public class Viewer extends JmolViewer implements AtomDataServer
Modifier and Type | Class and Description |
---|---|
static class |
Viewer.ACCESS |
Modifier and Type | Field and Description |
---|---|
private Viewer.ACCESS |
access |
(package private) ActionManager |
actionManager |
(package private) JmolList<java.lang.String> |
actionStates |
(package private) JmolList<java.lang.String> |
actionStatesRedo |
private boolean |
allowScripting |
(package private) AnimationManager |
animationManager |
private boolean |
antialiasDisplay |
(package private) JmolAppConsoleInterface |
appConsole |
(package private) java.lang.Object |
applet |
java.lang.String |
appletCodeBase |
java.lang.String |
appletDocumentBase |
boolean |
autoExit |
private boolean |
axesAreTainted |
(package private) BS |
bsFrameOffsets |
private BS |
bsRotateBranch |
JmolList<java.lang.String> |
chainList |
java.util.Map<java.lang.Object,java.lang.Object> |
chainMap |
(package private) ColorManager |
colorManager |
private CommandHistory |
commandHistory |
private java.lang.String |
commandOptions |
java.lang.Object |
compiler |
boolean |
creatingImage |
private int |
currentCursor |
private int |
currentShapeID |
private java.lang.String |
currentShapeState |
(package private) DataManager |
dataManager |
java.util.Map<java.lang.String,java.lang.Object> |
definedAtomSets |
(package private) Dimension |
dimScreen |
private java.lang.Object |
display |
boolean |
displayLoadErrors |
private java.lang.String |
errorMessage |
private java.lang.String |
errorMessageUntranslated |
(package private) JmolScriptEvaluator |
eval |
private java.lang.Object |
executor |
FileManager |
fileManager |
(package private) P3[] |
frameOffsets |
private boolean |
frankOn |
java.lang.String |
fullName |
(package private) GData |
gdata |
StateManager.GlobalSettings |
global |
boolean |
haveDisplay |
private boolean |
haveJDX |
private java.lang.Object[] |
headlessImage |
(package private) int |
hoverAtomIndex |
boolean |
hoverEnabled |
(package private) java.lang.String |
hoverText |
(package private) java.lang.String |
htmlName |
(package private) java.util.Map<java.lang.String,java.lang.String[][]> |
htPdbBondInfo |
private float |
imageFontScaling |
(package private) java.lang.String |
insertedCommand |
(package private) boolean |
isApplet |
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 |
(package private) boolean |
isSyntaxAndFileCheck |
(package private) boolean |
isSyntaxCheck |
(package private) boolean |
isTainted |
boolean |
isWebGL |
(package private) JmolPopupInterface |
jmolpopup |
static java.lang.String |
jsDocumentBase |
private JmolRendererInterface |
jsExporter3D |
private JmolJSpecView |
jsv |
private java.lang.String |
language |
(package private) java.util.Map<java.lang.String,java.lang.Object> |
ligandModels |
(package private) java.util.Map<java.lang.String,java.lang.Boolean> |
ligandModelSet |
(package private) boolean |
listCommands |
(package private) java.util.Map<java.lang.String,JmolScriptFunction> |
localFunctions |
(package private) java.lang.String |
logFile |
private java.lang.String |
logFilePath |
private int |
maximumSize |
private MinimizerInterface |
minimizer |
private JmolAdapter |
modelAdapter |
private JmolPopupInterface |
modelkitPopup |
private ModelManager |
modelManager |
ModelSet |
modelSet |
(package private) int |
motionEventNumber |
private JmolMouseInterface |
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 |
(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 |
private JmolThread |
scriptDelayThread |
(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 java.util.Map<java.lang.String,JmolScriptFunction> |
staticFunctions |
(package private) StatusManager |
statusManager |
private static java.lang.String |
strJavaVendor |
private static java.lang.String |
strJavaVersion |
private static java.lang.String |
strOSName |
private SymmetryInterface |
symmetry |
static java.lang.String |
SYNC_GRAPHICS_MESSAGE |
static java.lang.String |
SYNC_NO_GRAPHICS_MESSAGE |
private java.lang.String |
syncId |
private TempArray |
tempArray |
(package private) java.util.Map<java.lang.String,java.lang.Object> |
timeouts |
(package private) TransformManager |
transformManager |
private boolean |
useCommandThread |
private static java.lang.String |
version_date |
private java.util.Map<java.lang.String,java.lang.Object> |
viewerOptions |
(package private) boolean |
wasInMotion |
apiPlatform, menuStructure
Constructor and Description |
---|
Viewer(java.util.Map<java.lang.String,java.lang.Object> info)
new way...
|
Modifier and Type | Method and Description |
---|---|
(package private) void |
actionRotateBond(int deltaX,
int deltaY,
int x,
int y) |
void |
addCommand(java.lang.String command)
Adds one or more commands to the command history
|
void |
addFunction(JmolScriptFunction function) |
BS |
addHydrogens(BS bsAtoms,
boolean is2DLoad,
boolean isSilent) |
private BS |
addHydrogensInline(BS bsAtoms,
JmolList<Atom> vConnections,
P3[] pts) |
void |
addSelectionListener(JmolSelectionListener listener) |
ModelCollection.StateScript |
addStateScript(java.lang.String script,
boolean addFrameNumber,
boolean postDefinitions) |
ModelCollection.StateScript |
addStateScriptRet(java.lang.String script1,
BS bsBonds,
BS bsAtoms1,
BS bsAtoms2,
java.lang.String script2,
boolean addFrameNumber,
boolean postDefinitions) |
void |
addUnitCellOffset(P3 pt) |
protected static JmolViewer |
allocateViewer(java.lang.Object display,
JmolAdapter modelAdapter,
java.lang.String fullName,
java.net.URL documentBase,
java.net.URL codeBase,
java.lang.String commandOptions,
JmolStatusListener statusListener,
ApiPlatform implementedPlatform)
old way...
