getInsertedCommand()

script

public java.lang.String script(java.lang.String strScript)

Specified by:: script in class JmolViewer

evalString

public java.lang.String evalString(java.lang.String strScript)

Specified by:: evalString in class JmolViewer

evalStringQuiet

public java.lang.String evalStringQuiet(java.lang.String strScript)

Specified by:: evalStringQuiet in class JmolViewer

evalStringQuietSync

public java.lang.String evalStringQuietSync(java.lang.String strScript,
                                            boolean isQuiet,
                                            boolean allowSyncScript)

clearScriptQueue
```
public void clearScriptQueue()
```

setScriptQueue

private void setScriptQueue(boolean TF)

checkHalt

public boolean checkHalt(java.lang.String str,
                         boolean isInsert)

Specified by:: checkHalt in class JmolViewer

scriptWait

public java.lang.String scriptWait(java.lang.String strScript)

Specified by:: scriptWait in class JmolViewer

scriptWaitStatus

public java.lang.Object scriptWaitStatus(java.lang.String strScript,
                                         java.lang.String statusList)

Specified by:: scriptWaitStatus in class JmolViewer

evalWait

private java.lang.Object evalWait(java.lang.String returnType,
                                  java.lang.String strScript,
                                  java.lang.String statusList)

evalStringWaitStatusQueued

public java.lang.Object evalStringWaitStatusQueued(java.lang.String returnType,
                                                   java.lang.String strScript,
                                                   java.lang.String statusList,
                                                   boolean isScriptFile,
                                                   boolean isQuiet,
                                                   boolean isQueued)

exitJmol
```
public void exitJmol()
```

scriptCheckRet

private java.lang.Object scriptCheckRet(java.lang.String strScript,
                                        boolean returnContext)

scriptCheck

public java.lang.Object scriptCheck(java.lang.String strScript)

Specified by:: scriptCheck in class JmolViewer

isScriptExecuting
```
public boolean isScriptExecuting()
```
Specified by:

isScriptExecuting in class JmolViewer

haltScriptExecution
```
public void haltScriptExecution()
```
Specified by:

haltScriptExecution in class JmolViewer

pauseScriptExecution
```
public void pauseScriptExecution()
```

getDefaultLoadFilter

public java.lang.String getDefaultLoadFilter()

getDefaultLoadScript

public java.lang.String getDefaultLoadScript()

resolveDatabaseFormat

java.lang.String resolveDatabaseFormat(java.lang.String fileName)

isDatabaseCode

public static boolean isDatabaseCode(char ch)

hasDatabasePrefix

public static boolean hasDatabasePrefix(java.lang.String fileName)

setLoadFormat
```
public java.lang.Object setLoadFormat(java.lang.String name,
                                      char type,
                                      boolean withPrefix)
```
Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first. Starting with Jmol 13.1.13, we allow a generalized search using =xxx= where xxx is a known or user-specified database designation.

Parameters:

name -

type -

withPrefix -

Returns:

String or String[]

getElectronDensityLoadInfo

public java.lang.String[] getElectronDensityLoadInfo()

getStandardLabelFormat

public java.lang.String getStandardLabelFormat(int type)

getAdditionalHydrogens

public javajs.util.P3[] getAdditionalHydrogens(BS bsAtoms,
                                               boolean doAll,
                                               boolean justCarbon,
                                               javajs.util.List<Atom> vConnections)

setMarBond
```
public void setMarBond(short marBond)
```
Specified by:

setMarBond in class JmolViewer

setHoverLabel

public void setHoverLabel(java.lang.String strLabel)

hoverOn

void hoverOn(int atomIndex,
             boolean isLabel)

hoverOnPt

public void hoverOnPt(int x,
                      int y,
                      java.lang.String text,
                      java.lang.String id,
                      javajs.util.P3 pt)

hoverOff
```
void hoverOff()
```

getBfactor100Hi
```
public int getBfactor100Hi()
```

getColix

short getColix(java.lang.Object object)

setDebugScript
```
public void setDebugScript(boolean debugScript)
```
Specified by:

setDebugScript in class JmolViewer

clearClickCount
```
void clearClickCount()
```

getCursor
```
public int getCursor()
```

setCursor
```
public void setCursor(int cursor)
```

setPickingMode

void setPickingMode(java.lang.String strMode,
                    int pickingMode)

getPickingMode
```
public int getPickingMode()
```

setPickingStyle

void setPickingStyle(java.lang.String style,
                     int pickingStyle)

getDrawHover
```
public boolean getDrawHover()
```

getAtomInfo

public java.lang.String getAtomInfo(int atomOrPointIndex)

Specified by:: getAtomInfo in class JmolViewer

getAtomInfoXYZ

public java.lang.String getAtomInfoXYZ(int atomIndex,
                                       boolean useChimeFormat)

setSync
```
private void setSync()
```

setJmolCallbackListener

public void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)

Specified by:: setJmolCallbackListener in class JmolViewer

setJmolStatusListener

public void setJmolStatusListener(JmolStatusListener jmolStatusListener)

Specified by:: setJmolStatusListener in class JmolViewer

getMessageQueue

public java.util.Map<java.lang.String,javajs.util.List<javajs.util.List<java.lang.Object>>> getMessageQueue()

getStatusChanged

public javajs.util.List<javajs.util.List<javajs.util.List<java.lang.Object>>> getStatusChanged(java.lang.String statusNameList)

menuEnabled
```
public boolean menuEnabled()
```

popupMenu

void popupMenu(int x,
               int y,
               char type)

getMenu

public java.lang.String getMenu(java.lang.String type)

getPopupMenu

private java.lang.Object getPopupMenu()

setMenu

public void setMenu(java.lang.String fileOrText,
                    boolean isFile)

Specified by:: setMenu in class JmolViewer

setStatusFrameChanged

void setStatusFrameChanged(boolean isVib,
                           boolean doNotify)

Parameters:: isVib -; doNotify - ignored; not implemented

doHaveJDX
```
private boolean doHaveJDX()
```

getJSV
```
JmolJSpecView getJSV()
```

getJDXBaseModelIndex
```
public int getJDXBaseModelIndex(int modelIndex)
```
get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file. This might then allow pointing off a peak in JSpecView to switch to the model that is involved in HNMR or CNMR

