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<String>`	`actionStates`
`(package private) javajs.util.List<String>`	`actionStatesRedo`
`private boolean`	`allowScripting`
`(package private) AnimationManager`	`animationManager`
`private boolean`	`antialiasDisplay`
`(package private) JmolAppConsoleInterface`	`appConsole`
`(package private) Object`	`applet`
`String`	`appletCodeBase`
`String`	`appletDocumentBase`
`String`	`appletIdiomaBase`
`boolean`	`autoExit`
`private boolean`	`axesAreTainted`
`(package private) BS`	`bsFrameOffsets`
`private BS`	`bsRotateBranch`
`(package private) BS`	`bsUserVdws`
`Map<String,Object>`	`captureParams`
`javajs.util.List<String>`	`chainList`
`Map<Object,Object>`	`chainMap`
`(package private) ColorManager`	`colorManager`
`private CommandHistory`	`commandHistory`
`private String`	`commandOptions`
`Object`	`compiler`
`boolean`	`creatingImage`
`private int`	`currentCursor`
`private int`	`currentShapeID`
`private String`	`currentShapeState`
`(package private) JmolDataManager`	`dataManager`
`(package private) EnumVdw`	`defaultVdw`
`Map<String,Object>`	`definedAtomSets`
`(package private) javajs.awt.Dimension`	`dimScreen`
`private Object`	`display`
`boolean`	`displayLoadErrors`
`private String`	`errorMessage`
`private String`	`errorMessageUntranslated`
`JmolScriptEvaluator`	`eval`
`private Object`	`executor`
`FileManager`	`fileManager`
`(package private) javajs.util.P3[]`	`frameOffsets`
`private boolean`	`frankOn`
`String`	`fullName`
`(package private) GData`	`gdata`
`GlobalSettings`	`global`
`boolean`	`haveDisplay`
`private boolean`	`haveJDX`
`private Map<String,Object>`	`headlessImageParams`
`(package private) int`	`hoverAtomIndex`
`boolean`	`hoverEnabled`
`(package private) String`	`hoverText`
`(package private) String`	`htmlName`
`(package private) Map<String,String[][]>`	`htPdbBondInfo`
`private float`	`imageFontScaling`
`private boolean`	`inMotion`
`private 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`
`boolean`	`isSyntaxAndFileCheck`
`boolean`	`isSyntaxCheck`
`(package private) boolean`	`isTainted`
`boolean`	`isWebGL`
`(package private) javajs.api.GenericMenuInterface`	`jmolpopup`
`static String`	`jsDocumentBase`
`private JmolRendererInterface`	`jsExporter3D`
`private Map<String,Object>`	`jsParams`
`private JmolJSpecView`	`jsv`
`private String`	`language`
`(package private) Map<String,Object>`	`ligandModels`
`(package private) Map<String,Boolean>`	`ligandModelSet`
`boolean`	`listCommands`
`(package private) Map<String,JmolScriptFunction>`	`localFunctions`
`(package private) String`	`logFileName`
`private String`	`logFilePath`
`private int`	`maximumSize`
`private MinimizerInterface`	`minimizer`
`private JmolAdapter`	`modelAdapter`
`private javajs.api.GenericMenuInterface`	`modelkitPopup`
`private ModelManager`	`modelManager`
`ModelSet`	`modelSet`
`private int`	`motionEventNumber`
`private javajs.api.GenericMouseInterface`	`mouse`
`private boolean`	`mouseEnabled`
`private boolean`	`movingSelected`
`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 double`	`privateKey`
`boolean`	`queueOnHold`
`private RadiusData`	`rd`
`private boolean`	`refreshing`
`(package private) JmolRepaintManager`	`repaintManager`
`private int`	`rotateBondIndex`
`private int`	`rotatePrev1`
`private int`	`rotatePrev2`
`(package private) JmolStateCreator`	`sc`
`(package private) JmolScriptEditorInterface`	`scriptEditor`
`boolean`	`scriptEditorVisible`
`private JmolScriptManager`	`scriptManager`
`(package private) SelectionManager`	`selectionManager`
`(package private) ShapeManager`	`shapeManager`
`private boolean`	`showSelected`
`private SmilesMatcherInterface`	`smilesMatcher`
`private StateManager`	`stateManager`
`private int`	`stateScriptVersionInt`
`(package private) static Map<String,JmolScriptFunction>`	`staticFunctions`
`StatusManager`	`statusManager`
`private static String`	`strJavaVendor`
`private static String`	`strJavaVersion`
`private static String`	`strOSName`
`private SymmetryInterface`	`symmetry`
`static String`	`SYNC_GRAPHICS_MESSAGE`
`static String`	`SYNC_NO_GRAPHICS_MESSAGE`
`private String`	`syncId`
`private TempArray`	`tempArray`
`(package private) Map<String,Object>`	`timeouts`
`(package private) TransformManager`	`transformManager`
`private boolean`	`useCommandThread`
`(package private) int[]`	`userVdwMars`
`(package private) float[]`	`userVdws`
`private static String`	`version_date`
`private Map<String,Object>`	`viewerOptions`