|
EnumStructure[] |
allocTempEnum(int size) |
P3[] |
allocTempPoints(int size) |
P3i[] |
allocTempScreens(int size) |
boolean |
allowEmbeddedScripts() |
boolean |
allowSpecAtom() |
boolean |
areAxesTainted() |
void |
assignAromaticBonds() |
void |
assignAtom(int atomIndex,
P3 pt,
java.lang.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(java.lang.String desc,
java.lang.String name,
P3 range1,
P3 range2) |
void |
cacheClear() |
void |
cacheFile(java.lang.String fileName,
byte[] bytes)
JmolViewer interface -- allows saving files in memory for later retrieval
|
int |
cacheFileByName(java.lang.String fileName,
boolean isAdd) |
java.lang.Object |
cacheGet(java.lang.String key) |
java.util.Map<java.lang.String,java.lang.Integer> |
cacheList() |
boolean |
cachePngFiles() |
void |
cachePut(java.lang.String key,
java.lang.Object data) |
void |
calcAtomsMinMax(BS bs,
BoxInfo boxInfo) |
void |
calcBoundBoxDimensions(BS bs,
float scale) |
float |
calcRotationRadius(P3 center) |
float |
calcRotationRadiusBs(BS bs) |
void |
calcSelectedGroupsCount() |
void |
calcSelectedMoleculesCount() |
void |
calcSelectedMonomersCount() |
int |
calculateFormalCharges(BS bs) |
V3 |
calculateMolecularDipole() |
void |
calculatePartialCharges(BS bsSelected) |
java.lang.String |
calculatePointGroup() |
void |
calculateStraightness() |
java.lang.String |
calculateStructures(BS bsAtoms,
boolean asDSSP,
boolean setStructure) |
int |
calculateStruts(BS bs1,
BS bs2) |
P3[] |
calculateSurface(BS bsSelected,
float envelopeRadius) |
java.lang.String |
cd(java.lang.String dir) |
(package private) void |
centerAt(int x,
int y,
P3 pt) |
void |
checkCoordinatesChanged() |
private static float |
checkFloatRange(float value,
float min,
float max) |
boolean |
checkHalt(java.lang.String str,
boolean isInsert) |
void |
checkInheritedShapes() |
private static int |
checkIntRange(int value,
int min,
int max) |
private void |
checkMinimization() |
(package private) java.util.Map<java.lang.String,java.lang.Object> |
checkObjectClicked(int x,
int y,
int modifiers) |
(package private) void |
checkObjectDragged(int prevX,
int prevY,
int x,
int y,
int action) |
boolean |
checkObjectHovered(int x,
int y) |
private boolean |
checkOption2(java.lang.String key1,
java.lang.String key2) |
boolean |
checkPrivateKey(double privateKey)
Simple method to ensure that the image creator (which writes files) was in
fact opened by this viewer and not by some manipulation of the applet.
|
boolean |
checkPropertyParameter(java.lang.String name) |
void |
clearAllMeasurements() |
private void |
clearAtomSets() |
void |
clearBfactorRange() |
(package private) void |
clearClickCount() |
void |
clearConsole() |
void |
clearFunctions() |
void |
clearMeasurements() |
(package private) void |
clearMinimization() |
private void |
clearModelDependentObjects() |
void |
clearMouse() |
private void |
clearRepaintManager(int iShape) |
void |
clearScriptQueue() |
void |
clearSelection() |
void |
clearShapeRenderers() |
(package private) void |
clearThreads() |
void |
clearTimeout(java.lang.String name) |
void |
clearTimeouts() |
java.lang.String |
clipImage(java.lang.String text) |
void |
connect(float[][] connections) |
java.lang.Object |
createImage(java.lang.String fileName,
java.lang.String type,
java.lang.Object text_or_bytes,
int quality,
int width,
int height) |
java.lang.Object |
createImage(java.lang.String fileName,
java.lang.String type,
java.lang.String text,
byte[] bytes,
int quality,
int width,
int height) |
java.lang.String |
createImageSet(java.lang.String fileName,
java.lang.String type,
java.lang.String text,
byte[] bytes,
java.lang.String[] scripts,
int quality,
int width,
int height,
BS bsFrames,
int nVibes,
java.lang.String[] fullPath)
from eval write command only includes option to write set of files
|
void |
createModels(int n) |
private java.lang.String |
createModelSetAndReturnError(java.lang.Object atomSetCollection,
boolean isAppend,
SB loadScript,
java.util.Map<java.lang.String,java.lang.Object> htParams)
finally(!) we are ready to create the "model set" from the
"atom set collection"
|
java.lang.Object |
createZip(java.lang.String fileName,
java.lang.String type,
java.lang.String stateInfo,
java.lang.String[] scripts) |
void |
defineAtomSets(java.util.Map<java.lang.String,java.lang.Object> info) |
void |
delayScript(JmolScriptEvaluator eval,
int millis) |
int |
deleteAtoms(BS bs,
boolean fullModels) |
void |
deleteBonds(BS bsDeleted) |
void |
deleteMeasurement(int i) |
void |
deleteModelAtoms(int firstAtomIndex,
int nAtoms,
BS bsDeleted) |
void |
deleteSavedState(java.lang.String saveName) |
void |
deleteShapeAtoms(java.lang.Object[] value,
BS bs) |
(package private) void |
depthByPixels(int pixels) |
void |
depthToPercent(int percentDepth) |
(package private) java.lang.String |
dialogAsk(java.lang.String type,
java.lang.String fileName) |
void |
displayAtoms(BS bs,
boolean isDisplay,
boolean isGroup,
int addRemove,
boolean isQuiet) |
void |
displayBonds(Bond.BondSet bs,
boolean isDisplay) |
void |
disposeMouse() |
private boolean |
doHaveJDX() |
(package private) void |
echoMessage(java.lang.String msg) |
java.lang.String |
evalFile(java.lang.String strFilename) |
float |
evalFunctionFloat(java.lang.Object func,
java.lang.Object params,
float[] values) |
boolean |
evalParallel(ScriptContext context,
ShapeManager shapeManager) |
java.lang.String |
evalString(java.lang.String strScript) |
java.lang.String |
evalStringQuiet(java.lang.String strScript) |
(package private) java.lang.String |
evalStringQuietSync(java.lang.String strScript,
boolean isQuiet,
boolean allowSyncScript) |
java.lang.Object |
evalStringWaitStatusQueued(java.lang.String returnType,
java.lang.String strScript,
java.lang.String statusList,
boolean isScriptFile,
boolean isQuiet,
boolean isQueued) |
java.lang.Object |
evaluateExpression(java.lang.Object stringOrTokens) |
SV |
evaluateExpressionAsVariable(java.lang.Object stringOrTokens) |
private java.lang.Object |
evalWait(java.lang.String returnType,
java.lang.String strScript,
java.lang.String statusList) |
void |
excludeAtoms(BS bs,
boolean ignoreSubset) |
void |
exitJmol() |
java.lang.Object |
extractProperty(java.lang.Object property,
SV[] args,
int pt) |
void |
fillAtomData(AtomData atomData,
int mode) |
protected void |
finalize() |
void |
finalizeTransformParameters() |
(package private) BS |
findAtomsInRectangle(Rectangle rect) |
int |
findNearestAtomIndex(int x,
int y) |
int |
findNearestAtomIndexMovable(int x,
int y,
boolean mustBeMovable) |
static java.lang.String |
fixInlineString(java.lang.String strModel,
char newLine) |
java.lang.String |
formatText(java.lang.String text0) |
boolean |
frankClicked(int x,
int y) |
boolean |
frankClickedModelKit(int x,
int y) |
void |
freeTempEnum(EnumStructure[] temp) |
void |
freeTempPoints(P3[] tempPoints) |
void |
freeTempScreens(P3i[] tempScreens) |
float[][] |
functionXY(java.lang.String functionName,
int nX,
int nY)
fills an array with data -- if nX < 0 and this would involve JavaScript,
then this reads a full set of Double[][] in one function call.