Parameters:

modelIndex -

Returns:

modelIndex

getJspecViewProperties

public java.lang.Object getJspecViewProperties(java.lang.Object myParam)

scriptEcho

public void scriptEcho(java.lang.String strEcho)

isScriptQueued
```
private boolean isScriptQueued()
```

notifyError

public void notifyError(java.lang.String errType,
                        java.lang.String errMsg,
                        java.lang.String errMsgUntranslated)

jsEval

public java.lang.String jsEval(java.lang.String strEval)

setStatusAtomHovered

public void setStatusAtomHovered(int atomIndex,
                                 java.lang.String info)

setStatusObjectHovered

public void setStatusObjectHovered(java.lang.String id,
                                   java.lang.String info,
                                   javajs.util.P3 pt)

setFileLoadStatus

private void setFileLoadStatus(FIL ptLoad,
                               java.lang.String fullPathName,
                               java.lang.String fileName,
                               java.lang.String modelName,
                               java.lang.String strError,
                               java.lang.Boolean isAsync)

getZapName
```
public java.lang.String getZapName()
```

setStatusMeasuring

public void setStatusMeasuring(java.lang.String status,
                               int intInfo,
                               java.lang.String strMeasure,
                               float value)

notifyMinimizationStatus

public void notifyMinimizationStatus()

setStatusAtomPicked

public void setStatusAtomPicked(int atomIndex,
                                java.lang.String info,
                                java.util.Map<java.lang.String,java.lang.Object> map)

setStatusResized

public void setStatusResized(int width,
                             int height)

scriptStatus

public void scriptStatus(java.lang.String strStatus)

scriptStatusMsg

public void scriptStatusMsg(java.lang.String strStatus,
                            java.lang.String statusMessage)

setScriptStatus

public void setScriptStatus(java.lang.String strStatus,
                            java.lang.String statusMessage,
                            int msWalltime,
                            java.lang.String strErrorMessageUntranslated)

getModelTitle

private java.lang.String getModelTitle(int modelIndex)

getModelFileName
```
public java.lang.String getModelFileName(int modelIndex)
```
Specified by:

getModelFileName in class JmolViewer

dialogAsk

java.lang.String dialogAsk(java.lang.String type,
                           java.lang.String fileName)

showUrl

public void showUrl(java.lang.String urlString)

Specified by:: showUrl in class JmolViewer

setMeshCreator
```
public void setMeshCreator(java.lang.Object meshCreator)
```
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.

Parameters:

meshCreator -

showConsole

public void showConsole(boolean showConsole)

clearConsole
```
public void clearConsole()
```

getParameterEscaped

public java.lang.Object getParameterEscaped(java.lang.String key)

getParameter

public java.lang.Object getParameter(java.lang.String key)

Specified by:: getParameter in class JmolViewer

getOrSetNewVariable

public SV getOrSetNewVariable(java.lang.String key,
                              boolean doSet)

setUserVariable

public SV setUserVariable(java.lang.String name,
                          SV value)

unsetProperty

public void unsetProperty(java.lang.String key)

getVariableList

public java.lang.Object getVariableList()

notifyStatusReady
```
public void notifyStatusReady(boolean isReady)
```
Specified by:

notifyStatusReady in class JmolViewer

getBooleanProperty
```
public boolean getBooleanProperty(java.lang.String key)
```
Specified by:

getBooleanProperty in class JmolViewer

getInt
```
public int getInt(int tok)
```
Specified by:

getInt in class JmolViewer

getDelayMaximumMs
```
public int getDelayMaximumMs()
```

getHermiteLevel
```
public int getHermiteLevel()
```

getHoverDelay
```
public int getHoverDelay()
```

getBoolean
```
public boolean getBoolean(int tok)
```
Specified by:

getBoolean in class JmolViewer

allowEmbeddedScripts
```
public boolean allowEmbeddedScripts()
```

getDragSelected
```
boolean getDragSelected()
```

getBondPicking
```
boolean getBondPicking()
```

useMinimizationThread

public boolean useMinimizationThread()

getFloat
```
public float getFloat(int tok)
```
Specified by:

getFloat in class JmolViewer

setStringProperty

public void setStringProperty(java.lang.String key,
                              java.lang.String value)

Specified by:: setStringProperty in class JmolViewer

setStringPropertyTok

private void setStringPropertyTok(java.lang.String key,
                                  int tok,
                                  java.lang.String value)

setFloatProperty

public void setFloatProperty(java.lang.String key,
                             float value)

Specified by:: setFloatProperty in class JmolViewer

setFloatPropertyTok

private void setFloatPropertyTok(java.lang.String key,
                                 int tok,
                                 float value)

setIntProperty

public void setIntProperty(java.lang.String key,
                           int value)

Specified by:: setIntProperty in class JmolViewer

setIntPropertyTok

private void setIntPropertyTok(java.lang.String key,
                               int tok,
                               int value)

checkIntRange

private static int checkIntRange(int value,
                                 int min,
                                 int max)

checkFloatRange

private static float checkFloatRange(float value,
                                     float min,
                                     float max)

setBooleanProperty

public void setBooleanProperty(java.lang.String key,
                               boolean value)

Specified by:: setBooleanProperty in class JmolViewer

setBooleanPropertyTok

private void setBooleanPropertyTok(java.lang.String key,
                                   int tok,
                                   boolean value)

setModelKitMode

private void setModelKitMode(boolean value)

getLanguage
```
public java.lang.String getLanguage()
```

setSmilesString

public void setSmilesString(java.lang.String s)

removeUserVariable

public void removeUserVariable(java.lang.String key)

isJmolVariable

public boolean isJmolVariable(java.lang.String key)

jmolTest
```
private void jmolTest()
```

showParameter

public void showParameter(java.lang.String key,
                          boolean ifNotSet,
                          int nMax)

showString

public void showString(java.lang.String str,
                       boolean isPrint)

getAllSettings

public java.lang.String getAllSettings(java.lang.String prefix)

getBindingInfo

public java.lang.String getBindingInfo(java.lang.String qualifiers)

getIsosurfacePropertySmoothing

public int getIsosurfacePropertySmoothing(boolean asPower)

setNavigationDepthPercent

public void setNavigationDepthPercent(float percent)

getShowNavigationPoint

public boolean getShowNavigationPoint()

getCurrentSolventProbeRadius

public float getCurrentSolventProbeRadius()

getTestFlag
```
public boolean getTestFlag(int i)
```

setPerspectiveDepth
```
public void setPerspectiveDepth(boolean perspectiveDepth)
```
Specified by:

setPerspectiveDepth in class JmolViewer

setAxesOrientationRasmol
```
public void setAxesOrientationRasmol(boolean TF)
```
Specified by:

setAxesOrientationRasmol in class JmolViewer

setAxesScale
```
void setAxesScale(float scale)
```

getAxisPoints

public javajs.util.P3[] getAxisPoints()

resetError
```
public void resetError()
```

setAxesModeMolecular

private void setAxesModeMolecular(boolean TF)

setAxesModeUnitCell
```
void setAxesModeUnitCell(boolean TF)
```

getAxesMode
```
public AXES getAxesMode()
```

getPerspectiveDepth
```
public boolean getPerspectiveDepth()
```
Specified by:

getPerspectiveDepth in class JmolViewer

setSelectionHalos
```
public void setSelectionHalos(boolean TF)
```
Specified by:

setSelectionHalos in class JmolViewer

getSelectionHaloEnabled

public boolean getSelectionHaloEnabled(boolean isRenderer)

setStrandCount

private void setStrandCount(int type,
                            int value)

getStrandCount
```
public int getStrandCount(int type)
```

setNavigationMode

public void setNavigationMode(boolean TF)

setTransformManagerDefaults

private void setTransformManagerDefaults()

getCameraFactors

public javajs.util.P3[] getCameraFactors()

getCameraDepth
```
public float getCameraDepth()
```

getLoadState

java.lang.String getLoadState(java.util.Map<java.lang.String,java.lang.Object> htParams)

setAutoBond
```
public void setAutoBond(boolean TF)
```
Specified by:

setAutoBond in class JmolViewer

makeConnections

public int[] makeConnections(float minDistance,
                             float maxDistance,
                             int order,
                             int connectOperation,
                             BS bsA,
                             BS bsB,
                             BS bsBonds,
                             boolean isBonds,
                             boolean addGroup,
                             float energy)

rebond
```
public void rebond()
```
Specified by:

rebond in class JmolViewer

rebondState

public void rebondState(boolean isStateScript)

setPdbConectBonding

public void setPdbConectBonding(boolean isAuto,
                                boolean isStateScript)

setPercentVdwAtom
```
public void setPercentVdwAtom(int value)
```
Specified by:

setPercentVdwAtom in class JmolViewer

getDefaultRadiusData

public RadiusData getDefaultRadiusData()

getMadBond
```
public short getMadBond()
```
Specified by:

getMadBond in class JmolViewer

getMarBond
```
public short getMarBond()
```

getModeMultipleBond
```
public byte getModeMultipleBond()
```

setShowHydrogens
```
public void setShowHydrogens(boolean TF)
```
Specified by:

setShowHydrogens in class JmolViewer

setShowBbcage
```
public void setShowBbcage(boolean value)
```
Specified by:

setShowBbcage in class JmolViewer

getShowBbcage
```
public boolean getShowBbcage()
```
Specified by:

getShowBbcage in class JmolViewer

setShowUnitCell

public void setShowUnitCell(boolean value)

getShowUnitCell
```
public boolean getShowUnitCell()
```

setShowAxes
```
public void setShowAxes(boolean value)
```
Specified by:

setShowAxes in class JmolViewer

getShowAxes
```
public boolean getShowAxes()
```
Specified by:

getShowAxes in class JmolViewer

setFrankOn
```
public void setFrankOn(boolean TF)
```
Specified by:

setFrankOn in class JmolViewer

getShowFrank
```
public boolean getShowFrank()
```

setShowMeasurements
```
public void setShowMeasurements(boolean TF)
```
Specified by:

setShowMeasurements in class JmolViewer

setUnits

public void setUnits(java.lang.String units,
                     boolean isDistance)

getMeasureDistanceUnits

public java.lang.String getMeasureDistanceUnits()

getEnergyUnits

public java.lang.String getEnergyUnits()

setAppendNew

public void setAppendNew(boolean value)

setRasmolDefaults
```
public void setRasmolDefaults()
```
Specified by:

setRasmolDefaults in class JmolViewer

setJmolDefaults
```
public void setJmolDefaults()
```
Specified by:

setJmolDefaults in class JmolViewer

setDefaultsType

private void setDefaultsType(java.lang.String type)

setAntialias

private void setAntialias(int tok,
                          boolean TF)

allocTempPoints

public javajs.util.P3[] allocTempPoints(int size)

freeTempPoints

public void freeTempPoints(javajs.util.P3[] tempPoints)

allocTempScreens

public javajs.util.P3i[] allocTempScreens(int size)

freeTempScreens

public void freeTempScreens(javajs.util.P3i[] tempScreens)

allocTempEnum
```
public STR[] allocTempEnum(int size)
```

freeTempEnum
```
public void freeTempEnum(STR[] temp)
```

getFont3D

public javajs.awt.Font getFont3D(java.lang.String fontFace,
                                 java.lang.String fontStyle,
                                 float fontSize)

formatText

public java.lang.String formatText(java.lang.String text0)

getElementSymbol

java.lang.String getElementSymbol(int i)

getElementNumber
```
int getElementNumber(int i)
```

getAtomName
```
public java.lang.String getAtomName(int i)
```
Specified by:

getAtomName in class JmolViewer

getAtomNumber
```
public int getAtomNumber(int i)
```
Specified by:

getAtomNumber in class JmolViewer

getAtomGroupQuaternions

public javajs.util.Quat[] getAtomGroupQuaternions(BS bsAtoms,
                                                  int nMax)

getAtomQuaternion

public javajs.util.Quat getAtomQuaternion(int i)

getAtomPoint3f
```
public javajs.util.P3 getAtomPoint3f(int i)
```
Specified by:

getAtomPoint3f in class JmolViewer

getAtomPointVector

public javajs.util.List<javajs.util.P3> getAtomPointVector(BS bs)

getAtomRadius
```
public float getAtomRadius(int i)
```
Specified by:

getAtomRadius in class JmolViewer

getAtomArgb
```
public int getAtomArgb(int i)
```
Specified by:

getAtomArgb in class JmolViewer

getAtomModelIndex
```
public int getAtomModelIndex(int i)
```
Specified by:

getAtomModelIndex in class JmolViewer

getBondRadius
```
public float getBondRadius(int i)
```
Specified by:

getBondRadius in class JmolViewer

getBondOrder
```
public int getBondOrder(int i)
```
Specified by:

getBondOrder in class JmolViewer

assignAromaticBonds
```
public void assignAromaticBonds()
```

resetAromatic
```
public void resetAromatic()
```

getBondArgb1
```
public int getBondArgb1(int i)
```
Specified by:

getBondArgb1 in class JmolViewer

getBondModelIndex
```
public int getBondModelIndex(int i)
```
Specified by:

getBondModelIndex in class JmolViewer

getBondArgb2
```
public int getBondArgb2(int i)
```
Specified by:

getBondArgb2 in class JmolViewer

getPolymerLeadMidPoints

public javajs.util.P3[] getPolymerLeadMidPoints(int modelIndex,
                                                int polymerIndex)