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

Constructor Summary

Constructors
Constructor and Description

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

Constructors
Constructor and Description
`Viewer(Map<String,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(String command)` Adds one or more commands to the command history
`void`	`addFunction(JmolScriptFunction function)`
`BS`	`addHydrogens(BS bsAtoms, boolean is2DLoad, boolean isSilent)`
`private BS`	`addHydrogensInline(BS bsAtoms, javajs.util.List<Atom> vConnections, javajs.util.P3[] pts)`
`void`	`addSelectionListener(JmolSelectionListener listener)`
`StateScript`	`addStateScript(String script, boolean addFrameNumber, boolean postDefinitions)`
`StateScript`	`addStateScriptRet(String script1, BS bsBonds, BS bsAtoms1, BS bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)`
`void`	`addUnitCellOffset(javajs.util.P3 pt)`
`protected static JmolViewer`	`allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener, javajs.api.GenericPlatform implementedPlatform)` old way...
`EnumStructure[]`	`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`	`assignAtom(int atomIndex, javajs.util.P3 pt, String type)`
`void`	`assignBond(int bondIndex, char type)`
`void`	`assignConnect(int index, int index2)`
`void`	`autoCalculate(int tokProperty)`
`int`	`autoHbond(BS bsFrom, BS bsTo, boolean onlyIfHaveCalculated)`
`private void`	`beginRendering(boolean isDouble, boolean isImageWrite)`
`void`	`bindAction(String desc, String name)`
`void`	`cacheClear()`
`int`	`cacheFileByName(String fileName, boolean isAdd)` used in JSmolApplet.js for drag-drop behavior.
`Object`	`cacheGet(String key)`
`Map<String,Integer>`	`cacheList()`
`boolean`	`cachePngFiles()`
`void`	`cachePut(String key, 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)`
`String`	`calculatePointGroup()`
`void`	`calculateStraightness()`
`String`	`calculateStructures(BS bsAtoms, boolean asDSSP, boolean setStructure)`
`int`	`calculateStruts(BS bs1, BS bs2)`
`javajs.util.P3[]`	`calculateSurface(BS bsSelected, float envelopeRadius)`
`String`	`cd(String dir)`
`void`	`checkCoordinatesChanged()`
`private static float`	`checkFloatRange(float value, float min, float max)`
`boolean`	`checkHalt(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) Map<String,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(String key1, String key2)`
`boolean`	`checkPrivateKey(double privateKey)` Simple method to ensure that the image creator (which writes files) was in fact opened by this viewer and not by some manipulation of the applet.
`boolean`	`checkPropertyParameter(String name)`
`void`	`clearAllMeasurements()`
`private void`	`clearAtomSets()`
`void`	`clearBfactorRange()`
`(package private) void`	`clearClickCount()`
`void`	`clearConsole()`
`void`	`clearFunctions()`
`void`	`clearMeasurements()`
`(package private) void`	`clearMinimization()`
`private void`	`clearModelDependentObjects()`
`void`	`clearMouse()`
`private void`	`clearRepaintManager(int iShape)`
`void`	`clearScriptQueue()`
`void`	`clearSelection()`
`void`	`clearShapeRenderers()`
`void`	`clearThreads()`
`void`	`clearTimeout(String name)`
`void`	`clearTimeouts()`
`String`	`clipImageOrPasteText(String text)`
`void`	`connect(float[][] connections)`
`void`	`createModels(int n)`
`private String`	`createModelSetAndReturnError(Object atomSetCollection, boolean isAppend, javajs.util.SB loadScript, Map<String,Object> htParams)` finally(!) we are ready to create the "model set" from the "atom set collection" - does NOT repaint
`String`	`createZip(String fileName, String type, String[] scripts)`
`void`	`defineAtomSets(Map<String,Object> info)`
`int`	`deleteAtoms(BS bs, boolean fullModels)`
`void`	`deleteBonds(BS bsDeleted)`
`void`	`deleteMeasurement(int i)`
`void`	`deleteModelAtoms(int firstAtomIndex, int nAtoms, BS bsDeleted)`
`void`	`deleteSavedState(String saveName)`
`void`	`deleteShapeAtoms(Object[] value, BS bs)`
`(package private) void`	`depthByPixels(int pixels)`
`void`	`depthToPercent(int percentDepth)`
`(package private) String`	`dialogAsk(String type, String fileName)`
`void`	`displayAtoms(BS bs, boolean isDisplay, boolean isGroup, int addRemove, boolean isQuiet)`
`void`	`displayBonds(BondSet bs, boolean isDisplay)`
`void`	`disposeMouse()`
`private boolean`	`doHaveJDX()`
`(package private) void`	`echoMessage(String msg)`
`String`	`evalFile(String strFilename)`
`float`	`evalFunctionFloat(Object func, Object params, float[] values)`
`boolean`	`evalParallel(ScriptContext context, ShapeManager shapeManager)`
`String`	`evalString(String strScript)`
`String`	`evalStringQuiet(String strScript)`
`String`	`evalStringQuietSync(String strScript, boolean isQuiet, boolean allowSyncScript)`
`Object`	`evalStringWaitStatusQueued(String returnType, String strScript, String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)`
`Object`	`evaluateExpression(Object stringOrTokens)`
`SV`	`evaluateExpressionAsVariable(Object stringOrTokens)`
`private Object`	`evalWait(String returnType, String strScript, String statusList)`
`void`	`excludeAtoms(BS bs, boolean ignoreSubset)`
`void`	`exitJmol()`
`String`	`extractMolData(String what)`
`Object`	`extractProperty(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 String`	`fixInlineString(String strModel, char newLine)`
`String`	`formatText(String text0)`
`boolean`	`frankClicked(int x, int y)`
`boolean`	`frankClickedModelKit(int x, int y)`
`void`	`freeTempEnum(EnumStructure[] temp)`
`void`	`freeTempPoints(javajs.util.P3[] tempPoints)`
`void`	`freeTempScreens(javajs.util.P3i[] tempScreens)`
`float[][]`	`functionXY(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(String functionName, int nX, int nY, int nZ)`
`String`	`generateOutputForExport(Map<String,Object> params)`
`ActionManager`	`getActionManager()`
`javajs.util.P3[]`	`getAdditionalHydrogens(BS bsAtoms, boolean doAll, boolean justCarbon, javajs.util.List<Atom> vConnections)`
`BS`	`getAllAtoms()`
`String`	`getAllSettings(String prefix)`
`String`	`getAltLocListInModel(int modelIndex)`
`(package private) int`	`getAnimationDirection()`
`(package private) Map<String,Object>`	`getAnimationInfo()`
`EnumAnimationMode`	`getAnimationReplayMode()`
`Object`	`getApplet()`
`(package private) Map<String,Object>`	`getAppletInfo()`
`int`	`getArgbMinMax(float val, float min, float max)`
`int`	`getAtomArgb(int i)`
`BS`	`getAtomBits(int tokType, Object specInfo)`
`BS`	`getAtomBitSet(Object atomExpression)`
`(package private) BS`	`getAtomBitSetEval(JmolScriptEvaluator eval, Object atomExpression)`
`(package private) javajs.util.List<Integer>`	`getAtomBitSetVector(Object atomExpression)`
`int`	`getAtomCount()`
`int`	`getAtomCountInModel(int modelIndex)`
`String`	`getAtomDefs(Map<String,Object> names)`
`Quaternion[]`	`getAtomGroupQuaternions(BS bsAtoms, int nMax)`
`float[]`	`getAtomicCharges()`
`(package private) void`	`getAtomicPropertyState(javajs.util.SB commands, byte type, BS bs, String name, float[] data)`
`void`	`getAtomIdentityInfo(int atomIndex, Map<String,Object> info)`
`int`	`getAtomIndexFromAtomNumber(int atomNumber)`
`int[]`	`getAtomIndices(BS bs)`
`String`	`getAtomInfo(int atomOrPointIndex)`
`String`	`getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)`
`int`	`getAtomModelIndex(int i)`
`String`	`getAtomName(int i)`
`int`	`getAtomNumber(int i)`
`javajs.util.P3`	`getAtomPoint3f(int i)`
`javajs.util.List<javajs.util.P3>`	`getAtomPointVector(BS bs)`
`Quaternion`	`getAtomQuaternion(int i)`
`float`	`getAtomRadius(int i)`
`BS`	`getAtomsConnected(float min, float max, int intType, BS bs)`
`javajs.util.P3`	`getAtomSetCenter(BS bs)`
`String`	`getAtomShapeSetState(Shape shape, AtomShape[] shapes)`
`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)`
`Map<String,Object>`	`getAuxiliaryInfo(Object atomExpression)`
`(package private) javajs.util.P3`	`getAverageAtomPoint()`
`EnumAxesMode`	`getAxesMode()`
`void`	`getAxisAngle(javajs.util.A4 axisAngle)`
`javajs.util.P3[]`	`getAxisPoints()`
`int`	`getBackgroundArgb()`
`BS`	`getBaseModelBitSet()`
`int`	`getBfactor100Hi()`
`String`	`getBindingInfo(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)`
`String`	`getBondState(Shape shape, BS bsOrderSet, boolean reportAll)`
`boolean`	`getBoolean(int tok)`
`boolean`	`getBooleanProperty(String key)`
`javajs.util.P3`	`getBoundBoxCenter()`
`int`	`getBoundBoxCenterX()`
`int`	`getBoundBoxCenterY()`
`String`	`getBoundBoxCommand(boolean withOptions)`
`javajs.util.V3`	`getBoundBoxCornerVector()`
`(package private) Map<String,Object>`	`getBoundBoxInfo()`
`BS`	`getBoundBoxModels()`
`javajs.util.P3[]`	`getBoundBoxVertices()`
`BoxInfo`	`getBoxInfo(BS bs, float scale)`
`BS`	`getBranchBitSet(int atomIndex, int atomIndexNot, boolean allowCyclic)`
`BS[]`	`getBsBranches(float[] dihedralList)`
`BufferedInputStream`	`getBufferedInputStream(String fullPathName)`
`Object`	`getBufferedReaderOrErrorMessageFromName(String name, String[] fullPathNameReturn, boolean isBinary)`
`javajs.util.P3`	`getCamera()`
`float`	`getCameraDepth()`
`javajs.util.P3[]`	`getCameraFactors()`
`javajs.util.P3[][]`	`getCenterAndPoints(javajs.util.List<Object[]> atomSets, boolean addCenter)`
`int`	`getChainCount()`
`int`	`getChainCountInModel(int modelIndex)`
`int`	`getChainCountInModelWater(int modelIndex, boolean countWater)`
`int`	`getChainID(String id)` Create a unique integer for any chain string.
`String`	`getChainIDStr(int id)`
`String`	`getChemicalInfo(String smiles, char type, String info)`
`String`	`getChimeInfo(int tok)`
`Map<String,Object>`	`getCifData(int modelIndex)`
`BS`	`getClickableSet()`
`String`	`getClipboardText()`
`(package private) short`	`getColix(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(String colorScheme)`
`javajs.util.P3`	`getColorPointForPropertyValue(float val)`
`String`	`getColorSchemeList(String colorScheme)`
`String`	`getCommands(Map<String,BS> htDefine, Map<String,BS> htMore, String select)`
`BS`	`getConformation(int iModel, int conformationIndex, boolean doSet)`
`Map<String,SV>`	`getContextVariables()`
`String`	`getCoordinateState(BS bsSelected)`
`int`	`getCurrentAtom()`
`float[]`	`getCurrentColorRange()`
`String`	`getCurrentFileAsString()`
`int`	`getCurrentModelIndex()`
`float`	`getCurrentSolventProbeRadius()`
`SymmetryInterface`	`getCurrentUnitCell()`
`int`	`getCursor()`
`int`	`getCursorX()`
`int`	`getCursorY()`
`Object[]`	`getData(String type)`
`String`	`getData(String atomExpression, String type)`
`float[]`	`getDataFloat(String label)`
`float[][]`	`getDataFloat2D(String label)`
`float[][][]`	`getDataFloat3D(String label)`
`float`	`getDataFloatAt(String label, int atomIndex)`
`private JmolDataManager`	`getDataManager()`
`(package private) String`	`getDataSeparator()`
`(package private) String`	`getDefaultDirectory()`
`javajs.util.P3`	`getDefaultLattice()`
`String`	`getDefaultLoadFilter()`
`String`	`getDefaultLoadScript()`
`String`	`getDefaultMeasurementLabel(int nPoints)`
`String`	`getDefaultPropertyParam(int propertyID)`
`RadiusData`	`getDefaultRadiusData()`
`String`	`getDefaultStructure(BS bsAtoms, BS bsAllAtoms)`
`String`	`getDefaultVdwNameOrData(int mode, EnumVdw type, BS bs)`
`BS`	`getDefinedAtomSet(String name)`
`int`	`getDelayMaximumMs()`
`BS`	`getDeletedAtoms()`
`int[][]`	`getDihedralMap(int[] atoms)`
`Object`	`getDisplay()`
`int`	`getDisplayModelIndex()`
`String`	`getDistanceUnits(String s)`
`(package private) boolean`	`getDragSelected()`
`boolean`	`getDrawHover()`
`boolean`	`getEchoStateActive()`
`String[]`	`getElectronDensityLoadInfo()`
`(package private) int`	`getElementNumber(int i)`
`BS`	`getElementsPresentBitSet(int modelIndex)`
`(package private) String`	`getElementSymbol(int i)`
`String`	`getEmbeddedFileState(String filename)`
`String`	`getEnergyUnits()`
`String`	`getErrorMessage()`
`String`	`getErrorMessageUn()`
`ScriptContext`	`getEvalContextAndHoldQueue(JmolScriptEvaluator jse)`
`Object`	`getExecutor()`
`String`	`getExportDriverList()`
`Object`	`getFileAsBytes(String pathName, javajs.util.OC out)`
`String`	`getFileAsString(String name)`
`String`	`getFileAsString4(String name, int nBytesMax, boolean doSpecialLoad, boolean allowBinary, boolean checkProtected)`
`boolean`	`getFileAsStringBin(String[] data)`
`(package private) Object`	`getFileData()`
`(package private) String`	`getFileHeader()`
`String[]`	`getFileInfo()`
`String`	`getFileName()`
`String`	`getFilePath(String name, boolean asShortName)`
`float`	`getFloat(int tok)`
`javajs.awt.Font`	`getFont3D(String fontFace, String fontStyle, float fontSize)`
`String`	`getFontLineShapeState(String s, String myType, TickInfo[] tickInfos)`
`String`	`getFontState(String myType, javajs.awt.Font font3d)`
`int`	`getFrameCount()`
`long`	`getFrameDelayMs(int i)`
`BS`	`getFrameOffsets()`
`String`	`getFrameTitle()`
`int`	`getFrontPlane()`
`String`	`getFullPathName(boolean orPrevious)`
`String[]`	`getFullPathNameOrError(String filename)`
`JmolScriptFunction`	`getFunction(String name)`
`String`	`getFunctionCalls(String selectedFunction)`
`Map<String,JmolScriptFunction>`	`getFunctions(boolean isStatic)`
`GData`	`getGraphicsData()`
`int`	`getGroupCount()`
`int`	`getGroupCountInModel(int modelIndex)`
`BS`	`getGroupsWithin(int nResidues, BS bs)`
`Object`	`getHelixData(BS bs, int tokType)`
`void`	`getHelp(String what)`
`int`	`getHermiteLevel()`
`Map<String,String>`	`getHeteroList(int modelIndex)`
`BS`	`getHiddenSet()`
`int`	`getHoverDelay()`
`String`	`getHtmlName()`
`String`	`getHybridizationAndAxes(int atomIndex, javajs.util.V3 z, javajs.util.V3 x, String lcaoType)`
`private Object`	`getImage(boolean isDouble, boolean isImageWrite)`
`byte[]`	`getImageAsBytes(String type, int width, int height, int quality, String[] errMsg)`
`float`	`getImageFontScaling()`
`char`	`getInlineChar()`