|
float[][][] |
functionXYZ(java.lang.String functionName,
int nX,
int nY,
int nZ) |
java.lang.String |
generateOutputForExport(java.lang.String type,
java.lang.String[] fileName,
int width,
int height) |
P3[] |
getAdditionalHydrogens(BS bsAtoms,
boolean doAll,
boolean justCarbon,
JmolList<Atom> vConnections) |
java.lang.String |
getAllSettings(java.lang.String prefix) |
java.lang.String |
getAltLocListInModel(int modelIndex) |
(package private) int |
getAnimationDirection() |
(package private) java.util.Map<java.lang.String,java.lang.Object> |
getAnimationInfo() |
(package private) EnumAnimationMode |
getAnimationReplayMode() |
(package private) java.util.Map<java.lang.String,java.lang.Object> |
getAppletInfo() |
int |
getAtomArgb(int i) |
BS |
getAtomBits(int tokType,
java.lang.Object specInfo) |
BS |
getAtomBitSet(java.lang.Object atomExpression) |
(package private) BS |
getAtomBitSetEval(JmolScriptEvaluator eval,
java.lang.Object atomExpression) |
(package private) JmolList<java.lang.Integer> |
getAtomBitSetVector(java.lang.Object atomExpression) |
int |
getAtomCount() |
int |
getAtomCountInModel(int modelIndex) |
java.lang.String |
getAtomDefs(java.util.Map<java.lang.String,java.lang.Object> names) |
Quaternion[] |
getAtomGroupQuaternions(BS bsAtoms,
int nMax) |
float[] |
getAtomicCharges() |
float[] |
getAtomicPotentials(boolean isMep,
BS bsSelected,
BS bsIgnore,
java.lang.String fileName) |
(package private) void |
getAtomicPropertyState(SB commands,
byte type,
BS bs,
java.lang.String name,
float[] data) |
void |
getAtomIdentityInfo(int atomIndex,
java.util.Map<java.lang.String,java.lang.Object> info) |
int |
getAtomIndexFromAtomNumber(int atomNumber) |
int[] |
getAtomIndices(BS bs) |
java.lang.String |
getAtomInfo(int atomOrPointIndex) |
java.lang.String |
getAtomInfoXYZ(int atomIndex,
boolean useChimeFormat) |
int |
getAtomModelIndex(int i) |
java.lang.String |
getAtomName(int i) |
int |
getAtomNumber(int i) |
P3 |
getAtomPoint3f(int i) |
JmolList<P3> |
getAtomPointVector(BS bs) |
Quaternion |
getAtomQuaternion(int i) |
float |
getAtomRadius(int i) |
BS |
getAtomsConnected(float min,
float max,
int intType,
BS bs) |
P3 |
getAtomSetCenter(BS bs) |
java.lang.String |
getAtomShapeSetState(Shape shape,
AtomShape[] shapes) |
java.lang.String |
getAtomShapeState(AtomShape shape) |
float |
getAtomShapeValue(int tok,
Group group,
int atomIndex) |
BS |
getAtomsNearPlane(float distance,
P4 plane) |
BS |
getAtomsNearPt(float distance,
P3 coord) |
BS |
getAtomsNearPts(float distance,
P3[] points,
BS bsInclude) |
BS |
getAtomsWithinRadius(float distance,
BS bs,
boolean withinAllModels,
RadiusData rd) |
java.util.Map<java.lang.String,java.lang.Object> |
getAuxiliaryInfo(java.lang.Object atomExpression) |
(package private) P3 |
getAverageAtomPoint() |
EnumAxesMode |
getAxesMode() |
void |
getAxisAngle(AxisAngle4f axisAngle) |
P3[] |
getAxisPoints() |
int |
getBackgroundArgb() |
BS |
getBaseModelBitSet() |
int |
getBfactor100Hi() |
java.lang.String |
getBindingInfo(java.lang.String qualifiers) |
BS |
getBitSetTrajectories() |
int |
getBondArgb1(int i) |
int |
getBondArgb2(int i) |
int |
getBondCount()
For use in setting a for() construct max value
|
int |
getBondCountInModel(int modelIndex)
from JmolPopup.udateModelSetComputedMenu
|
int |
getBondModelIndex(int i) |
int |
getBondOrder(int i) |
(package private) boolean |
getBondPicking() |
P3 |
getBondPoint3f1(int i) |
P3 |
getBondPoint3f2(int i) |
float |
getBondRadius(int i) |
BS |
getBondsForSelectedAtoms(BS bsAtoms) |
java.lang.String |
getBondState(Shape shape,
BS bsOrderSet,
boolean reportAll) |
boolean |
getBoolean(int tok) |
boolean |
getBooleanProperty(java.lang.String key) |
P3 |
getBoundBoxCenter() |
int |
getBoundBoxCenterX() |
int |
getBoundBoxCenterY() |
java.lang.String |
getBoundBoxCommand(boolean withOptions) |
V3 |
getBoundBoxCornerVector() |
(package private) java.util.Map<java.lang.String,java.lang.Object> |
getBoundBoxInfo() |
BS |
getBoundBoxModels() |
P3[] |
getBoundBoxVertices() |
BoxInfo |
getBoxInfo(BS bs,
float scale) |
BS |
getBranchBitSet(int atomIndex,
int atomIndexNot,
boolean allowCyclic) |
BS[] |
getBsBranches(float[] dihedralList) |
java.io.BufferedInputStream |
getBufferedInputStream(java.lang.String fullPathName) |
java.lang.Object |
getBufferedReaderOrErrorMessageFromName(java.lang.String name,
java.lang.String[] fullPathNameReturn,
boolean isBinary) |
P3 |
getCamera() |
float |
getCameraDepth() |
P3[] |
getCameraFactors() |
P3[][] |
getCenterAndPoints(JmolList<BS[]> atomSets,
boolean addCenter) |
int |
getChainCount() |
int |
getChainCountInModel(int modelIndex) |
int |
getChainCountInModelWater(int modelIndex,
boolean countWater) |
int |
getChainID(java.lang.String id)
Create a unique integer for any chain string.