Specified by:: getPolymerLeadMidPoints in class JmolViewer

setStereoMode

public void setStereoMode(int[] twoColors,
                          STER stereoMode,
                          float degrees)

isStereoDouble
```
boolean isStereoDouble()
```

getGraphicsData
```
public GData getGraphicsData()
```

getProperty
```
public java.lang.Object getProperty(java.lang.String returnType,
                                    java.lang.String infoType,
                                    java.lang.Object paramInfo)
```
Specified by:

getProperty in class JmolViewer

Parameters:

returnType - "JSON", "string", "readable", and anything else returns the Java object.

Returns:

property data -- see org.jmol.viewer.PropertyManager.java

showEditor

public void showEditor(java.lang.String[] file_text)

getPropertyManager

private JmolPropertyManager getPropertyManager()

getModelExtract

public java.lang.String getModelExtract(java.lang.Object atomExpression,
                                        boolean doTransform,
                                        boolean isModelKit,
                                        java.lang.String type)

setTainted
```
public void setTainted(boolean TF)
```

notifyMouseClicked

public int notifyMouseClicked(int x,
                              int y,
                              int action,
                              int mode)

checkObjectClicked

java.util.Map<java.lang.String,java.lang.Object> checkObjectClicked(int x,
                                                                    int y,
                                                                    int modifiers)

checkObjectHovered

public boolean checkObjectHovered(int x,
                                  int y)

checkObjectDragged

void checkObjectDragged(int prevX,
                        int prevY,
                        int x,
                        int y,
                        int action)

rotateAxisAngleAtCenter

public boolean rotateAxisAngleAtCenter(JmolScriptEvaluator eval,
                                       javajs.util.P3 rotCenter,
                                       javajs.util.V3 rotAxis,
                                       float degreesPerSecond,
                                       float endDegrees,
                                       boolean isSpin,
                                       BS bsSelected)

rotateAboutPointsInternal

public boolean rotateAboutPointsInternal(JmolScriptEvaluator eval,
                                         javajs.util.P3 point1,
                                         javajs.util.P3 point2,
                                         float degreesPerSecond,
                                         float endDegrees,
                                         boolean isSpin,
                                         BS bsSelected,
                                         javajs.util.V3 translation,
                                         javajs.util.List<javajs.util.P3> finalPoints,
                                         float[] dihedralList)

startSpinningAxis

public void startSpinningAxis(javajs.util.P3 pt1,
                              javajs.util.P3 pt2,
                              boolean isClockwise)

getModelDipole

public javajs.util.V3 getModelDipole()

calculateMolecularDipole

public javajs.util.V3 calculateMolecularDipole()

getAtomIdentityInfo

public void getAtomIdentityInfo(int atomIndex,
                                java.util.Map<java.lang.String,java.lang.Object> info)

setDefaultLattice

public void setDefaultLattice(javajs.util.P3 p)

getDefaultLattice

public javajs.util.P3 getDefaultLattice()

getTaintedAtoms
```
public BS getTaintedAtoms(byte type)
```

setTaintedAtoms

public void setTaintedAtoms(BS bs,
                            byte type)

getData

public java.lang.String getData(java.lang.String atomExpression,
                                java.lang.String type)

Specified by:: getData in class JmolViewer

getModelCml

public java.lang.String getModelCml(BS bs,
                                    int nAtomsMax,
                                    boolean addBonds)

getHelixData

public java.lang.Object getHelixData(BS bs,
                                     int tokType)

getPdbAtomData

public java.lang.String getPdbAtomData(BS bs,
                                       javajs.util.OC sb)

isJmolDataFrameForModel

public boolean isJmolDataFrameForModel(int modelIndex)

isJmolDataFrame
```
public boolean isJmolDataFrame()
```

getJmolDataFrameIndex

public int getJmolDataFrameIndex(int modelIndex,
                                 java.lang.String type)

setJmolDataFrame

public void setJmolDataFrame(java.lang.String type,
                             int modelIndex,
                             int dataIndex)

setFrameTitle

public void setFrameTitle(int modelIndex,
                          java.lang.String title)

setFrameTitleObj

public void setFrameTitleObj(java.lang.Object title)

getFrameTitle

public java.lang.String getFrameTitle()

getJmolFrameType

java.lang.String getJmolFrameType(int modelIndex)

getJmolDataSourceFrame

public int getJmolDataSourceFrame(int modelIndex)

setAtomProperty

public void setAtomProperty(BS bs,
                            int tok,
                            int iValue,
                            float fValue,
                            java.lang.String sValue,
                            float[] values,
                            java.lang.String[] list)

checkCoordinatesChanged
```
public void checkCoordinatesChanged()
```

setAtomCoord

public void setAtomCoord(int atomIndex,
                         float x,
                         float y,
                         float z)

setAtomCoordRelative

public void setAtomCoordRelative(int atomIndex,
                                 float x,
                                 float y,
                                 float z)

setAtomCoords

public void setAtomCoords(BS bs,
                          int tokType,
                          java.lang.Object xyzValues)

setAtomCoordsRelative

public void setAtomCoordsRelative(javajs.util.T3 offset,
                                  BS bs)

invertAtomCoordPt

public void invertAtomCoordPt(javajs.util.P3 pt,
                              BS bs)

invertAtomCoordPlane

public void invertAtomCoordPlane(javajs.util.P4 plane,
                                 BS bs)

invertSelected

public void invertSelected(javajs.util.P3 pt,
                           javajs.util.P4 plane,
                           int iAtom,
                           BS invAtoms)

moveAtoms

public void moveAtoms(javajs.util.M3 mNew,
                      javajs.util.M3 matrixRotate,
                      javajs.util.V3 translation,
                      javajs.util.P3 center,
                      boolean isInternal,
                      BS bsAtoms,
                      boolean translationOnly)

moveSelected

public void moveSelected(int deltaX,
                         int deltaY,
                         int deltaZ,
                         int x,
                         int y,
                         BS bsSelected,
                         boolean isTranslation,
                         boolean asAtoms)

highlightBond

public void highlightBond(int index,
                          boolean isHover)

highlight
```
public void highlight(BS bs)
```

setRotateBondIndex

public void setRotateBondIndex(int index)

getRotateBondIndex
```
int getRotateBondIndex()
```

actionRotateBond

void actionRotateBond(int deltaX,
                      int deltaY,
                      int x,
                      int y)

refreshMeasures

public void refreshMeasures(boolean andStopMinimization)

functionXY
```
public float[][] functionXY(java.lang.String functionName,
                            int nX,
                            int nY)
```
fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call. Otherwise it reads the values using individual function calls, which each return Double. If the functionName begins with "file:" then data are read from a file specified after the colon. The sign of nX is not relevant in that case. The file may contain mixed numeric and non-numeric values; the non-numeric values will be skipped by Parser.parseFloatArray