`boolean`	`getInMotion(boolean includeAnim)`
`String`	`getInsertedCommand()`
`int`	`getInt(int tok)`
`int`	`getIsosurfacePropertySmoothing(boolean asPower)`
`String`	`getJavaVendor()`
`String`	`getJavaVersion()`
`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, String type)`
`int`	`getJmolDataSourceFrame(int modelIndex)`
`(package private) String`	`getJmolFrameType(int modelIndex)`
`static String`	`getJmolVersion()`
`Object`	`getJspecViewProperties(Object myParam)`
`private JmolJSpecView`	`getJSV()`
`String`	`getLanguage()`
`Object`	`getLigandModel(String id, String prefix, String suffix, String terminator)` obtain CIF data for a ligand for purposes of adding hydrogens
`(package private) String`	`getLoadState(Map<String,Object> htParams)`
`String`	`getLocalUrl(String fileName)`
`String`	`getLogFileName()`
`(package private) String`	`getLogFilePath()`
`short`	`getMadBond()`
`short`	`getMarBond()`
`(package private) javajs.util.M3`	`getMatrixRotate()`
`javajs.util.M4`	`getMatrixtransform()`
`float`	`getMaxZoomPercent()`
`String`	`getMeasureDistanceUnits()`
`int`	`getMeasurementCount()`
`int[]`	`getMeasurementCountPlusIndices(int i)`
`(package private) javajs.util.List<Map<String,Object>>`	`getMeasurementInfo()`
`String`	`getMeasurementInfoAsString()`
`String`	`getMeasurementState(Measures measures, javajs.util.List<Measurement> mList, int measurementCount, javajs.awt.Font font3d, TickInfo ti)`
`String`	`getMeasurementStringValue(int i)`
`String`	`getMenu(String type)`
`Map<String,javajs.util.List<javajs.util.List<Object>>>`	`getMessageQueue()`
`String`	`getMinimizationInfo()`
`MinimizerInterface`	`getMinimizer(boolean createNew)`
`JmolAdapter`	`getModelAdapter()`
`String`	`getModelAtomProperty(Atom atom, String text)`
`Map<String,Object>`	`getModelAuxiliaryInfo(int modelIndex)`
`Object`	`getModelAuxiliaryInfoValue(int modelIndex, String keyName)`
`BS`	`getModelBitSet(BS atomList, boolean allTrajectories)`
`String`	`getModelCml(BS bs, int nAtomsMax, boolean addBonds)`
`int`	`getModelCount()`
`javajs.util.V3`	`getModelDipole()`
`String`	`getModelExtract(Object atomExpression, boolean doTransform, boolean isModelKit, String type)`
`String`	`getModelFileInfo()`
`String`	`getModelFileInfoAll()`
`String`	`getModelFileName(int modelIndex)`
`int`	`getModelFileNumber(int modelIndex)`
`int`	`getModelIndexFromId(String id)`
`String`	`getModelInfoAsString()`
`(package private) BS`	`getModelKitStateBitSet(BS bs, BS bsDeleted)`
`String`	`getModelName(int modelIndex)`
`int`	`getModelNumber(int modelIndex)`
`String`	`getModelNumberDotted(int modelIndex)`
`int`	`getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)`
`Properties`	`getModelProperties(int modelIndex)`
`String`	`getModelProperty(int modelIndex, String propertyName)`
`ModelSet`	`getModelSet()`
`Map<String,Object>`	`getModelSetAuxiliaryInfo()`
`Object`	`getModelSetAuxiliaryInfoValue(String strKey)`
`String`	`getModelSetFileName()`
`String`	`getModelSetName()`
`String`	`getModelSetPathName()`
`Properties`	`getModelSetProperties()`
`String`	`getModelSetProperty(String strProp)`
`String`	`getModelSetTypeName()`
`private String`	`getModelTitle(int modelIndex)`
`BS`	`getModelUndeletedAtomsBitSet(int modelIndex)`
`BS`	`getModelUndeletedAtomsBitSetBs(BS bsModels)`
`SymmetryInterface`	`getModelUnitCell(int modelIndex)`
`byte`	`getModeMultipleBond()`
`javajs.util.List<Object>`	`getModulationList(BS bs, String type, javajs.util.P3 t456)`
`String`	`getMoInfo(int modelIndex)`
`BS`	`getMoleculeBitSet(int atomIndex)`
`int`	`getMotionEventNumber()`
`BS`	`getMotionFixedAtoms()`
`boolean`	`getMouseEnabled()`
`Object`	`getMouseInfo()`
`String`	`getMoveToText(float timespan)`
`MeasurementPending`	`getMP()`
`javajs.util.P3`	`getNavigationCenter()`
`float`	`getNavigationDepthPercent()`
`javajs.util.P3`	`getNavigationOffset()`
`float`	`getNavigationOffsetPercent(char XorY)`
`boolean`	`getNavOn()`
`JmolNMRInterface`	`getNMRCalculation()`
`String`	`getNMRPredict(boolean openURL)`
`Boolean`	`getNoneSelected()`
`(package private) int`	`getObjectArgb(int objId)`
`short`	`getObjectColix(int objId)`
`int`	`getObjectMad(int objId)`
`void`	`getObjectMap(Map<String,?> map, char c)` used in autocompletion in console using TAB
`String`	`getOperatingSystemName()`
`Orientation`	`getOrientation()`
`(package private) Map<String,Object>`	`getOrientationInfo()`
`String`	`getOrientationText(int type, String name)`
`SV`	`getOrSetNewVariable(String key, boolean doSet)`
`javajs.util.OC`	`getOutputChannel(String localName, String[] fullPath)`
`private OutputManager`	`getOutputManager()`
`Object`	`getParameter(String key)`
`Object`	`getParameterEscaped(String key)`
`float[]`	`getPartialCharges()`
`String`	`getPathForAllFiles()`
`String`	`getPdbAtomData(BS bs, javajs.util.OC sb)`
`String[][]`	`getPdbBondInfo(String group3)`
`String`	`getPdbData(int modelIndex, String type, Object[] parameters)`
`String`	`getPDBHeader()`
`(package private) MeasurementPending`	`getPendingMeasurement()`
`boolean`	`getPerspectiveDepth()`
`int`	`getPickingMode()`
`javajs.util.List<Object>`	`getPlaneIntersection(int type, javajs.util.P4 plane, float scale, int flags)`
`String`	`getPointGroupAsString(boolean asDraw, String type, int index, float scale)`
`Map<String,Object>`	`getPointGroupInfo(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 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.
`Object`	`getProperty(String returnType, String infoType, Object paramInfo)`
`String`	`getPropertyColorScheme()`
`private JmolPropertyManager`	`getPropertyManager()`
`int`	`getPropertyNumber(String name)`
`String`	`getProteinStructureState()`
`char`	`getQuaternionFrame()`
`boolean`	`getRefreshing()`
`BS`	`getRenderableBitSet()`
`(package private) int`	`getRotateBondIndex()`
`void`	`getRotation(javajs.util.M3 matrixRotation)`
`javajs.util.P3`	`getRotationCenter()`
`Quaternion`	`getRotationQuaternion()`
`Rectangle`	`getRubberBandSelection()`
`String`	`getSavedCoordinates(String saveName)`
`String`	`getSavedState(String saveName)`
`String`	`getSavedStructure(String saveName)`
`float`	`getScalePixelsPerAngstrom(boolean asAntialiased)`
`String[]`	`getSceneList()`
`int`	`getScreenDim()`
`int`	`getScreenHeight()`
`Object`	`getScreenImageBuffer(Object graphic, boolean isImageWrite)` Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo
`int`	`getScreenWidth()`
`ScriptContext`	`getScriptContext(String why)`
`private JmolScriptManager`	`getScriptManager()`
`Boolean`	`getScriptQueueInfo()`
`AtomIndexIterator`	`getSelectedAtomIterator(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel)`
`int`	`getSelectionCount()`
`boolean`	`getSelectionHaloEnabled(boolean isRenderer)`
`BS`	`getSelectionSet(boolean includeDeleted)`
`BS`	`getSelectionSubset()`
`BS`	`getSequenceBits(String specInfo, BS bs)`
`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;
`String`	`getShapeErrorState()`
`Map<String,Object>`	`getShapeInfo()`
`ShapeManager`	`getShapeManager()`
`Object`	`getShapeProperty(int shapeType, String propertyName)`
`private int`	`getShapePropertyAsInt(int shapeID, String propertyName)`
`boolean`	`getShapePropertyData(int shapeType, String propertyName, Object[] data)`
`Object`	`getShapePropertyIndex(int shapeType, String propertyName, int index)`
`void`	`getShapeSetState(AtomShape atomShape, Shape shape, int monomerCount, Group[] monomers, BS bsSizeDefault, Map<String,BS> temp, Map<String,BS> temp2)`
`String`	`getShapeState(Shape shape)`
`boolean`	`getShowAxes()`
`boolean`	`getShowBbcage()`
`boolean`	`getShowFrank()`
`boolean`	`getShowNavigationPoint()`
`boolean`	`getShowUnitCell()`
`boolean`	`getSlabEnabled()`
`BS`	`getSmartsMatch(String smarts, BS bsSelected)`
`String`	`getSmiles(int index1, int index2, BS bsSelected, boolean isBioSmiles, boolean allowUnmatchedRings, boolean addCrossLinks, boolean addComment)` returns the SMILES string for a sequence or atom set does not include attached protons on groups
`SmilesMatcherInterface`	`getSmilesMatcher()`
`Map<String,Object>`	`getSpaceGroupInfo(String spaceGroup)`
`String`	`getSpecularState()`
`boolean`	`getSpinOn()`
`String`	`getSpinState()`
`String`	`getStandardLabelFormat(int type)`
`JmolStateCreator`	`getStateCreator()`
`String`	`getStateInfo()`
`String`	`getStateInfo3(String type, int width, int height)`
`javajs.util.List<javajs.util.List<javajs.util.List<Object>>>`	`getStatusChanged(String statusNameList)`
`(package private) StatusManager`	`getStatusManager()`
`int`	`getStrandCount(int type)`
`Map<EnumStructure,float[]>`	`getStructureList()`
`String`	`getStructureState()`
`(package private) int`	`getSurfaceDistanceMax()`
`SymmetryInterface`	`getSymmetry()`
`Object`	`getSymmetryInfo(BS bsAtoms, String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, String id, int type)`
`String`	`getSymmetryInfoAsString()`
`String`	`getSymmetryOperation(String spaceGroup, int symop, javajs.util.P3 pt1, javajs.util.P3 pt2, boolean labelOnly)`
`BS`	`getTaintedAtoms(byte type)`
`boolean`	`getTestFlag(int i)`
`Map<String,Object>`	`getTimeouts()`
`String`	`getTrajectoryState()`
`String`	`getTransformText()`
`String`	`getTranslationScript()`
`float`	`getTranslationXPercent()`
`float`	`getTranslationYPercent()`
`(package private) float`	`getTranslationZPercent()`
`private BS`	`getUndeletedGroupAtomBits(BS bs)`
`float`	`getUnitCellInfo(int infoType)`
`String`	`getUnitCellInfoText()`
`javajs.util.M4`	`getUnscaledTransformMatrix()`
`int`	`getVanderwaalsMar(int i)`
`int`	`getVanderwaalsMarType(int atomicAndIsotopeNumber, EnumVdw type)`
`Object`	`getVariableList()`
`Vibration`	`getVibration(int atomIndex)`
`Point3fi`	`getVibrationPoint(Vibration vibration, Point3fi pt)`
`Map<String,Object>`	`getViewerOptions()`
`BS`	`getVisibleFramesBitSet()`
`BS`	`getVisibleSet()`
`String`	`getWrappedStateScript()`
`String`	`getZapName()`
`boolean`	`getZoomEnabled()`
`int`	`getZoomPercent()`
`float`	`getZoomPercentFloat()`
`float`	`getZoomSetting()`
`int`	`getZShadeStart()`
`void`	`haltScriptExecution()`
`void`	`handleError(Error er, boolean doClear)`
`static boolean`	`hasDatabasePrefix(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, String text, String id, javajs.util.P3 pt)`
`void`	`initialize(boolean clearUserVariables)`
`JmolRendererInterface`	`initializeExporter(Map<String,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(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(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(String name)`
`(package private) boolean`	`isStereoDouble()`
`boolean`	`isTrajectory(int modelIndex)`
`boolean`	`isVibrationOn()`
`boolean`	`isWindowCentered()`
`private void`	`jmolTest()`
`String`	`jsEval(String strEval)`
`String`	`listSavedStates()`
`private String`	`loadAtomDataAndReturnError(Object atomSetCollection, int tokType)` or just apply the data to the current model set
`void`	`loadImage(String pathName, String echoName)`
`(package private) void`	`loadImageData(Object image, String nameOrError, String echoName, ScriptContext sc)`
`String`	`loadInline(List<Object> arrayData, boolean isAppend)` External applications only; does not preserver state -- intentionally!
`String`	`loadInline(String strModel)` from Applet and external applications only
`String`	`loadInline(String[] arrayModels)` external apps only
`String`	`loadInline(String[] arrayModels, boolean isAppend)` external apps and applet only
`String`	`loadInline(String strModel, char newLine)` external apps only
`String`	`loadInlineAppend(String strModel, boolean isAppend)` used by applet and console
`private String`	`loadInlineScript(String strModel, char newLine, boolean isAppend, Map<String,Object> htParams)` used by loadInline and openFileFull
`private String`	`loadInlineScriptRepaint(String strModel, char newLine, boolean isAppend)`
`String`	`loadModelFromFile(String fullPathName, String fileName, String[] fileNames, Object reader, boolean isAppend, Map<String,Object> htParams, javajs.util.SB loadScript, int tokType)` Used by the ScriptEvaluator LOAD command to open one or more files.
`private String`	`loadModelFromFileRepaint(String fullPathName, String fileName, String[] fileNames, Object reader)`
`void`	`loadShape(int shapeID)`
`void`	`log(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<Object[]> list)`
`void`	`navigatePt(javajs.util.P3 center)`
`void`	`navTranslatePercent(float x, float y)`
`boolean`	`noGraphicsAllowed()`
`void`	`notifyError(String errType, String errMsg, String errMsgUntranslated)`
`void`	`notifyMinimizationStatus()`
`int`	`notifyMouseClicked(int x, int y, int action, int mode)`
`void`	`notifyStatusReady(boolean isReady)`
`void`	`notifyViewerRepaintDone()`
`String`	`openDOM(Object DOMNode)` applet DOM method -- does not preserve state
`javajs.util.OC`	`openExportChannel(double privateKey, String fileName, boolean asWriter)`
`String`	`openFile(String fileName)` for JmolSimpleViewer -- external applications only (and no-script JavaScript)
`void`	`openFileAsyncSpecial(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 Object`	`openFileFull(String fileName, boolean isAppend, Map<String,Object> htParams, javajs.util.SB loadScript)` does NOT repaint
`String`	`openFiles(String[] fileNames)` for JmolSimpleViewer -- external applications only
`String`	`openReader(String fullPathName, String fileName, Reader reader)` Opens the file, given an already-created reader.
`String`	`openStringInline(String strModel)` only used by file dropper.
`String`	`openStringInlineParamsAppend(String strModel, Map<String,Object> htParams, boolean isAppend)` Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.
`private String`	`openStringsInlineParamsAppend(String[] arrayModels, Map<String,Object> htParams, boolean isAppend)` opens multiple files inline; does NOT repaint