|
java.lang.String |
getChainIDStr(int id) |
java.lang.String |
getChemicalInfo(java.lang.String smiles,
char type,
java.lang.String info) |
java.lang.String |
getChimeInfo(int tok) |
java.util.Map<java.lang.String,java.lang.Object> |
getCifData(int modelIndex) |
BS |
getClickableSet() |
(package private) short |
getColix(java.lang.Object object) |
short |
getColixAtomPalette(Atom atom,
byte pid) |
short |
getColixBackgroundContrast() |
short |
getColixBondPalette(Bond bond,
int pid) |
short |
getColixForPropertyValue(float val) |
short |
getColixRubberband() |
int |
getColorArgbOrGray(short colix) |
ColorEncoder |
getColorEncoder(java.lang.String colorScheme) |
P3 |
getColorPointForPropertyValue(float val) |
java.lang.String |
getColorSchemeList(java.lang.String colorScheme) |
BS |
getConformation(int iModel,
int conformationIndex,
boolean doSet) |
java.util.Map<java.lang.String,SV> |
getContextVariables() |
java.lang.String |
getCoordinateState(BS bsSelected) |
float[] |
getCurrentColorRange() |
java.lang.String |
getCurrentFileAsString() |
int |
getCurrentModelIndex() |
float |
getCurrentSolventProbeRadius() |
SymmetryInterface |
getCurrentUnitCell() |
int |
getCursor() |
int |
getCursorX() |
int |
getCursorY() |
java.lang.Object[] |
getData(java.lang.String type) |
java.lang.String |
getData(java.lang.String atomExpression,
java.lang.String type) |
float[] |
getDataFloat(java.lang.String label) |
float[][] |
getDataFloat2D(java.lang.String label) |
float[][][] |
getDataFloat3D(java.lang.String label) |
float |
getDataFloatAt(java.lang.String label,
int atomIndex) |
(package private) java.lang.String |
getDataSeparator() |
(package private) java.lang.String |
getDefaultDirectory() |
P3 |
getDefaultLattice() |
java.lang.String |
getDefaultLoadFilter() |
java.lang.String |
getDefaultLoadScript() |
java.lang.String |
getDefaultMeasurementLabel(int nPoints) |
java.lang.String |
getDefaultPropertyParam(int propertyID) |
RadiusData |
getDefaultRadiusData() |
java.lang.String |
getDefaultStructure(BS bsAtoms,
BS bsAllAtoms) |
java.lang.String |
getDefaultVdwTypeNameOrData(int iMode,
EnumVdw vType) |
BS |
getDefinedAtomSet(java.lang.String name) |
int |
getDelayMaximumMs() |
BS |
getDeletedAtoms() |
int[][] |
getDihedralMap(int[] atoms) |
java.lang.Object |
getDisplay() |
int |
getDisplayModelIndex() |
java.lang.String |
getDistanceUnits(java.lang.String s) |
(package private) boolean |
getDragSelected() |
boolean |
getDrawHover() |
boolean |
getEchoStateActive() |
java.lang.String[] |
getElectronDensityLoadInfo() |
(package private) int |
getElementNumber(int i) |
BS |
getElementsPresentBitSet(int modelIndex) |
(package private) java.lang.String |
getElementSymbol(int i) |
java.lang.String |
getEmbeddedFileState(java.lang.String filename) |
java.lang.String |
getEnergyUnits() |
java.lang.String |
getErrorMessage() |
java.lang.String |
getErrorMessageUn() |
ScriptContext |
getEvalContextAndHoldQueue(JmolScriptEvaluator jse) |
java.lang.Object |
getExecutor() |
java.lang.String |
getExportDriverList() |
java.lang.Object |
getFileAsBytes(java.lang.String pathName,
java.io.OutputStream os) |
java.lang.String |
getFileAsString(java.lang.String name) |
java.lang.String |
getFileAsString4(java.lang.String name,
int nBytesMax,
boolean doSpecialLoad,
boolean allowBinary) |
boolean |
getFileAsStringBin(java.lang.String[] data,
int nBytesMax,
boolean doSpecialLoad) |
private boolean |
getFileAsStringFM(java.lang.String[] data,
int nBytesMax,
boolean doSpecialLoad,
boolean allowBinary) |
(package private) java.lang.Object |
getFileData() |
(package private) java.lang.String |
getFileHeader() |
java.lang.String[] |
getFileInfo() |
java.lang.String |
getFileName() |
java.lang.String |
getFilePath(java.lang.String name,
boolean asShortName) |
float |
getFloat(int tok) |
JmolFont |
getFont3D(java.lang.String fontFace,
java.lang.String fontStyle,
float fontSize) |
java.lang.String |
getFontLineShapeState(java.lang.String s,
java.lang.String myType,
TickInfo[] tickInfos) |
java.lang.String |
getFontState(java.lang.String myType,
JmolFont font3d) |
int |
getFrameCount() |
long |
getFrameDelayMs(int i) |
BS |
getFrameOffsets() |
java.lang.String |
getFrameTitle() |
int |
getFrontPlane() |
java.lang.String |
getFullPathName() |
java.lang.String[] |
getFullPathNameOrError(java.lang.String filename) |
JmolScriptFunction |
getFunction(java.lang.String name) |
java.lang.String |
getFunctionCalls(java.lang.String selectedFunction) |
java.util.Map<java.lang.String,JmolScriptFunction> |
getFunctions(boolean isStatic) |
StateManager.GlobalSettings |
getGlobalSettings() |
GData |
getGraphicsData() |
int |
getGroupCount() |
int |
getGroupCountInModel(int modelIndex) |
BS |
getGroupsWithin(int nResidues,
BS bs) |
java.lang.Object |
getHelixData(BS bs,
int tokType) |
void |
getHelp(java.lang.String what) |
int |
getHermiteLevel() |
java.util.Map<java.lang.String,java.lang.String> |
getHeteroList(int modelIndex) |
BS |
getHiddenSet() |
int |
getHoverDelay() |
java.lang.String |
getHtmlName() |
java.lang.String |
getHybridizationAndAxes(int atomIndex,
V3 z,
V3 x,
java.lang.String lcaoType) |
private java.lang.Object |