Parameters:

functionName -

nX -

nY -

Returns:

nX by nY array of floating values

functionXYZ

public float[][][] functionXYZ(java.lang.String functionName,
                               int nX,
                               int nY,
                               int nZ)

extractMolData

public java.lang.String extractMolData(java.lang.String what)

Specified by:: extractMolData in class JmolViewer

getNMRPredict

public java.lang.String getNMRPredict(boolean openURL)

getHelp

public void getHelp(java.lang.String what)

show2D

public void show2D(java.lang.String smiles)

getChemicalInfo

public java.lang.String getChemicalInfo(java.lang.String smiles,
                                        T t)

addCommand
```
public void addCommand(java.lang.String command)
```
Adds one or more commands to the command history

Parameters:

command - the command to add

removeCommand
```
public java.lang.String removeCommand()
```
Removes one command from the command history

Returns:

command removed

getSetHistory
```
public java.lang.String getSetHistory(int howFarBack)
```
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;

Specified by:

getSetHistory in class JmolViewer

Parameters:

howFarBack - number of lines (-1 for next line)

Returns:

one or more lines of command history

getOutputChannel

public javajs.util.OC getOutputChannel(java.lang.String localName,
                                       java.lang.String[] fullPath)

writeTextFile

public void writeTextFile(java.lang.String fileName,
                          java.lang.String data)

Specified by:: writeTextFile in class JmolViewer

clipImageOrPasteText
```
public java.lang.String clipImageOrPasteText(java.lang.String text)
```
Specified by:

clipImageOrPasteText in class JmolViewer

Parameters:

text - null here clips image; String pastes text

Returns:

"OK image to clipboard: [width] * [height] or "OK text to clipboard: [length]

getClipboardText
```
public java.lang.String getClipboardText()
```
Specified by:

getClipboardText in class JmolViewer

processWriteOrCapture
```
public java.lang.String processWriteOrCapture(java.util.Map<java.lang.String,java.lang.Object> params)
```
from eval write command only includes option to write set of files

Parameters:

params -

Returns:

message starting with "OK" or an error message

createZip

public java.lang.String createZip(java.lang.String fileName,
                                  java.lang.String type,
                                  java.lang.Object data)

outputToFile
```
public java.lang.String outputToFile(java.util.Map<java.lang.String,java.lang.Object> params)
```
Specified by:

outputToFile in class JmolViewer

Parameters:

params - include type, fileName, text, bytes, quality, width, height

Returns:

null (canceled) or a message starting with OK or an error message

getOutputManager

private OutputManager getOutputManager()

setSyncTarget

private void setSyncTarget(int mode,
                           boolean TF)

syncScript

public void syncScript(java.lang.String script,
                       java.lang.String applet,
                       int port)

Specified by:: syncScript in class JmolViewer

getModelIndexFromId
```
public int getModelIndexFromId(java.lang.String id)
```
Specified by:

getModelIndexFromId in class JmolViewer

Parameters:

id - some_id, filename#id, or ~fileNo.modelNo added ".basemodel" indicates to get the first model in a series from a JDX-MOL file.

Returns:

model index if found; -2 if file found but model not found -2 if no file indicated and no model found -1 if no such file

setSyncDriver
```
public void setSyncDriver(int mode)
```

getPartialCharges
```
public float[] getPartialCharges()
```

setProteinType

public void setProteinType(STR type,
                           BS bs)

getBondPoint3f1
```
public javajs.util.P3 getBondPoint3f1(int i)
```
Specified by:

getBondPoint3f1 in class JmolViewer

getBondPoint3f2
```
public javajs.util.P3 getBondPoint3f2(int i)
```
Specified by:

getBondPoint3f2 in class JmolViewer

getVibration

public Vibration getVibration(int atomIndex)

getVanderwaalsMar
```
public int getVanderwaalsMar(int i)
```

getVanderwaalsMarType

public int getVanderwaalsMarType(int atomicAndIsotopeNumber,
                                 VDW type)

setVdwStr
```
void setVdwStr(java.lang.String name)
```

setUserVdw
```
void setUserVdw(VDW mode)
```

getDefaultVdwNameOrData

public java.lang.String getDefaultVdwNameOrData(int mode,
                                                VDW type,
                                                BS bs)

deleteAtoms

public int deleteAtoms(BS bs,
                       boolean fullModels)

deleteBonds

public void deleteBonds(BS bsDeleted)

deleteModelAtoms

public void deleteModelAtoms(int modelIndex,
                             int firstAtomIndex,
                             int nAtoms,
                             BS bsDeleted)

getDeletedAtoms
```
public BS getDeletedAtoms()
```

getQuaternionFrame
```
public char getQuaternionFrame()
```

calculatePointGroup

public java.lang.String calculatePointGroup()

getPointGroupInfo

public java.util.Map<java.lang.String,java.lang.Object> getPointGroupInfo(java.lang.Object atomExpression)

getPointGroupAsString

public java.lang.String getPointGroupAsString(boolean asDraw,
                                              java.lang.String type,
                                              int index,
                                              float scale)

loadImage

public void loadImage(java.lang.String pathName,
                      java.lang.String echoName)

loadImageData

void loadImageData(java.lang.Object image,
                   java.lang.String nameOrError,
                   java.lang.String echoName,
                   ScriptContext sc)

cd

public java.lang.String cd(java.lang.String dir)

setErrorMessage

public java.lang.String setErrorMessage(java.lang.String errMsg,
                                        java.lang.String errMsgUntranslated)

getErrorMessage
```
public java.lang.String getErrorMessage()
```
Specified by:

getErrorMessage in class JmolViewer

getErrorMessageUn
```
public java.lang.String getErrorMessageUn()
```
Specified by:

getErrorMessageUn in class JmolViewer

setShapeErrorState

public void setShapeErrorState(int shapeID,
                               java.lang.String state)

getShapeErrorState

public java.lang.String getShapeErrorState()

handleError

public void handleError(java.lang.Error er,
                        boolean doClear)

getAtomicCharges
```
public float[] getAtomicCharges()
```

getFunctions

public java.util.Map<java.lang.String,JmolScriptFunction> getFunctions(boolean isStatic)

removeFunction

public void removeFunction(java.lang.String name)

getFunction

public JmolScriptFunction getFunction(java.lang.String name)

isStaticFunction

private static boolean isStaticFunction(java.lang.String name)

isFunction

public boolean isFunction(java.lang.String name)

clearFunctions
```
public void clearFunctions()
```

addFunction

public void addFunction(JmolScriptFunction function)

getFunctionCalls

public java.lang.String getFunctionCalls(java.lang.String selectedFunction)

showMessage

public void showMessage(java.lang.String s)

getMoInfo

public java.lang.String getMoInfo(int modelIndex)

checkPrivateKey
```
public boolean checkPrivateKey(double privateKey)
```
Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet. When the image creator is used it requires both a vwr object and that vwr's private key. But the private key is private, so it is not possible to create a useable image creator without working through a vwr's own methods. Bob Hanson, 9/20/2009

Parameters:

privateKey -

Returns:

true if privateKey matches

bindAction

public void bindAction(java.lang.String desc,
                       java.lang.String name)

unBindAction

public void unBindAction(java.lang.String desc,
                         java.lang.String name)

getFrontPlane
```
public int getFrontPlane()
```

getPlaneIntersection

public javajs.util.List<java.lang.Object> getPlaneIntersection(int type,
                                                               javajs.util.P4 plane,
                                                               float scale,
                                                               int flags)

calculateStruts

public int calculateStruts(BS bs1,
                           BS bs2)

getPreserveState
```
public boolean getPreserveState()
```
This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.

Returns:

TRUE or FALSE

isKiosk
```
boolean isKiosk()
```

hasFocus
```
public boolean hasFocus()
```

setFocus
```
public void setFocus()
```

stopMinimization
```
void stopMinimization()
```

clearMinimization
```
void clearMinimization()
```

getMinimizationInfo

public java.lang.String getMinimizationInfo()

checkMinimization
```
private void checkMinimization()
```

minimize

public void minimize(int steps,
                     float crit,
                     BS bsSelected,
                     BS bsFixed,
                     float rangeFixed,
                     boolean addHydrogen,
                     boolean isOnly,
                     boolean isSilent,
                     boolean isLoad2D)

Parameters:: steps - Integer.MAX_VALUE --> use defaults; crit - -1 --> use defaults; bsSelected -; bsFixed -; rangeFixed -; addHydrogen -; isOnly -; isSilent -; isLoad2D -

setMotionFixedAtoms

public void setMotionFixedAtoms(BS bs)

getMotionFixedAtoms
```
public BS getMotionFixedAtoms()
```

rotateArcBall

void rotateArcBall(int x,
                   int y,
                   float factor)

getAtomicPropertyState

void getAtomicPropertyState(javajs.util.SB commands,
                            byte type,
                            BS bs,
                            java.lang.String name,
                            float[] data)

getCenterAndPoints

public javajs.util.P3[][] getCenterAndPoints(javajs.util.List<java.lang.Object[]> atomSets,
                                             boolean addCenter)

writeFileData

public java.lang.String writeFileData(java.lang.String fileName,
                                      java.lang.String type,
                                      int modelIndex,
                                      java.lang.Object[] parameters)

getPdbData

public java.lang.String getPdbData(int modelIndex,
                                   java.lang.String type,
                                   java.lang.Object[] parameters)

getGroupsWithin

public BS getGroupsWithin(int nResidues,
                          BS bs)

getExecutor
```
public java.lang.Object getExecutor()
```

togglePickingLabel

public void togglePickingLabel(BS bs)

loadShape
```
public void loadShape(int shapeID)
```

setShapeSize

public void setShapeSize(int shapeID,
                         int mad,
                         BS bsSelected)

setShapeSizeRD

public void setShapeSizeRD(int shapeID,
                           RadiusData rd,
                           BS bsAtoms)

setShapeProperty

public void setShapeProperty(int shapeID,
                             java.lang.String propertyName,
                             java.lang.Object value)

getShapeProperty

public java.lang.Object getShapeProperty(int shapeType,
                                         java.lang.String propertyName)

getShapePropertyData

public boolean getShapePropertyData(int shapeType,
                                    java.lang.String propertyName,
                                    java.lang.Object[] data)

getShapePropertyIndex

public java.lang.Object getShapePropertyIndex(int shapeType,
                                              java.lang.String propertyName,
                                              int index)

getShapePropertyAsInt

private int getShapePropertyAsInt(int shapeID,
                                  java.lang.String propertyName)

setModelVisibility
```
public void setModelVisibility()
```

resetShapes

public void resetShapes(boolean andCreateNew)

setAtomLabel

public void setAtomLabel(java.lang.String value,
                         int i)

deleteShapeAtoms

public void deleteShapeAtoms(java.lang.Object[] value,
                             BS bs)

resetBioshapes

public void resetBioshapes(BS bsAllAtoms)

getAtomShapeValue

public float getAtomShapeValue(int tok,
                               Group group,
                               int atomIndex)

mergeShapes

public void mergeShapes(Shape[] newShapes)

getShapeManager
```
public ShapeManager getShapeManager()
```

setParallel

public boolean setParallel(boolean TF)

isParallel
```
public boolean isParallel()
```

getRenderableBitSet
```
public BS getRenderableBitSet()
```

setAtomPickingOption

private void setAtomPickingOption(java.lang.String option)

setBondPickingOption

private void setBondPickingOption(java.lang.String option)

undoClear
```
void undoClear()
```

undoMoveAction
```
public void undoMoveAction(int action,
                           int n)
```
Parameters:

action - Token.undo or Token.redo

n - number of steps to go back/forward; 0 for all; -1 for clear; -2 for clear BOTH

undoMoveActionClear

void undoMoveActionClear(int taintedAtom,
                         int type,
                         boolean clearRedo)

moveAtomWithHydrogens

protected void moveAtomWithHydrogens(int atomIndex,
                                     int deltaX,
                                     int deltaY,
                                     int deltaZ,
                                     BS bsAtoms)

isAtomPDB
```
public boolean isAtomPDB(int i)
```

isModelPDB
```
public boolean isModelPDB(int i)
```

isAtomAssignable
```
boolean isAtomAssignable(int i)
```

deleteMeasurement
```
public void deleteMeasurement(int i)
```
Specified by:

deleteMeasurement in class JmolViewer

haveModelKit
```
boolean haveModelKit()
```

getModelKitStateBitSet

BS getModelKitStateBitSet(BS bs,
                          BS bsDeleted)

getSmiles

public java.lang.String getSmiles(BS bs)
                           throws java.lang.Exception