`String`	`outputToFile(Map<String,Object> params)`
`void`	`pauseScriptExecution()`
`void`	`popHoldRepaint(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)`
`String`	`processWriteOrCapture(Map<String,Object> params)` from eval write command only includes option to write set of files
`String`	`prompt(String label, String data, String[] list, boolean asButtons)`
`void`	`pushHoldRepaint()`
`void`	`pushHoldRepaintWhy(String why)`
`void`	`rebond()`
`void`	`rebondState(boolean isStateScript)`
`void`	`refresh(int mode, String strWhy)` initiate a repaint/update sequence if it has not already been requested.
`void`	`refreshMeasures(boolean andStopMinimization)`
`void`	`releaseScreenImage()`
`String`	`removeCommand()` Removes one command from the command history
`void`	`removeFunction(String name)`
`void`	`removeSelectionListener(JmolSelectionListener listener)`
`void`	`removeUserVariable(String key)`
`private void`	`render()`
`private void`	`render1(Object graphic, Object img, int x, int y)`
`void`	`renderScreenImage(Object g, int width, int height)`
`void`	`renderScreenImageStereo(Object gLeft, Object gRight, int width, int height)` an added class for rendering stereo in two independent applets
`(package private) void`	`reportSelection(String msg)`
`void`	`requestRepaintAndWait(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) String`	`resolveDatabaseFormat(String fileName)`
`boolean`	`restoreBonds(String saveName)`
`(package private) void`	`restoreModelOrientation(int modelIndex)`
`(package private) void`	`restoreModelRotation(int modelIndex)`
`boolean`	`restoreOrientation(String saveName, float timeSeconds)`
`void`	`restoreRotation(String saveName, float timeSeconds)`
`void`	`restoreScene(String saveName, float timeSeconds)`
`boolean`	`restoreSelection(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)`
`String`	`runScript(String script)` run a script immediately and return output buffer string Jmol 13.1.15
`void`	`saveBonds(String saveName)`
`void`	`saveCoordinates(String saveName, BS bsSelected)`
`(package private) void`	`saveModelOrientation()`
`void`	`saveOrientation(String saveName, float[] pymolView)`
`void`	`saveScene(String saveName, Map<String,Object> scene)`
`void`	`saveSelection(String saveName)`
`void`	`saveState(String saveName)`
`void`	`saveStructure(String saveName)`
`float`	`scaleToPerspective(int z, float sizeAngstroms)`
`float`	`scaleToScreen(int z, int milliAngstroms)`
`String`	`script(String strScript)`
`Object`	`scriptCheck(String strScript)`
`private Object`	`scriptCheckRet(String strScript, boolean returnContext)`
`void`	`scriptEcho(String strEcho)`
`void`	`scriptStatus(String strStatus)`
`void`	`scriptStatusMsg(String strStatus, String statusMessage)`
`String`	`scriptWait(String strScript)`
`Object`	`scriptWaitStatus(String strScript, 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(String mode)`
`void`	`setAnimationOn(boolean animationOn)`
`void`	`setAnimationRange(int modelIndex1, int modelIndex2)`
`void`	`setAnimationReplayMode(EnumAnimationMode 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, Object xyzValues)`
`void`	`setAtomCoordsRelative(javajs.util.T3 offset, BS bs)`
`void`	`setAtomData(int type, String name, String coordinateData, boolean isDefault)`
`void`	`setAtomLabel(String value, int i)`
`private void`	`setAtomPickingOption(String option)`
`void`	`setAtomProperty(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, 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(String fileName, Object image)`
`void`	`setBackgroundModelIndex(int modelIndex)`
`void`	`setBondParameters(int modelIndex, int i, BS bsBonds, float rad, float pymolValence, int argb, float trans)`
`private void`	`setBondPickingOption(String option)`
`void`	`setBondTolerance(float bondTolerance)`
`void`	`setBooleanProperty(String key, boolean value)`
`private void`	`setBooleanPropertyTok(String key, int tok, boolean value)`
`void`	`setBoundBox(javajs.util.P3 pt1, javajs.util.P3 pt2, boolean byCorner, float scale)`
`void`	`setCenterAt(String relativeTo, javajs.util.P3 pt)`
`void`	`setCenterBitSet(BS bsCenter, boolean doScale)`
`void`	`setCenterSelected()`
`void`	`setCentroid(BS bs, int[] minmax)`
`void`	`setCGO(javajs.util.List<Object> info)`
`void`	`setColorBackground(String colorName)`
`BS`	`setConformation()`
`void`	`setCurrentAtom(int iAtom)`
`void`	`setCurrentCage(String isosurfaceId)`
`void`	`setCurrentCagePts(javajs.util.P3[] points)`
`void`	`setCurrentColorRange(float min, float max)`
`void`	`setCurrentColorRange(String label)`
`void`	`setCurrentColorRangeData(float[] data, BS bs)`
`void`	`setCurrentModelID(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(String type, 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 ptLattice)`
`private void`	`setDefaults()`
`private void`	`setDefaultsType(String type)`
`void`	`setDihedrals(float[] dihedralList, BS[] bsBranches, float rate)`
`void`	`setDisplay(Object canvas)`
`void`	`setEchoStateActive(boolean TF)`
`void`	`setElementArgb(int elementNumber, int argb)`
`String`	`setErrorMessage(String errMsg, String errMsgUntranslated)`
`void`	`setFileInfo(String[] fileInfo)`
`private void`	`setFileLoadStatus(EnumFileStatus ptLoad, String fullPathName, String fileName, String modelName, String strError, Boolean isAsync)`
`void`	`setFloatProperty(String key, float value)`
`private void`	`setFloatPropertyTok(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, String title)`
`void`	`setFrameTitleObj(Object title)`
`(package private) void`	`setFrameVariables()`
`void`	`setFrankOn(boolean TF)`
`void`	`setHoverLabel(String strLabel)`
`void`	`setInMotion(boolean inMotion)`
`void`	`setInsertedCommand(String strScript)`
`void`	`setIntProperty(String key, int value)`
`private void`	`setIntPropertyTok(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(String type, int modelIndex, int dataIndex)`
`void`	`setJmolDefaults()`
`void`	`setJmolStatusListener(JmolStatusListener jmolStatusListener)`
`void`	`setLigandModel(String key, String data)`
`Object`	`setLoadFormat(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 Map<String,Object>`	`setLoadParameters(Map<String,Object> htParams, boolean isAppend)`
`void`	`setMarBond(short marBond)`
`private void`	`setMaximumSize(int x)`
`void`	`setMenu(String fileOrText, boolean isFile)`
`void`	`setMeshCreator(Object meshCreator)` an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer viewer = applet.getViewer(); viewer.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`	`setModeMouse(int modeMouse)`
`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(Map<String,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(String name, int argb)`
`(package private) void`	`setObjectColor(String name, String colorName)`
`void`	`setObjectMad(int iShape, String name, int mad)`
`String`	`setObjectProp(String id, int tokCommand)`
`void`	`setObjectVisibility(String name, boolean b)`
`private void`	`setOptions(Map<String,Object> info)`
`boolean`	`setParallel(boolean TF)`
`void`	`setPdbConectBonding(boolean isAuto, boolean isStateScript)`
`(package private) void`	`setPendingMeasurement(MeasurementPending measurementPending)`
`void`	`setPercentVdwAtom(int value)`
`void`	`setPerspectiveDepth(boolean perspectiveDepth)`
`void`	`setPicked(int iAtom)`
`(package private) void`	`setPickingMode(String strMode, int pickingMode)`
`(package private) void`	`setPickingStyle(String style, int pickingStyle)`
`void`	`setPropertyColorScheme(String scheme, boolean isTranslucent, boolean isOverloaded)`
`void`	`setProteinType(EnumStructure type, BS bs)`
`void`	`setRasmolDefaults()`
`private void`	`setRefreshing(boolean TF)`
`(package private) 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(String strStatus, String statusMessage, int msWalltime, String strErrorMessageUntranslated)`
`void`	`setSelectedAtom(int atomIndex, boolean TF)`
`void`	`setSelectionHalos(boolean TF)`
`void`	`setSelectionSet(BS set)`
`void`	`setSelectionSubset(BS subset)`
`void`	`setShapeErrorState(int shapeID, String state)`
`void`	`setShapeProperty(int shapeID, String propertyName, 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(String s)`
`void`	`setSpin(String key, int value)`
`void`	`setSpinOn(boolean spinOn)`
`private void`	`setStartupBooleans()`
`void`	`setStateScriptVersion(String version)`
`void`	`setStatusAtomHovered(int atomIndex, String info)`
`void`	`setStatusAtomPicked(int atomIndex, String info)`
`(package private) void`	`setStatusFrameChanged(boolean isVib, boolean doNotify)`
`void`	`setStatusMeasuring(String status, int intInfo, String strMeasure, float value)`
`void`	`setStatusObjectHovered(String id, String info, javajs.util.P3 pt)`
`void`	`setStatusResized(int width, int height)`
`void`	`setStereoMode(int[] twoColors, EnumStereoMode stereoMode, float degrees)`
`private void`	`setStrandCount(int type, int value)`
`void`	`setStringProperty(String key, String value)`
`private void`	`setStringPropertyTok(String key, int tok, String value)`
`void`	`setStructureList(float[] list, EnumStructure 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(String name, int mSec, String script)`
`(package private) void`	`setTrajectory(int modelIndex)`
`void`	`setTrajectoryBs(BS bsModels)`
`private void`	`setTransformManagerDefaults()`
`void`	`setUnits(String units, boolean isDistance)`
`void`	`setUserScale(int[] scale)`
`SV`	`setUserVariable(String name, SV value)`
`(package private) void`	`setUserVdw(EnumVdw mode)`
`(package private) void`	`setVdwStr(String name)`
`void`	`setVectorScale(float scale)`
`void`	`setVibrationOff()`
`void`	`setVibrationPeriod(float period)`
`void`	`setVibrationScale(float scale)`
`void`	`setZslabPoint(javajs.util.P3 pt)`
`void`	`show2D(String smiles)`
`void`	`showConsole(boolean showConsole)`
`void`	`showEditor(String[] file_text)`
`void`	`showMessage(String s)`
`void`	`showParameter(String key, boolean ifNotSet, int nMax)`
`void`	`showString(String str, boolean isPrint)`
`String`	`showTimeout(String name)`
`void`	`showUrl(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(String script, 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(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(String name)`
`void`	`unBindAction(String desc, 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(String key)`
`void`	`unTransformPoint(javajs.util.P3 pointScreen, javajs.util.P3 pointAngstroms)`
`void`	`updateJS(int width, int height)` for JavaScript only
`private boolean`	`updateWindow(int width, int height)`
`boolean`	`useMinimizationThread()`
`String`	`writeFileData(String fileName, String type, int modelIndex, Object[] parameters)`
`void`	`writeTextFile(String fileName, String data)`
`void`	`zap(boolean notify, boolean resetUndo, boolean zapModelKit)`
`private void`	`zapMsg(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 String fullName
```

appletDocumentBase
```
public String appletDocumentBase
```

appletCodeBase
```
public String appletCodeBase
```

appletIdiomaBase
```
public String appletIdiomaBase
```

jsDocumentBase
```
public static String jsDocumentBase
```

compiler
```
public Object compiler
```

definedAtomSets

public Map<String,Object> definedAtomSets

modelSet
```
public ModelSet modelSet
```

fileManager
```
public FileManager fileManager
```

isApplet
```
private boolean isApplet
```

isJNLP
```
private boolean isJNLP
```

isSyntaxAndFileCheck
```
public boolean isSyntaxAndFileCheck
```

isSyntaxCheck
```
public boolean isSyntaxCheck
```

listCommands
```
public boolean listCommands
```

mustRender
```
boolean mustRender
```

htmlName
```
String htmlName
```

insertedCommand
```
private String insertedCommand
```

gdata
```
GData gdata
```

applet
```
Object applet
```

actionManager
```
ActionManager actionManager
```

animationManager
```
AnimationManager animationManager
```

colorManager
```
ColorManager colorManager
```

dataManager
```
JmolDataManager dataManager
```

shapeManager
```
ShapeManager shapeManager
```

selectionManager
```
SelectionManager selectionManager
```

repaintManager
```
JmolRepaintManager repaintManager
```

global
```
public GlobalSettings global
```

statusManager
```
public StatusManager statusManager
```

transformManager
```
TransformManager transformManager
```

strJavaVendor

private static final String strJavaVendor

strOSName
```
private static final String strOSName
```

strJavaVersion

private static final String strJavaVersion

syncId
```
private String syncId
```

logFilePath
```
private 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 String commandOptions
```

viewerOptions

private Map<String,Object> viewerOptions

display
```
private Object display
```

modelAdapter
```
private JmolAdapter modelAdapter
```

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

commandHistory
```
private CommandHistory commandHistory
```

symmetry
```
private SymmetryInterface symmetry
```

smilesMatcher

private SmilesMatcherInterface smilesMatcher

modelManager
```
private ModelManager modelManager
```

stateManager
```
private StateManager stateManager
```

scriptManager

private JmolScriptManager scriptManager

eval
```
public JmolScriptEvaluator eval
```

tempArray
```
private TempArray tempArray
```

version_date
```
private static String version_date
```

isPreviewOnly
```
private boolean isPreviewOnly
```

mouse

private javajs.api.GenericMouseInterface mouse

mouseEnabled
```
private boolean mouseEnabled
```

noneSelected
```
private boolean noneSelected
```

ligandModels
```
Map<String,Object> ligandModels
```

ligandModelSet
```
Map<String,Boolean> ligandModelSet
```

sc
```
JmolStateCreator sc
```

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
```