getImage(boolean isDouble,
boolean isImageWrite) |
java.lang.Object |
getImageAs(java.lang.String type,
int quality,
int width,
int height,
java.lang.String fileName,
java.io.OutputStream os) |
java.lang.Object |
getImageAsWithComment(java.lang.String type,
int quality,
int width,
int height,
java.lang.String fileName,
java.lang.String[] scripts,
java.io.OutputStream os,
java.lang.String comment) |
(package private) JmolImageCreatorInterface |
getImageCreator() |
float |
getImageFontScaling() |
char |
getInlineChar() |
static void |
getInlineData(SB loadScript,
java.lang.String strModel,
boolean isAppend) |
boolean |
getInMotion(boolean includeAnim) |
java.lang.String |
getInsertedCommand() |
int |
getInt(int tok) |
int |
getIsosurfacePropertySmoothing(boolean asPower) |
java.lang.String |
getJavaVendor() |
java.lang.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,
java.lang.String type) |
int |
getJmolDataSourceFrame(int modelIndex) |
(package private) java.lang.String |
getJmolFrameType(int modelIndex) |
static java.lang.String |
getJmolVersion() |
java.lang.Object |
getJspecViewProperties(java.lang.Object myParam) |
private JmolJSpecView |
getJSV() |
java.lang.String |
getLanguage() |
java.lang.Object |
getLigandModel(java.lang.String id)
obtain CIF data for a ligand for purposes of adding hydrogens
|
(package private) java.lang.String |
getLoadState(java.util.Map<java.lang.String,java.lang.Object> htParams) |
java.lang.String |
getLogFile() |
short |
getMadBond() |
short |
getMarBond() |
(package private) Matrix3f |
getMatrixRotate() |
Matrix4f |
getMatrixtransform() |
float |
getMaxZoomPercent() |
java.lang.String |
getMeasureDistanceUnits() |
int |
getMeasurementCount() |
int[] |
getMeasurementCountPlusIndices(int i) |
(package private) JmolList<java.util.Map<java.lang.String,java.lang.Object>> |
getMeasurementInfo() |
java.lang.String |
getMeasurementInfoAsString() |
java.lang.String |
getMeasurementState(Measures measures,
JmolList<Measurement> mList,
int measurementCount,
JmolFont font3d,
TickInfo ti) |
java.lang.String |
getMeasurementStringValue(int i) |
java.lang.String |
getMenu(java.lang.String type) |
java.util.Map<java.lang.String,JmolList<JmolList<java.lang.Object>>> |
getMessageQueue() |
java.lang.String |
getMinimizationInfo() |
MinimizerInterface |
getMinimizer(boolean createNew) |
JmolAdapter |
getModelAdapter() |
java.lang.String |
getModelAtomProperty(Atom atom,
java.lang.String text) |
java.util.Map<java.lang.String,java.lang.Object> |
getModelAuxiliaryInfo(int modelIndex) |
java.lang.Object |
getModelAuxiliaryInfoValue(int modelIndex,
java.lang.String keyName) |
BS |
getModelBitSet(BS atomList,
boolean allTrajectories) |
java.lang.String |
getModelCml(BS bs,
int nAtomsMax,
boolean addBonds) |
int |
getModelCount() |
V3 |
getModelDipole() |
java.lang.String |
getModelExtract(java.lang.Object atomExpression,
boolean doTransform,
boolean isModelKit,
java.lang.String type) |
java.lang.String |
getModelFileInfo() |
java.lang.String |
getModelFileInfoAll() |
java.lang.String |
getModelFileName(int modelIndex) |
int |
getModelFileNumber(int modelIndex) |
int |
getModelIndexFromId(java.lang.String id) |
java.lang.String |
getModelInfoAsString() |
(package private) BS |
getModelKitStateBitSet(BS bs,
BS bsDeleted) |
java.lang.String |
getModelName(int modelIndex) |
int |
getModelNumber(int modelIndex) |
java.lang.String |
getModelNumberDotted(int modelIndex) |
int |
getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory) |
java.util.Properties |
getModelProperties(int modelIndex) |
java.lang.String |
getModelProperty(int modelIndex,
java.lang.String propertyName) |
ModelSet |
getModelSet() |
java.util.Map<java.lang.String,java.lang.Object> |
getModelSetAuxiliaryInfo() |
java.lang.Object |
getModelSetAuxiliaryInfoValue(java.lang.String strKey) |
java.lang.String |
getModelSetFileName() |
java.lang.String |
getModelSetName() |
java.lang.String |
getModelSetPathName() |
java.util.Properties |
getModelSetProperties() |
java.lang.String |
getModelSetProperty(java.lang.String strProp) |
java.lang.String |
getModelSetTypeName() |
private java.lang.String |
getModelTitle(int modelIndex) |
BS |
getModelUndeletedAtomsBitSet(int modelIndex) |
BS |
getModelUndeletedAtomsBitSetBs(BS bsModels) |
SymmetryInterface |
getModelUnitCell(int modelIndex) |
byte |
getModeMultipleBond() |
java.lang.String |
getMoInfo(int modelIndex) |
BS |
getMoleculeBitSet(int atomIndex) |
int |
getMotionEventNumber() |
BS |
getMotionFixedAtoms() |
boolean |
getMouseEnabled() |
java.lang.Object |
getMouseInfo() |
(package private) java.lang.String |
getMoveToText(float timespan) |
P3 |
getNavigationCenter() |
float |
getNavigationDepthPercent() |
P3 |
getNavigationOffset() |
(package private) float |
getNavigationOffsetPercent(char XorY) |
boolean |
getNavOn() |
JmolNMRInterface |
getNMRCalculation() |
java.lang.Boolean |
getNoneSelected() |
(package private) int |
getObjectArgb(int objId) |
short |
getObjectColix(int objId) |
int |
getObjectMad(int objId) |
void |
getObjectMap(java.util.Map<java.lang.String,?> map,
char c)
used in autocompletion in console using TAB
|
java.lang.String |
getOperatingSystemName() |