Specified by:: getSmiles in class JmolViewer
Throws:: java.lang.Exception

getSmilesOpt

public java.lang.String getSmilesOpt(BS bsSelected,
                                     int index1,
                                     int index2,
                                     boolean explicitH,
                                     boolean isBioSmiles,
                                     boolean bioAllowUnmatchedRings,
                                     boolean bioAddCrossLinks,
                                     boolean bioAddComment)
                              throws java.lang.Exception

returns the SMILES string for a sequence or atom set does not include attached protons on groups

Parameters:: bsSelected - selected atom set or null for current or specified range; index1 - when bsSeleced == null, first atomIndex or -1 for current; index2 - when bsSeleced == null, end atomIndex or -1 for current; explicitH - include all H atoms, not just stereochemical ones; isBioSmiles -; bioAllowUnmatchedRings -; bioAddCrossLinks -; bioAddComment -
Returns:: SMILES string
Throws:: java.lang.Exception

connect

public void connect(float[][] connections)

prompt

public java.lang.String prompt(java.lang.String label,
                               java.lang.String data,
                               java.lang.String[] list,
                               boolean asButtons)

getColorEncoder

public ColorEncoder getColorEncoder(java.lang.String colorScheme)

displayBonds

public void displayBonds(BondSet bs,
                         boolean isDisplay)

getModelAtomProperty

public java.lang.String getModelAtomProperty(Atom atom,
                                             java.lang.String text)

initializeExporter

public JmolRendererInterface initializeExporter(java.util.Map<java.lang.String,java.lang.Object> params)

getMouseEnabled
```
public boolean getMouseEnabled()
```

setZslabPoint

public void setZslabPoint(javajs.util.P3 pt)

calcAtomsMinMax

public void calcAtomsMinMax(BS bs,
                            BoxInfo boxInfo)

Specified by:: calcAtomsMinMax in class JmolViewer

getObjectMap

public void getObjectMap(java.util.Map<java.lang.String,?> map,
                         char c)

used in autocompletion in console using TAB

Parameters:: map -; c -

getPdbBondInfo

public java.lang.String[][] getPdbBondInfo(java.lang.String group3)

setPicked
```
public void setPicked(int iAtom)
```

runScript
```
public java.lang.String runScript(java.lang.String script)
```
Description copied from class: JmolViewer

run a script immediately and return output buffer string Jmol 13.1.15

Specified by:

runScript in class JmolViewer

Returns:

string from ScriptEvaluator#outputBuffer

allowSpecAtom
```
public boolean allowSpecAtom()
```

setFrameDelayMs

public void setFrameDelayMs(long millis)

getFrameDelayMs
```
public long getFrameDelayMs(int i)
```

getBaseModelBitSet
```
public BS getBaseModelBitSet()
```

getTimeouts

public java.util.Map<java.lang.String,java.lang.Object> getTimeouts()

clearTimeouts
```
public void clearTimeouts()
```

setTimeout

public void setTimeout(java.lang.String name,
                       int mSec,
                       java.lang.String script)

triggerTimeout

public void triggerTimeout(java.lang.String name)

clearTimeout

public void clearTimeout(java.lang.String name)

showTimeout

public java.lang.String showTimeout(java.lang.String name)

calculatePartialCharges

public void calculatePartialCharges(BS bsSelected)

setCurrentModelID

public void setCurrentModelID(java.lang.String id)

setCentroid

public void setCentroid(BS bs,
                        int[] minmax)

getPathForAllFiles

public java.lang.String getPathForAllFiles()

cacheGet

public java.lang.Object cacheGet(java.lang.String key)

cacheClear
```
public void cacheClear()
```

cachePut
```
public void cachePut(java.lang.String key,
                     java.lang.Object data)
```
JmolViewer interface -- allows saving files in memory for later retrieval

Specified by:

cachePut in interface javajs.api.JSInterface

Specified by:

cachePut in class JmolViewer

Parameters:

key -

data -

cacheFileByName
```
public int cacheFileByName(java.lang.String fileName,
                           boolean isAdd)
```
Description copied from class: JmolViewer

used in JSmolApplet.js for drag-drop behavior.

Specified by:

cacheFileByName in interface javajs.api.JSInterface

Specified by:

cacheFileByName in class JmolViewer

Returns:

number of bytes cached

cacheList

public java.util.Map<java.lang.String,java.lang.Integer> cacheList()

clearThreads
```
public void clearThreads()
```

getEvalContextAndHoldQueue

public ScriptContext getEvalContextAndHoldQueue(JmolScriptEvaluator jse)

checkInheritedShapes
```
public void checkInheritedShapes()
```

resizeInnerPanel

public javajs.awt.Dimension resizeInnerPanel(int width,
                                             int height)

Specified by:: resizeInnerPanel in class JmolViewer

getFontLineShapeState

public java.lang.String getFontLineShapeState(java.lang.String s,
                                              java.lang.String myType,
                                              TickInfo[] tickInfos)

getShapeSetState

public void getShapeSetState(AtomShape atomShape,
                             Shape shape,
                             int monomerCount,
                             Group[] monomers,
                             BS bsSizeDefault,
                             java.util.Map<java.lang.String,BS> temp,
                             java.util.Map<java.lang.String,BS> temp2)

getMeasurementState

public java.lang.String getMeasurementState(Measures measures,
                                            javajs.util.List<Measurement> mList,
                                            int measurementCount,
                                            javajs.awt.Font font3d,
                                            TickInfo ti)

getBondState

public java.lang.String getBondState(Shape shape,
                                     BS bsOrderSet,
                                     boolean reportAll)

getAtomShapeSetState

public java.lang.String getAtomShapeSetState(Shape shape,
                                             AtomShape[] shapes)

getShapeState

public java.lang.String getShapeState(Shape shape)

getAtomShapeState

public java.lang.String getAtomShapeState(AtomShape shape)

getDefaultPropertyParam

public java.lang.String getDefaultPropertyParam(int propertyID)

getPropertyNumber

public int getPropertyNumber(java.lang.String name)

checkPropertyParameter

public boolean checkPropertyParameter(java.lang.String name)

extractProperty

public java.lang.Object extractProperty(java.lang.Object property,
                                        SV[] args,
                                        int pt)

addHydrogens

public BS addHydrogens(BS bsAtoms,
                       boolean is2DLoad,
                       boolean isSilent)

addHydrogensInline

public BS addHydrogensInline(BS bsAtoms,
                             javajs.util.List<Atom> vConnections,
                             javajs.util.P3[] pts)
                      throws java.lang.Exception