captureParams

public Map<String,Object> captureParams

jsParams
```
private Map<String,Object> jsParams
```

antialiasDisplay
```
private boolean antialiasDisplay
```

hoverAtomIndex
```
int hoverAtomIndex
```

hoverText
```
String hoverText
```

hoverEnabled
```
public boolean hoverEnabled
```

currentCursor
```
private int currentCursor
```

prevFrame
```
int prevFrame
```

haveJDX
```
private boolean haveJDX
```

jsv
```
private JmolJSpecView jsv
```

language
```
private 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 Map<String,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 String SYNC_GRAPHICS_MESSAGE

See Also:: Constant Field Values

SYNC_NO_GRAPHICS_MESSAGE

public static final String SYNC_NO_GRAPHICS_MESSAGE

See Also:: Constant Field Values

bsUserVdws
```
BS bsUserVdws
```

userVdws
```
float[] userVdws
```

userVdwMars
```
int[] userVdwMars
```

defaultVdw
```
EnumVdw defaultVdw
```

errorMessage
```
private String errorMessage
```

errorMessageUntranslated

private String errorMessageUntranslated

currentShapeID
```
private int currentShapeID
```

currentShapeState
```
private String currentShapeState
```

staticFunctions

static final Map<String,JmolScriptFunction> staticFunctions

localFunctions

Map<String,JmolScriptFunction> localFunctions

privateKey
```
private double privateKey
```

isKiosk
```
boolean isKiosk
```

minimizer
```
private MinimizerInterface minimizer
```

executor
```
private Object executor
```

nProcessors
```
public static int nProcessors
```

displayLoadErrors
```
public boolean displayLoadErrors
```

isParallel
```
boolean isParallel
```

actionStates

final javajs.util.List<String> actionStates

actionStatesRedo

final javajs.util.List<String> actionStatesRedo

stateScriptVersionInt
```
private int stateScriptVersionInt
```

jsExporter3D

private JmolRendererInterface jsExporter3D

htPdbBondInfo
```
Map<String,String[][]> htPdbBondInfo
```

timeouts
```
Map<String,Object> timeouts
```

chainMap
```
public Map<Object,Object> chainMap
```

chainList

public javajs.util.List<String> chainList

nmrCalculation
```
JmolNMRInterface nmrCalculation
```

logFileName
```
String logFileName
```

Constructor Detail
- Viewer
```
public Viewer(Map<String,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 Throwable

Overrides:: finalize in class Object
Throws:: Throwable

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

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

isApplet in class JmolViewer

setInsertedCommand

public void setInsertedCommand(String strScript)

getActionManager

public ActionManager getActionManager()

getLogFilePath
```
String getLogFilePath()
```

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

getJmolVersion
```
public static String getJmolVersion()
```

allocateViewer

protected static JmolViewer allocateViewer(Object display,
                                           JmolAdapter modelAdapter,
                                           String fullName,
                                           URL documentBase,
                                           URL codeBase,
                                           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

getSymmetry

public SymmetryInterface getSymmetry()

getSymmetryInfo

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

getSmilesMatcher

public SmilesMatcherInterface getSmilesMatcher()

getSmartsMatch

public BS getSmartsMatch(String smarts,
                         BS bsSelected)

Specified by:: getSmartsMatch in class JmolViewer

getViewerOptions

public Map<String,Object> getViewerOptions()

setOptions

private void setOptions(Map<String,Object> info)

setDisplay

public void setDisplay(Object canvas)

getDataManager

private JmolDataManager getDataManager()

getScriptManager

private JmolScriptManager getScriptManager()

checkOption2

private boolean checkOption2(String key1,
                             String key2)

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

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

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

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

getExportDriverList
```
public String getExportDriverList()
```

getHtmlName
```
public String getHtmlName()
```

getDisplay
```
public Object getDisplay()
```
Specified by:

getDisplay in class JmolViewer

clearMouse
```
public void clearMouse()
```

disposeMouse
```
public void disposeMouse()
```

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

reset

public void reset(boolean includingSpin)