StateManager.Orientation |
getOrientation() |
(package private) java.util.Map<java.lang.String,java.lang.Object> |
getOrientationInfo() |
java.lang.String |
getOrientationText(int type,
java.lang.String name) |
SV |
getOrSetNewVariable(java.lang.String key,
boolean doSet) |
java.io.OutputStream |
getOutputStream(java.lang.String localName,
java.lang.String[] fullPath) |
java.lang.Object |
getParameter(java.lang.String key) |
java.lang.Object |
getParameterEscaped(java.lang.String key) |
float[] |
getPartialCharges() |
java.lang.String |
getPathForAllFiles() |
java.lang.String[][] |
getPdbBondInfo(java.lang.String group3) |
java.lang.String |
getPdbData(BS bs,
OutputStringBuilder sb) |
java.lang.String |
getPdbData(int modelIndex,
java.lang.String type,
java.lang.Object[] parameters) |
java.lang.String |
getPDBHeader() |
(package private) MeasurementPending |
getPendingMeasurement() |
boolean |
getPerspectiveDepth() |
int |
getPickingMode() |
JmolList<java.lang.Object> |
getPlaneIntersection(int type,
P4 plane,
float scale,
int flags) |
java.lang.String |
getPointGroupAsString(boolean asDraw,
java.lang.String type,
int index,
float scale) |
java.util.Map<java.lang.String,java.lang.Object> |
getPointGroupInfo(java.lang.Object atomExpression) |
int |
getPolymerCount() |
int |
getPolymerCountInModel(int modelIndex) |
P3[] |
getPolymerLeadMidPoints(int modelIndex,
int polymerIndex) |
void |
getPolymerPointsAndVectors(BS bs,
JmolList<P3[]> vList) |
private java.lang.Object |
getPopupMenu() |
boolean |
getPreserveState()
This flag if set FALSE:
1) turns UNDO off for the application 2) turns history off 3) prevents
saving of inlinedata for later LOAD "" commands 4) turns off the saving of
changed atom properties 5) does not guarantee accurate state representation
6) disallows generation of the state
It is useful in situations such as web sites where memory is an issue and
there is no need for such.
|
java.lang.Object |
getProperty(java.lang.String returnType,
java.lang.String infoType,
java.lang.Object paramInfo) |
java.lang.String |
getPropertyColorScheme() |
private JmolPropertyManager |
getPropertyManager() |
int |
getPropertyNumber(java.lang.String name) |
java.lang.String |
getProteinStructureState() |
char |
getQuaternionFrame() |
boolean |
getRefreshing() |
BS |
getRenderableBitSet() |
(package private) int |
getRotateBondIndex() |
(package private) void |
getRotation(Matrix3f matrixRotation) |
P3 |
getRotationCenter() |
Quaternion |
getRotationQuaternion() |
Rectangle |
getRubberBandSelection() |
java.lang.String |
getSavedCoordinates(java.lang.String saveName) |
java.lang.String |
getSavedState(java.lang.String saveName) |
java.lang.String |
getSavedStructure(java.lang.String saveName) |
float |
getScalePixelsPerAngstrom(boolean asAntialiased) |
java.lang.String[] |
getSceneList() |
int |
getScreenDim() |
int |
getScreenHeight() |
java.lang.Object |
getScreenImageBuffer(java.lang.Object graphic,
boolean isImageWrite)
Image.getJpgImage, ImageCreator.clipImage, getImageBytes,
Viewer.renderScreenImageStereo
|
int |
getScreenWidth() |
ScriptContext |
getScriptContext() |
private JmolScriptManager |
getScriptManager() |
java.lang.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(java.lang.String specInfo,
BS bs) |
java.lang.String |
getSetHistory(int howFarBack)
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n ==
-1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off;
return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
|
java.lang.String |
getShapeErrorState() |
java.util.Map<java.lang.String,java.lang.Object> |
getShapeInfo() |
ShapeManager |
getShapeManager() |
java.lang.Object |
getShapeProperty(int shapeType,
java.lang.String propertyName) |
private int |
getShapePropertyAsInt(int shapeID,
java.lang.String propertyName) |
boolean |
getShapePropertyData(int shapeType,
java.lang.String propertyName,
java.lang.Object[] data) |
java.lang.Object |
getShapePropertyIndex(int shapeType,
java.lang.String propertyName,
int index) |
void |
getShapeSetState(AtomShape atomShape,
Shape shape,
int monomerCount,
Group[] monomers,
BS bsSizeDefault,
java.util.Map<java.lang.String,BS> temp,
java.util.Map<java.lang.String,BS> temp2) |
java.lang.String |
getShapeState(Shape shape) |
boolean |
getShowAxes() |
boolean |
getShowBbcage() |
boolean |
getShowFrank() |
boolean |
getShowNavigationPoint() |
boolean |
getShowUnitCell() |
boolean |
getSlabEnabled() |
BS |
getSmartsMatch(java.lang.String smarts,
BS bsSelected) |
java.lang.String |
getSmiles(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() |
java.util.Map<java.lang.String,java.lang.Object> |
getSpaceGroupInfo(java.lang.String spaceGroup) |
java.lang.String |
getSpecularState() |
boolean |
getSpinOn() |
java.lang.String |
getSpinState() |
java.lang.String |
getStandardLabelFormat(int type) |
JmolStateCreator |
getStateCreator() |
java.lang.String |
getStateInfo() |
java.lang.String |
getStateInfo3(java.lang.String type,
int width,
int height) |
(package private) JmolList<JmolList<JmolList<java.lang.Object>>> |
getStatusChanged(java.lang.String statusNameList) |
(package private) StatusManager |
getStatusManager() |