Throws:: java.lang.Exception

evalFunctionFloat

public float evalFunctionFloat(java.lang.Object func,
                               java.lang.Object params,
                               float[] values)

Specified by:: evalFunctionFloat in interface AtomDataServer

evalParallel

public boolean evalParallel(ScriptContext context,
                            ShapeManager shapeManager)

evaluateExpression

public java.lang.Object evaluateExpression(java.lang.Object stringOrTokens)

Specified by:: evaluateExpression in class JmolViewer

evaluateExpressionAsVariable

public SV evaluateExpressionAsVariable(java.lang.Object stringOrTokens)

getAtomBitSet

public BS getAtomBitSet(java.lang.Object atomExpression)

getAtomBitSetVector

javajs.util.List<java.lang.Integer> getAtomBitSetVector(java.lang.Object atomExpression)

getContextVariables

public java.util.Map<java.lang.String,SV> getContextVariables()

getScriptContext

public ScriptContext getScriptContext(java.lang.String why)

getAtomDefs

public java.lang.String getAtomDefs(java.util.Map<java.lang.String,java.lang.Object> names)

Specified by:: getAtomDefs in class JmolViewer

createModels
```
public void createModels(int n)
```

setCGO

public void setCGO(javajs.util.List<java.lang.Object> info)

setFrame
```
public void setFrame(int i)
```

movePyMOL

public boolean movePyMOL(JmolScriptEvaluator eval,
                         float floatSecondsTotal,
                         float[] pymolView)

getCamera
```
public javajs.util.P3 getCamera()
```

setModelSet

public void setModelSet(ModelSet modelSet)

setObjectProp

public java.lang.String setObjectProp(java.lang.String id,
                                      int tokCommand)

getSceneList

public java.lang.String[] getSceneList()

getDihedralMap

public int[][] getDihedralMap(int[] atoms)

setDihedrals

public void setDihedrals(float[] dihedralList,
                         BS[] bsBranches,
                         float rate)

getBsBranches

public BS[] getBsBranches(float[] dihedralList)

getChainID
```
public int getChainID(java.lang.String id)
```
Create a unique integer for any chain string. Note that if there are any chains that are more than a single character, chainCaseSensitive is automatically set TRUE

Parameters:

id - < 256 is just the character of a single-character chain id; >= 256 indicates a list pointer into chainList.

Returns:

i

getChainIDStr

public java.lang.String getChainIDStr(int id)

getScriptQueueInfo

public java.lang.Boolean getScriptQueueInfo()

getNMRCalculation

public JmolNMRInterface getNMRCalculation()

getDistanceUnits

public java.lang.String getDistanceUnits(java.lang.String s)

calculateFormalCharges

public int calculateFormalCharges(BS bs)

cachePngFiles
```
public boolean cachePngFiles()
```

setModulation

public void setModulation(BS bs,
                          boolean isOn,
                          javajs.util.P3 t1,
                          boolean isQ)

checkInMotion
```
public void checkInMotion(int state)
```

checkMotionRendering
```
public boolean checkMotionRendering(int tok)
```
check motion for rendering during mouse movement, spin, vibration, and animation

Parameters:

tok -

Returns:

TRUE if allowed

openExportChannel

public javajs.util.OC openExportChannel(double privateKey,
                                        java.lang.String fileName,
                                        boolean asWriter)
                                 throws java.io.IOException

Throws:: java.io.IOException

log
```
public void log(java.lang.String data)
```
Specified by:

log in interface AtomDataServer

getLogFileName

public java.lang.String getLogFileName()

getCommands

public java.lang.String getCommands(java.util.Map<java.lang.String,BS> htDefine,
                                    java.util.Map<java.lang.String,BS> htMore,
                                    java.lang.String select)

allowCapture
```
public boolean allowCapture()
```

getApplet
```
public java.lang.Object getApplet()
```
Specified by:

getApplet in interface javajs.api.JSInterface

getModulationList

public javajs.util.List<java.lang.Object> getModulationList(BS bs,
                                                            java.lang.String type,
                                                            javajs.util.P3 t456)

getVibrationPoint

public Point3fi getVibrationPoint(Vibration vibration,
                                  Point3fi pt)

setCurrentAtom

public void setCurrentAtom(int iAtom)

getCurrentAtom
```
public int getCurrentAtom()
```

Class Viewer

Nested Class Summary

Field Summary

Fields inherited from class org.jmol.api.JmolViewer

Constructor Summary

Method Summary

Methods inherited from class org.jmol.api.JmolViewer

Methods inherited from class java.lang.Object

Field Detail

autoExit

haveDisplay

isJS

isWebGL

isSingleThreaded

queueOnHold

fullName

appletDocumentBase

appletCodeBase

appletIdiomaBase

jsDocumentBase

compiler

definedAtomSets

ms

fm

isApplet

isJNLP

isSyntaxAndFileCheck

isSyntaxCheck

listCommands

mustRender

htmlName

appletName

insertedCommand

gdata

applet

actionManager

am

cm

dm

shm

slm

rm

g

sm

tm

strJavaVendor

strOSName

strJavaVersion

syncId

logFilePath

allowScripting

isPrintOnly

isSignedApplet

isSignedAppletLocal

isSilent

multiTouch

noGraphicsAllowed

useCommandThread

commandOptions

vwrOptions

display

modelAdapter

access

commandHistory

mm

stm

scm

eval

tempArray

allowArrayDotNotation

version_date

isPreviewOnly

mouseEnabled

noneSelected

mouse

ligandModels

ligandModelSet

minimizer

smilesMatcher

jsc