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

homePosition in class JmolViewer

getAppletInfo
```
Map<String,Object> getAppletInfo()
```

initialize

public void initialize(boolean clearUserVariables)

listSavedStates
```
public String listSavedStates()
```

saveOrientation

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

saveScene

public void saveScene(String saveName,
                      Map<String,Object> scene)

restoreScene

public void restoreScene(String saveName,
                         float timeSeconds)

restoreOrientation

public boolean restoreOrientation(String saveName,
                                  float timeSeconds)

restoreRotation

public void restoreRotation(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(String saveName)

restoreBonds

public boolean restoreBonds(String saveName)

saveState

public void saveState(String saveName)

deleteSavedState

public void deleteSavedState(String saveName)

getSavedState

public String getSavedState(String saveName)

saveStructure

public void saveStructure(String saveName)

getSavedStructure

public String getSavedStructure(String saveName)

saveCoordinates

public void saveCoordinates(String saveName,
                            BS bsSelected)

getSavedCoordinates

public String getSavedCoordinates(String saveName)

saveSelection

public void saveSelection(String saveName)

restoreSelection

public boolean restoreSelection(String saveName)

getMatrixtransform

public javajs.util.M4 getMatrixtransform()

getRotationQuaternion

public Quaternion getRotationQuaternion()

setRotationRadius

public void setRotationRadius(float angstroms,
                              boolean doAll)

getRotationCenter

public javajs.util.P3 getRotationCenter()

setCenterAt

public void setCenterAt(String 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 String getMoveToText(float timespan)

navigateList

public void navigateList(JmolScriptEvaluator eval,
                         javajs.util.List<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 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(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(String key,
                    int value)

getSpinState
```
public 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 String getOrientationText(int type,
                                 String name)

getOrientationInfo

Map<String,Object> getOrientationInfo()

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

getAxisAngle

public void getAxisAngle(javajs.util.A4 axisAngle)

getTransformText
```
public 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(String name,
                    String colorName)

setObjectVisibility

public void setObjectVisibility(String name,
                                boolean b)

setObjectArgb

public void setObjectArgb(String name,
                          int argb)

setBackgroundImage

public void setBackgroundImage(String fileName,
                               Object image)

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

getObjectColix

public short getObjectColix(int objId)

getFontState

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

setColorBackground
```
public void setColorBackground(String colorName)
```
Specified by:

setColorBackground in class JmolViewer

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

getBackgroundArgb in class JmolViewer

setObjectMad

public void setObjectMad(int iShape,
                         String name,
                         int mad)

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

setPropertyColorScheme

public void setPropertyColorScheme(String scheme,
                                   boolean isTranslucent,
                                   boolean isOverloaded)

getPropertyColorScheme

public String getPropertyColorScheme()

getColixBackgroundContrast

public short getColixBackgroundContrast()

getSpecularState
```
public String getSpecularState()
```

getColixAtomPalette

public short getColixAtomPalette(Atom atom,
                                 byte pid)

getColixBondPalette

public short getColixBondPalette(Bond bond,
                                 int pid)

getColorSchemeList

public String getColorSchemeList(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(String msg)
```

getAtomSetCenter

public javajs.util.P3 getAtomSetCenter(BS bs)

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

getDefinedAtomSet

public BS getDefinedAtomSet(String name)

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

selectAll in class JmolViewer

setNoneSelected

public void setNoneSelected(boolean noneSelected)

getNoneSelected
```
public 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()
```

getSelectionSet

public BS getSelectionSet(boolean includeDeleted)

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,
                     Object atomExpression)

setModeMouse
```
public void setModeMouse(int modeMouse)
```
Specified by:

setModeMouse in class JmolViewer

getRubberBandSelection

public Rectangle getRubberBandSelection()

isBound

public boolean isBound(int action,
                       int gesture)

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

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

getDefaultDirectory
```
String getDefaultDirectory()
```

getLocalUrl

public String getLocalUrl(String fileName)

getBufferedInputStream
```
public BufferedInputStream getBufferedInputStream(String fullPathName)
```
Specified by:

getBufferedInputStream in interface AtomDataServer

getBufferedReaderOrErrorMessageFromName

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

setLoadParameters

private Map<String,Object> setLoadParameters(Map<String,Object> htParams,
                                             boolean isAppend)

openFileAsyncSpecial
```
public void openFileAsyncSpecial(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 String openFile(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 String openFiles(String[] fileNames)
```
for JmolSimpleViewer -- external applications only

Specified by:

openFiles in class JmolViewer

Parameters:

fileNames -

Returns:

null or error

openReader

public String openReader(String fullPathName,
                         String fileName,
                         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 String openDOM(Object DOMNode)
```
applet DOM method -- does not preserve state

Specified by:

openDOM in class JmolViewer

Parameters:

DOMNode -

Returns:

null or error

loadModelFromFileRepaint

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

loadModelFromFile

public String loadModelFromFile(String fullPathName,
                                String fileName,
                                String[] fileNames,
                                Object reader,
                                boolean isAppend,
                                Map<String,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(String key,
                           String data)

getLigandModel

public Object getLigandModel(String id,
                             String prefix,
                             String suffix,
                             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 Object openFileFull(String fileName,
                            boolean isAppend,
                            Map<String,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 String openStringInline(String strModel)
```
only used by file dropper.

Specified by:

openStringInline in class JmolViewer

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

Specified by:

loadInline in class JmolViewer

loadInline

public String loadInline(String strModel,
                         char newLine)

external apps only

Specified by:: loadInline in class JmolViewer

loadInlineAppend

public String loadInlineAppend(String strModel,
                               boolean isAppend)

used by applet and console

Specified by:: loadInlineAppend in class JmolViewer

loadInlineScriptRepaint

private String loadInlineScriptRepaint(String strModel,
                                       char newLine,
                                       boolean isAppend)

loadInline
```
public String loadInline(String[] arrayModels)
```
external apps only

Specified by:

loadInline in class JmolViewer

loadInline
```
public String loadInline(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 String loadInline(List<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 String loadInlineScript(String strModel,
                                char newLine,
                                boolean isAppend,
                                Map<String,Object> htParams)

used by loadInline and openFileFull

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

fixInlineString

public static String fixInlineString(String strModel,
                                     char newLine)

openStringInlineParamsAppend

public String openStringInlineParamsAppend(String strModel,
                                           Map<String,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 String openStringsInlineParamsAppend(String[] arrayModels,
                                             Map<String,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
```
String getDataSeparator()
```

createModelSetAndReturnError

private String createModelSetAndReturnError(Object atomSetCollection,
                                            boolean isAppend,
                                            javajs.util.SB loadScript,
                                            Map<String,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 String loadAtomDataAndReturnError(Object atomSetCollection,
                                          int tokType)

or just apply the data to the current model set

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

getEmbeddedFileState
```
public String getEmbeddedFileState(String filename)
```
Specified by:

getEmbeddedFileState in class JmolViewer

getFileAsBytes

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

Specified by:: getFileAsBytes in class JmolViewer

getCurrentFileAsString

public String getCurrentFileAsString()

getFullPathName

public String getFullPathName(boolean orPrevious)

getFileName
```
public String getFileName()
```

getFullPathNameOrError
```
public String[] getFullPathNameOrError(String filename)
```
Parameters:

filename -

Returns:

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

getFileAsString
```
public String getFileAsString(String name)
```
Specified by:

getFileAsString in class JmolViewer

getFileAsString4

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

getFileAsStringBin

public boolean getFileAsStringBin(String[] data)

getFilePath

public String getFilePath(String name,
                          boolean asShortName)

getFileInfo
```
public String[] getFileInfo()
```

setFileInfo

public void setFileInfo(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 Map<EnumStructure,float[]> getStructureList()

setStructureList

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

getDefaultStructure

public String getDefaultStructure(BS bsAtoms,
                                  BS bsAllAtoms)

calculateStructures

public 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(String script,
                                  boolean addFrameNumber,
                                  boolean postDefinitions)

addStateScriptRet

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

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

setEchoStateActive

public void setEchoStateActive(boolean TF)

clearModelDependentObjects

private void clearModelDependentObjects()

zap

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

zapMsg
```
private void zapMsg(String msg)
```

echoMessage
```
void echoMessage(String msg)
```

initializeModel

private void initializeModel(boolean isAppend)

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

startHoverWatcher in interface javajs.api.JSInterface

getModelSetName
```
public String getModelSetName()
```
Specified by:

getModelSetName in class JmolViewer

getModelSetFileName
```
public String getModelSetFileName()
```
Specified by:

getModelSetFileName in class JmolViewer

getUnitCellInfoText
```
public String getUnitCellInfoText()
```

getUnitCellInfo

public float getUnitCellInfo(int infoType)

getSpaceGroupInfo

public Map<String,Object> getSpaceGroupInfo(String spaceGroup)

getPolymerPointsAndVectors

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

getModelSetProperty

public String getModelSetProperty(String strProp)

getModelSetAuxiliaryInfoValue

public Object getModelSetAuxiliaryInfoValue(String strKey)

getModelSetPathName
```
public String getModelSetPathName()
```
Specified by:

getModelSetPathName in class JmolViewer

getModelSetTypeName
```
public String getModelSetTypeName()
```

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

haveFrame in class JmolViewer

haveModelSet
```
boolean haveModelSet()
```

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

getHybridizationAndAxes

public String getHybridizationAndAxes(int atomIndex,
                                      javajs.util.V3 z,
                                      javajs.util.V3 x,
                                      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 void excludeAtoms(BS bs,
                         boolean ignoreSubset)

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

getBoundBoxCommand

public 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()

getBoundBoxInfo
```
Map<String,Object> getBoundBoxInfo()
```

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

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

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

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

getModelCount in class JmolViewer

getModelInfoAsString
```
public String getModelInfoAsString()
```

getSymmetryInfoAsString

public String getSymmetryInfoAsString()

getSymmetryOperation

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

getModelSetProperties
```
public Properties getModelSetProperties()
```
Specified by:

getModelSetProperties in class JmolViewer

getModelSetAuxiliaryInfo
```
public Map<String,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 String getModelNumberDotted(int modelIndex)
```
Specified by:

getModelNumberDotted in class JmolViewer

getModelName
```
public String getModelName(int modelIndex)
```
Specified by:

getModelName in class JmolViewer

getModelProperties
```
public Properties getModelProperties(int modelIndex)
```
Specified by:

getModelProperties in class JmolViewer

getModelProperty

public String getModelProperty(int modelIndex,
                               String propertyName)

Specified by:: getModelProperty in class JmolViewer

getModelFileInfo
```
public String getModelFileInfo()
```

getModelFileInfoAll
```
public String getModelFileInfoAll()
```

getModelAuxiliaryInfo
```
public Map<String,Object> getModelAuxiliaryInfo(int modelIndex)
```
Specified by:

getModelAuxiliaryInfo in class JmolViewer

getModelAuxiliaryInfoValue

public Object getModelAuxiliaryInfoValue(int modelIndex,
                                         String keyName)

Specified by:: getModelAuxiliaryInfoValue in class JmolViewer

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(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,
                        String name,
                        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,
                      Object specInfo)

getSequenceBits

public BS getSequenceBits(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)

getAtomsConnected

public BS getAtomsConnected(float min,
                            float max,
                            int intType,
                            BS bs)