int |
getStrandCount(int type) |
java.util.Map<EnumStructure,float[]> |
getStructureList() |
java.lang.String |
getStructureState() |
(package private) int |
getSurfaceDistanceMax() |
SymmetryInterface |
getSymmetry() |
java.lang.Object |
getSymmetryInfo(BS bsAtoms,
java.lang.String xyz,
int op,
P3 pt,
P3 pt2,
java.lang.String id,
int type) |
java.lang.String |
getSymmetryInfoAsString() |
java.lang.String |
getSymmetryOperation(java.lang.String spaceGroup,
int symop,
P3 pt1,
P3 pt2,
boolean labelOnly) |
BS |
getTaintedAtoms(byte type) |
boolean |
getTestFlag(int i) |
java.util.Map<java.lang.String,java.lang.Object> |
getTimeouts() |
java.lang.String |
getTrajectoryState() |
java.lang.String |
getTransformText() |
java.lang.String |
getTranslationScript() |
float |
getTranslationXPercent() |
float |
getTranslationYPercent() |
(package private) float |
getTranslationZPercent() |
private BS |
getUndeletedGroupAtomBits(BS bs) |
float |
getUnitCellInfo(int infoType) |
java.lang.String |
getUnitCellInfoText() |
Matrix4f |
getUnscaledTransformMatrix() |
int |
getVanderwaalsMar(int i) |
int |
getVanderwaalsMarType(int atomicAndIsotopeNumber,
EnumVdw type) |
java.lang.String |
getVariableList() |
Vibration |
getVibration(int atomIndex) |
java.util.Map<java.lang.String,java.lang.Object> |
getViewerOptions() |
BS |
getVisibleFramesBitSet() |
BS |
getVisibleSet() |
java.lang.Object |
getWrappedState(java.lang.String fileName,
java.lang.String[] scripts,
boolean isImage,
boolean asJmolZip,
int width,
int height) |
java.lang.String |
getZapName() |
boolean |
getZoomEnabled() |
int |
getZoomPercent() |
float |
getZoomPercentFloat() |
float |
getZoomSetting() |
int |
getZShadeStart() |
void |
haltScriptExecution() |
void |
handleError(java.lang.Error er,
boolean doClear) |
boolean |
handleOldJvm10Event(int id,
int x,
int y,
int modifiers,
long time) |
static boolean |
hasDatabasePrefix(java.lang.String fileName) |
boolean |
hasFocus() |
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,
int action) |
void |
hoverOnPt(int x,
int y,
java.lang.String text,
java.lang.String id,
P3 pt) |
void |
initialize(boolean clearUserVariables) |
JmolRendererInterface |
initializeExporter(java.lang.String type,
java.lang.String fileName) |
private void |
initializeModel(boolean isAppend) |
void |
invertAtomCoordPlane(P4 plane,
BS bs) |
void |
invertAtomCoordPt(P3 pt,
BS bs) |
void |
invertSelected(P3 pt,
P4 plane,
int iAtom,
BS invAtoms) |
void |
invertSelection() |
(package private) boolean |
isAnimationOn() |
boolean |
isAntialiased() |
boolean |
isApplet() |
(package private) boolean |
isAtomAssignable(int i) |
boolean |
isAtomPDB(int i) |
boolean |
isAtomSelected(int atomIndex) |
boolean |
isBound(int action,
int gesture) |
static boolean |
isDatabaseCode(char ch) |
boolean |
isFunction(java.lang.String name) |
boolean |
isHeadless() |
boolean |
isInPosition(V3 axis,
float degrees) |
(package private) boolean |
isInSelectionSubset(int atomIndex) |
boolean |
isJmolDataFrame() |
boolean |
isJmolDataFrameForModel(int modelIndex) |
boolean |
isJmolVariable(java.lang.String key) |
boolean |
isJS() |
(package private) boolean |
isKiosk() |
boolean |
isModelPDB(int i) |
boolean |
isMovie() |
boolean |
isNavigating() |
boolean |
isParallel() |
boolean |
isPreviewOnly() |
boolean |
isRepaintPending() |
boolean |
isRestricted(Viewer.ACCESS a) |
boolean |
isScriptExecuting() |
private boolean |
isScriptQueued() |
boolean |
isSelected(int atomIndex) |
boolean |
isSignedApplet() |
private static boolean |
isStaticFunction(java.lang.String name) |
(package private) boolean |
isStereoDouble() |
boolean |
isTrajectory(int modelIndex) |
boolean |
isVibrationOn() |
boolean |
isWindowCentered() |
private void |
jmolTest() |
java.lang.String |
jsEval(java.lang.String strEval) |
java.lang.String |
listSavedStates() |
private java.lang.String |
loadAtomDataAndReturnError(java.lang.Object atomSetCollection,
int tokType)
or just apply the data to the current model set
|
void |
loadImage(java.lang.String pathName,
java.lang.String echoName) |
(package private) void |
loadImageData(java.lang.Object image,
java.lang.String nameOrError,
java.lang.String echoName,
ScriptContext sc) |
java.lang.String |
loadInline(java.util.List<java.lang.Object> arrayData,
boolean isAppend)
does not preserver state, intentionally!
|
java.lang.String |
loadInline(java.lang.String strModel) |
java.lang.String |
loadInline(java.lang.String[] arrayModels) |
java.lang.String |
loadInline(java.lang.String[] arrayModels,
boolean isAppend) |
java.lang.String |
loadInline(java.lang.String strModel,
boolean isAppend) |
java.lang.String |
loadInline(java.lang.String strModel,
char newLine) |
java.lang.String |
loadInlineScript(java.lang.String strModel,
char newLine,
boolean isAppend,
java.util.Map<java.lang.String,java.lang.Object> htParams) |
java.lang.String |
loadModelFromFile(java.lang.String fullPathName,
java.lang.String fileName,
java.lang.String[] fileNames,
java.lang.Object reader,
boolean isAppend,
java.util.Map<java.lang.String,java.lang.Object> htParams,
SB loadScript,
int tokType)
Used by the ScriptEvaluator LOAD command to open one or more files.