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 Map<String,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
```
String getFileHeader()
```

getFileData
```
Object getFileData()
```

getCifData

public Map<String,Object> getCifData(int modelIndex)

getPDBHeader
```
public String getPDBHeader()
```

getAuxiliaryInfo

public Map<String,Object> getAuxiliaryInfo(Object atomExpression)

getChimeInfo
```
public String getChimeInfo(int tok)
```

getStateCreator

public JmolStateCreator getStateCreator()

getWrappedStateScript
```
public String getWrappedStateScript()
```

getStateInfo
```
public String getStateInfo()
```
Specified by:

getStateInfo in class JmolViewer

getStateInfo3

public String getStateInfo3(String type,
                            int width,
                            int height)

getStructureState
```
public String getStructureState()
```

getProteinStructureState

public String getProteinStructureState()

getCoordinateState

public String getCoordinateState(BS bsSelected)

setCurrentColorRange

public void setCurrentColorRange(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(String type,
                    Object[] data,
                    int arrayCount,
                    int matchField,
                    int matchFieldColumnCount,
                    int field,
                    int fieldColumnCount)

getData
```
public Object[] getData(String type)
```

getDataFloat

public float[] getDataFloat(String label)

getDataFloat2D

public float[][] getDataFloat2D(String label)

getDataFloat3D

public float[][][] getDataFloat3D(String label)

getDataFloatAt

public float getDataFloatAt(String label,
                            int atomIndex)

getAltLocListInModel
```
public 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 String getDefaultMeasurementLabel(int nPoints)

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

getMeasurementCount in class JmolViewer

getMeasurementStringValue
```
public String getMeasurementStringValue(int i)
```
Specified by:

getMeasurementStringValue in class JmolViewer

getMeasurementInfo

javajs.util.List<Map<String,Object>> getMeasurementInfo()

getMeasurementInfoAsString

public String getMeasurementInfoAsString()

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

getMeasurementCountPlusIndices in class JmolViewer

setPendingMeasurement

void setPendingMeasurement(MeasurementPending measurementPending)

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()
```

getAnimationInfo
```
Map<String,Object> getAnimationInfo()
```

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

setAnimationFps in class JmolViewer

setAnimationMode

private void setAnimationMode(String mode)

setAnimationReplayMode

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

getAnimationReplayMode

public EnumAnimationMode 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(Map<String,Object> info)

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

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

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

defineAtomSets

public void defineAtomSets(Map<String,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 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(String why)

Parameters:: why -

popHoldRepaint
```
public void popHoldRepaint(String why)
```
Specified by:

popHoldRepaint in class JmolViewer

refresh
```
public void refresh(int mode,
                    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(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

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 String generateOutputForExport(Map<String,Object> params)
```
Specified by:

generateOutputForExport in class JmolViewer

clearRepaintManager

private void clearRepaintManager(int iShape)

renderScreenImageStereo

public void renderScreenImageStereo(Object gLeft,
                                    Object gRight,
                                    int width,
                                    int height)

Description copied from class: JmolViewer

an added class for rendering stereo in two independent applets

Specified by:: renderScreenImageStereo in class JmolViewer

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

Specified by:

updateJS in interface javajs.api.JSInterface

Parameters:

width -

height -

updateWindow

private boolean updateWindow(int width,
                             int height)

renderScreenImage

public void renderScreenImage(Object g,
                              int width,
                              int height)

Specified by:: renderScreenImage in class JmolViewer

getImage
```
private 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(Object graphic,
                     Object img,
                     int x,
                     int y)

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

Specified by:

getScreenImageBuffer in class JmolViewer

getImageAsBytes

public byte[] getImageAsBytes(String type,
                              int width,
                              int height,
                              int quality,
                              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 String evalFile(String strFilename)

Specified by:: evalFile in class JmolViewer

getInsertedCommand
```
public String getInsertedCommand()
```

script

public String script(String strScript)

Specified by:: script in class JmolViewer

evalString

public String evalString(String strScript)

Specified by:: evalString in class JmolViewer

evalStringQuiet
```
public String evalStringQuiet(String strScript)
```
Specified by:

evalStringQuiet in class JmolViewer

evalStringQuietSync

public String evalStringQuietSync(String strScript,
                                  boolean isQuiet,
                                  boolean allowSyncScript)

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

setScriptQueue

private void setScriptQueue(boolean TF)

checkHalt

public boolean checkHalt(String str,
                         boolean isInsert)

Specified by:: checkHalt in class JmolViewer

scriptWait

public String scriptWait(String strScript)

Specified by:: scriptWait in class JmolViewer

scriptWaitStatus

public Object scriptWaitStatus(String strScript,
                               String statusList)

Specified by:: scriptWaitStatus in class JmolViewer

evalWait

private Object evalWait(String returnType,
                        String strScript,
                        String statusList)

evalStringWaitStatusQueued

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

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

scriptCheckRet

private Object scriptCheckRet(String strScript,
                              boolean returnContext)

scriptCheck
```
public Object scriptCheck(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 String getDefaultLoadFilter()
```

getDefaultLoadScript
```
public String getDefaultLoadScript()
```

resolveDatabaseFormat

String resolveDatabaseFormat(String fileName)

isDatabaseCode

public static boolean isDatabaseCode(char ch)

hasDatabasePrefix

public static boolean hasDatabasePrefix(String fileName)

setLoadFormat
```
public Object setLoadFormat(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 String[] getElectronDensityLoadInfo()

getStandardLabelFormat

public 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(String strLabel)

hoverOn

void hoverOn(int atomIndex,
             boolean isLabel)

hoverOnPt

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

hoverOff
```
void hoverOff()
```

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

getColix
```
short getColix(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(String strMode,
                    int pickingMode)

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

setPickingStyle

void setPickingStyle(String style,
                     int pickingStyle)

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

getAtomInfo

public String getAtomInfo(int atomOrPointIndex)

Specified by:: getAtomInfo in class JmolViewer

getAtomInfoXYZ

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

getStatusChanged

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

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

popupMenu

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

getMenu
```
public String getMenu(String type)
```

getPopupMenu
```
private Object getPopupMenu()
```

setMenu

public void setMenu(String fileOrText,
                    boolean isFile)

setStatusFrameChanged

void setStatusFrameChanged(boolean isVib,
                           boolean doNotify)

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

getJSV
```
private 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 Object getJspecViewProperties(Object myParam)

scriptEcho

public void scriptEcho(String strEcho)

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

notifyError

public void notifyError(String errType,
                        String errMsg,
                        String errMsgUntranslated)

jsEval
```
public String jsEval(String strEval)
```

setStatusAtomHovered

public void setStatusAtomHovered(int atomIndex,
                                 String info)

setStatusObjectHovered

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

setFileLoadStatus

private void setFileLoadStatus(EnumFileStatus ptLoad,
                               String fullPathName,
                               String fileName,
                               String modelName,
                               String strError,
                               Boolean isAsync)

getZapName
```
public String getZapName()
```

setStatusMeasuring

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

notifyMinimizationStatus

public void notifyMinimizationStatus()

setStatusAtomPicked

public void setStatusAtomPicked(int atomIndex,
                                String info)

setStatusResized

public void setStatusResized(int width,
                             int height)

scriptStatus

public void scriptStatus(String strStatus)

scriptStatusMsg

public void scriptStatusMsg(String strStatus,
                            String statusMessage)

setScriptStatus

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

getModelTitle

private String getModelTitle(int modelIndex)

getModelFileName
```
public String getModelFileName(int modelIndex)
```
Specified by:

getModelFileName in class JmolViewer

dialogAsk

String dialogAsk(String type,
                 String fileName)

showUrl
```
public void showUrl(String urlString)
```
Specified by:

showUrl in class JmolViewer

setMeshCreator
```
public void setMeshCreator(Object meshCreator)
```
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer viewer = applet.getViewer(); viewer.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 Object getParameterEscaped(String key)

getParameter
```
public Object getParameter(String key)
```
Specified by:

getParameter in class JmolViewer

getOrSetNewVariable

public SV getOrSetNewVariable(String key,
                              boolean doSet)

setUserVariable

public SV setUserVariable(String name,
                          SV value)

unsetProperty

public void unsetProperty(String key)

getVariableList
```
public Object getVariableList()
```

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

notifyStatusReady in class JmolViewer

getBooleanProperty
```
public boolean getBooleanProperty(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(String key,
                              String value)

Specified by:: setStringProperty in class JmolViewer

setStringPropertyTok

private void setStringPropertyTok(String key,
                                  int tok,
                                  String value)

setFloatProperty

public void setFloatProperty(String key,
                             float value)

Specified by:: setFloatProperty in class JmolViewer

setFloatPropertyTok

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

setIntProperty

public void setIntProperty(String key,
                           int value)

Specified by:: setIntProperty in class JmolViewer

setIntPropertyTok

private void setIntPropertyTok(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(String key,
                               boolean value)

Specified by:: setBooleanProperty in class JmolViewer

setBooleanPropertyTok

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

setModelKitMode

private void setModelKitMode(boolean value)

getLanguage
```
public String getLanguage()
```

setSmilesString

public void setSmilesString(String s)

removeUserVariable

public void removeUserVariable(String key)

isJmolVariable

public boolean isJmolVariable(String key)

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

showParameter

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

showString

public void showString(String str,
                       boolean isPrint)

getAllSettings

public String getAllSettings(String prefix)

getBindingInfo

public String getBindingInfo(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 EnumAxesMode 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

String getLoadState(Map<String,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(String units,
                     boolean isDistance)

getMeasureDistanceUnits

public String getMeasureDistanceUnits()

getEnergyUnits
```
public 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(String type)

setDefaults
```
private void setDefaults()
```

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 EnumStructure[] allocTempEnum(int size)

freeTempEnum

public void freeTempEnum(EnumStructure[] temp)

getFont3D

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

formatText

public String formatText(String text0)

getElementSymbol
```
String getElementSymbol(int i)
```

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

getAtomName
```
public String getAtomName(int i)
```
Specified by:

getAtomName in class JmolViewer

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

getAtomNumber in class JmolViewer

getAtomGroupQuaternions

public Quaternion[] getAtomGroupQuaternions(BS bsAtoms,
                                            int nMax)

getAtomQuaternion

public Quaternion 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,
                          EnumStereoMode stereoMode,
                          float degrees)

isStereoDouble
```
boolean isStereoDouble()
```

getOperatingSystemName
```
public String getOperatingSystemName()
```
Specified by:

getOperatingSystemName in class JmolViewer

getJavaVendor
```
public String getJavaVendor()
```
Specified by:

getJavaVendor in class JmolViewer

getJavaVersion
```
public String getJavaVersion()
```
Specified by:

getJavaVersion in class JmolViewer

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

getProperty
```
public Object getProperty(String returnType,
                          String infoType,
                          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(String[] file_text)

getPropertyManager

private JmolPropertyManager getPropertyManager()

getModelExtract

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

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

notifyMouseClicked

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

checkObjectClicked

Map<String,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,
                                Map<String,Object> info)

setDefaultLattice

public void setDefaultLattice(javajs.util.P3 ptLattice)

getDefaultLattice

public javajs.util.P3 getDefaultLattice()

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

setTaintedAtoms

public void setTaintedAtoms(BS bs,
                            byte type)

getData

public String getData(String atomExpression,
                      String type)

Specified by:: getData in class JmolViewer

getModelCml

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

getHelixData

public Object getHelixData(BS bs,
                           int tokType)

getPdbAtomData

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

isJmolDataFrameForModel

public boolean isJmolDataFrameForModel(int modelIndex)

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

getJmolDataFrameIndex

public int getJmolDataFrameIndex(int modelIndex,
                                 String type)

setJmolDataFrame

public void setJmolDataFrame(String type,
                             int modelIndex,
                             int dataIndex)

setFrameTitle

public void setFrameTitle(int modelIndex,
                          String title)

setFrameTitleObj

public void setFrameTitleObj(Object title)

getFrameTitle
```
public String getFrameTitle()
```

getJmolFrameType

String getJmolFrameType(int modelIndex)

getJmolDataSourceFrame

public int getJmolDataSourceFrame(int modelIndex)

setAtomProperty

public void setAtomProperty(BS bs,
                            int tok,
                            int iValue,
                            float fValue,
                            String sValue,
                            float[] values,
                            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,
                          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
```
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(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(String functionName,
                               int nX,
                               int nY,
                               int nZ)

extractMolData
```
public String extractMolData(String what)
```
Specified by:

extractMolData in class JmolViewer

getNMRPredict

public String getNMRPredict(boolean openURL)

getHelp
```
public void getHelp(String what)
```

show2D
```
public void show2D(String smiles)
```

getChemicalInfo

public String getChemicalInfo(String smiles,
                              char type,
                              String info)

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

Parameters:

command - the command to add

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

Returns:

command removed

getSetHistory
```
public 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(String localName,
                                       String[] fullPath)

writeTextFile

public void writeTextFile(String fileName,
                          String data)

Specified by:: writeTextFile in class JmolViewer

clipImageOrPasteText
```
public String clipImageOrPasteText(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 String getClipboardText()
```
Specified by:

getClipboardText in class JmolViewer

processWriteOrCapture
```
public String processWriteOrCapture(Map<String,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 String createZip(String fileName,
                        String type,
                        String[] scripts)

outputToFile
```
public String outputToFile(Map<String,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(String script,
                       String applet,
                       int port)

Specified by:: syncScript in class JmolViewer

getModelIndexFromId

public int getModelIndexFromId(String id)

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

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

setProteinType

public void setProteinType(EnumStructure 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,
                                 EnumVdw type)

setVdwStr
```
void setVdwStr(String name)
```

setUserVdw
```
void setUserVdw(EnumVdw mode)
```

getDefaultVdwNameOrData

public String getDefaultVdwNameOrData(int mode,
                                      EnumVdw type,
                                      BS bs)

deleteAtoms

public int deleteAtoms(BS bs,
                       boolean fullModels)

deleteBonds

public void deleteBonds(BS bsDeleted)

deleteModelAtoms

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

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

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

calculatePointGroup
```
public String calculatePointGroup()
```

getPointGroupInfo

public Map<String,Object> getPointGroupInfo(Object atomExpression)

getPointGroupAsString

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

loadImage

public void loadImage(String pathName,
                      String echoName)

loadImageData

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

cd
```
public String cd(String dir)
```

setErrorMessage

public String setErrorMessage(String errMsg,
                              String errMsgUntranslated)

getErrorMessage
```
public String getErrorMessage()
```
Specified by:

getErrorMessage in class JmolViewer

getErrorMessageUn
```
public String getErrorMessageUn()
```
Specified by:

getErrorMessageUn in class JmolViewer

setShapeErrorState

public void setShapeErrorState(int shapeID,
                               String state)

getShapeErrorState
```
public String getShapeErrorState()
```

handleError

public void handleError(Error er,
                        boolean doClear)

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

getFunctions

public Map<String,JmolScriptFunction> getFunctions(boolean isStatic)

removeFunction

public void removeFunction(String name)

getFunction

public JmolScriptFunction getFunction(String name)

isStaticFunction

private static boolean isStaticFunction(String name)

isFunction

public boolean isFunction(String name)

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

addFunction

public void addFunction(JmolScriptFunction function)

getFunctionCalls

public String getFunctionCalls(String selectedFunction)

showMessage
```
public void showMessage(String s)
```

getMoInfo

public 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 viewer and not by some manipulation of the applet. When the image creator is used it requires both a viewer object and that viewer's private key. But the private key is private, so it is not possible to create a useable image creator without working through a viewer's own methods. Bob Hanson, 9/20/2009

Parameters:

privateKey -

Returns:

true if privateKey matches

bindAction

public void bindAction(String desc,
                       String name)

unBindAction

public void unBindAction(String desc,
                         String name)

getMouseInfo
```
public Object getMouseInfo()
```

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

getPlaneIntersection

public javajs.util.List<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()
```

getMinimizer

public MinimizerInterface getMinimizer(boolean createNew)

stopMinimization
```
void stopMinimization()
```

clearMinimization
```
void clearMinimization()
```

getMinimizationInfo
```
public 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,
                            String name,
                            float[] data)

getCenterAndPoints

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

writeFileData

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

getPdbData

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

getGroupsWithin

public BS getGroupsWithin(int nResidues,
                          BS bs)

getExecutor
```
public Object getExecutor()
```

getShapeInfo

public Map<String,Object> getShapeInfo()

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,
                             String propertyName,
                             Object value)

getShapeProperty

public Object getShapeProperty(int shapeType,
                               String propertyName)

getShapePropertyData

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

getShapePropertyIndex

public Object getShapePropertyIndex(int shapeType,
                                    String propertyName,
                                    int index)

getShapePropertyAsInt

private int getShapePropertyAsInt(int shapeID,
                                  String propertyName)

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

resetShapes

public void resetShapes(boolean andCreateNew)

setAtomLabel

public void setAtomLabel(String value,
                         int i)

deleteShapeAtoms

public void deleteShapeAtoms(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(String option)

setBondPickingOption

private void setBondPickingOption(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)

assignBond

public void assignBond(int bondIndex,
                       char type)

assignAtom

public void assignAtom(int atomIndex,
                       javajs.util.P3 pt,
                       String type)

assignConnect

public void assignConnect(int index,
                          int index2)

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 String getSmiles(int index1,
                        int index2,
                        BS bsSelected,
                        boolean isBioSmiles,
                        boolean allowUnmatchedRings,
                        boolean addCrossLinks,
                        boolean addComment)

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

Parameters:: index1 -; index2 -; bsSelected -; isBioSmiles -; allowUnmatchedRings - TODO; addCrossLinks - TODO; addComment -
Returns:: SMILES string

connect

public void connect(float[][] connections)

prompt

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

getColorEncoder

public ColorEncoder getColorEncoder(String colorScheme)

displayBonds

public void displayBonds(BondSet bs,
                         boolean isDisplay)

getModelAtomProperty

public String getModelAtomProperty(Atom atom,
                                   String text)

setStateScriptVersion

public void setStateScriptVersion(String version)

initializeExporter

public JmolRendererInterface initializeExporter(Map<String,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(Map<String,?> map,
                         char c)

used in autocompletion in console using TAB

Parameters:: map -; c -

getPdbBondInfo

public String[][] getPdbBondInfo(String group3)

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

runScript
```
public String runScript(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 Map<String,Object> getTimeouts()

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

setTimeout

public void setTimeout(String name,
                       int mSec,
                       String script)

triggerTimeout

public void triggerTimeout(String name)

clearTimeout

public void clearTimeout(String name)

showTimeout

public String showTimeout(String name)

calculatePartialCharges

public void calculatePartialCharges(BS bsSelected)

setCurrentModelID

public void setCurrentModelID(String id)

setCentroid

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

getPathForAllFiles
```
public String getPathForAllFiles()
```

cacheGet
```
public Object cacheGet(String key)
```

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

cachePut
```
public void cachePut(String key,
                     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(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 Map<String,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 String getFontLineShapeState(String s,
                                    String myType,
                                    TickInfo[] tickInfos)

getShapeSetState

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

getMeasurementState

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

getBondState

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

getAtomShapeSetState

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

getShapeState

public String getShapeState(Shape shape)

getAtomShapeState

public String getAtomShapeState(AtomShape shape)

getDefaultPropertyParam

public String getDefaultPropertyParam(int propertyID)

getPropertyNumber

public int getPropertyNumber(String name)

checkPropertyParameter

public boolean checkPropertyParameter(String name)

extractProperty

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

addHydrogens

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

addHydrogensInline

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

Throws:: Exception

evalFunctionFloat

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

Specified by:: evalFunctionFloat in interface AtomDataServer

evalParallel

public boolean evalParallel(ScriptContext context,
                            ShapeManager shapeManager)

evaluateExpression
```
public Object evaluateExpression(Object stringOrTokens)
```
Specified by:

evaluateExpression in class JmolViewer

evaluateExpressionAsVariable

public SV evaluateExpressionAsVariable(Object stringOrTokens)

getAtomBitSet

public BS getAtomBitSet(Object atomExpression)

getAtomBitSetVector

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

getContextVariables

public Map<String,SV> getContextVariables()

getScriptContext

public ScriptContext getScriptContext(String why)

getAtomDefs

public String getAtomDefs(Map<String,Object> names)

Specified by:: getAtomDefs in class JmolViewer

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

setCGO

public void setCGO(javajs.util.List<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 String setObjectProp(String id,
                            int tokCommand)

getSceneList
```
public String[] getSceneList()
```

setBondParameters

public void setBondParameters(int modelIndex,
                              int i,
                              BS bsBonds,
                              float rad,
                              float pymolValence,
                              int argb,
                              float trans)

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(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 String getChainIDStr(int id)
```

getScriptQueueInfo
```
public Boolean getScriptQueueInfo()
```

getNMRCalculation

public JmolNMRInterface getNMRCalculation()

getDistanceUnits

public String getDistanceUnits(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,
                                        String fileName,
                                        boolean asWriter)
                                 throws IOException

Throws:: IOException

log
```
public void log(String data)
```
Specified by:

log in interface AtomDataServer

getLogFileName
```
public String getLogFileName()
```

getCommands

public String getCommands(Map<String,BS> htDefine,
                          Map<String,BS> htMore,
                          String select)

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

getMP
```
public MeasurementPending getMP()
```

getApplet
```
public Object getApplet()
```
Specified by:

getApplet in interface javajs.api.JSInterface

getModulationList

public javajs.util.List<Object> getModulationList(BS bs,
                                                  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

modelSet

fileManager

isApplet

isJNLP

isSyntaxAndFileCheck

isSyntaxCheck

listCommands

mustRender

htmlName

insertedCommand

gdata

applet

actionManager

animationManager

colorManager

dataManager

shapeManager

selectionManager

repaintManager

global

statusManager

transformManager

strJavaVendor

strOSName

strJavaVersion

syncId

logFilePath

allowScripting

isPrintOnly

isSignedApplet

isSignedAppletLocal

isSilent

multiTouch

noGraphicsAllowed

useCommandThread

commandOptions

viewerOptions

display

modelAdapter

access

commandHistory

symmetry

smilesMatcher

modelManager

stateManager

scriptManager

eval

tempArray

version_date

isPreviewOnly

mouse

mouseEnabled

noneSelected

ligandModels

ligandModelSet

sc

bsFrameOffsets

frameOffsets