|
void |
loadShape(int shapeID) |
void |
log(java.lang.String data) |
int[] |
makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
BS bsA,
BS bsB,
BS bsBonds,
boolean isBonds,
boolean addGroup,
float energy) |
boolean |
menuEnabled() |
void |
mergeShapes(Shape[] newShapes) |
void |
minimize(int steps,
float crit,
BS bsSelected,
BS bsFixed,
float rangeFixed,
boolean addHydrogen,
boolean isSilent,
boolean isLoad2D) |
boolean |
modelHasVibrationVectors(int modelIndex) |
(package private) boolean |
modelSetHasVibrationVectors() |
void |
morph(float frame) |
void |
move(JmolScriptEvaluator eval,
V3 dRot,
float dZoom,
V3 dTrans,
float dSlab,
float floatSecondsTotal,
int fps) |
void |
moveAtoms(Matrix3f mNew,
Matrix3f matrixRotate,
V3 translation,
P3 center,
boolean isInternal,
BS bsAtoms) |
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,
P3 center,
V3 rotAxis,
float degrees,
Matrix3f rotationMatrix,
float zoom,
float xTrans,
float yTrans,
float rotationRadius,
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(V3 rotAxis,
float degrees) |
void |
navigateList(JmolScriptEvaluator eval,
JmolList<java.lang.Object[]> list) |
void |
navigatePt(P3 center) |
void |
navTranslatePercent(float x,
float y) |
boolean |
noGraphicsAllowed() |
void |
notifyError(java.lang.String errType,
java.lang.String errMsg,
java.lang.String errMsgUntranslated) |
void |
notifyMinimizationStatus() |
int |
notifyMouseClicked(int x,
int y,
int action,
int mode) |
void |
notifyViewerRepaintDone() |
java.lang.String |
openDOM(java.lang.Object DOMNode)
applet DOM method -- does not preserve state
|
java.lang.String |
openFile(java.lang.String fileName)
for JmolSimpleViewer -- external applications only (and no-script
JavaScript)
|
void |
openFileAsyncPDB(java.lang.String fileName,
boolean pdbCartoons)
opens a file as a model, a script, or a surface via the creation of a
script that is queued \t at the beginning disallows script option - used by
JmolFileDropper and JmolPanel file-open actions - sets up a script to load
the file
|
private java.lang.Object |
openFileFull(java.lang.String fileName,
boolean isAppend,
java.util.Map<java.lang.String,java.lang.Object> htParams,
SB loadScript) |
java.lang.String |
openFiles(java.lang.String[] fileNames)
for JmolSimpleViewer -- external applications only
|
java.lang.String |
openReader(java.lang.String fullPathName,
java.lang.String fileName,
java.io.Reader reader)
Opens the file, given an already-created reader.
|
java.lang.String |
openStringInline(java.lang.String strModel) |
private java.lang.String |
openStringInlineParams(java.lang.String strModel,
java.util.Map<java.lang.String,java.lang.Object> htParams,
boolean isAppend) |
private java.lang.String |
openStringsInline(java.lang.String[] arrayModels,
java.util.Map<java.lang.String,java.lang.Object> htParams,
boolean isAppend) |
void |
pauseScriptExecution() |
void |
popHoldRepaint() |
void |
popHoldRepaintWhy(java.lang.String why) |
(package private) void |
popupMenu(int x,
int y,
char type) |
void |
processEvent(int groupID,
int eventType,
int touchID,
int iData,
P3 pt,
long time) |
java.lang.String |
prompt(java.lang.String label,
java.lang.String data,
java.lang.String[] list,
boolean asButtons) |
void |
pushHoldRepaint() |
void |
pushHoldRepaintWhy(java.lang.String why) |
void |
rebond() |
void |
rebondState(boolean isStateScript) |
void |
refresh(int mode,
java.lang.String strWhy)
initiate a repaint/update sequence if it has not already been requested.
|
void |
refreshMeasures(boolean andStopMinimization) |
void |
releaseScreenImage() |
java.lang.String |
removeCommand()
Removes one command from the command history
|
void |
removeFunction(java.lang.String name) |
void |
removeSelectionListener(JmolSelectionListener listener) |
void |
removeUserVariable(java.lang.String key) |
private void |
render() |
private void |
render1(java.lang.Object graphic,
java.lang.Object img,
int x,
int y) |
void |
renderScreenImage(java.lang.Object g,
int width,
int height) |
void |
renderScreenImageStereo(java.lang.Object gLeft,
java.lang.Object gRight,
int width,
int height)
an added class for rendering stereo in two independent applets
|
(package private) void |
reportSelection(java.lang.String msg) |
void |
requestRepaintAndWait() |
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) |
Dimension |
resizeInnerPanel(int width,
int height) |
(package private) java.lang.String |
resolveDatabaseFormat(java.lang.String fileName) |
boolean |
restoreBonds(java.lang.String saveName) |
(package private) void |
restoreModelOrientation(int modelIndex) |
(package private) void |
restoreModelRotation(int modelIndex) |
boolean |
restoreOrientation(java.lang.String saveName,
float timeSeconds) |
void |
restoreRotation(java.lang.String saveName,
float timeSeconds) |
void |
restoreScene(java.lang.String saveName,
float timeSeconds) |
boolean |
restoreSelection(java.lang.String saveName) |
boolean |
rotateAboutPointsInternal(JmolScriptEvaluator eval,
P3 point1,
P3 point2,
float degreesPerSecond,
float endDegrees,
boolean isSpin,
BS bsSelected,
V3 translation,
JmolList<P3> finalPoints,
float[] dihedralList) |
(package private) void |
rotateArcBall(int x,
int y,
float factor) |
boolean |
rotateAxisAngleAtCenter(JmolScriptEvaluator eval,
P3 rotCenter,
V3 rotAxis,
float degreesPerSecond,
float endDegrees,
boolean isSpin,
BS bsSelected) |
void |
rotateFront() |
void |
rotatePoint(P3 pt,
P3 ptRot) |
(package private) void |
rotateSelected(float deltaX,
float deltaY,
BS bsSelected) |
void |
rotateX(float angleRadians) |
void |
rotateXDeg(int angleDegrees) |
(package private) void |
rotateXYBy(float xDelta,
float yDelta) |
void |
rotateY(float angleRadians) |
void |
rotateYDeg(int angleDegrees) |
void |
rotateZ(float angleRadians) |
void |
rotateZBy(int zDelta,
int x,
int y) |
java.lang.String |
runScript(java.lang.String script)
run a script immediately and return output buffer string
Jmol 13.1.15
|
void |
saveBonds(java.lang.String saveName) |
void |
saveCoordinates(java.lang.String saveName,
BS bsSelected) |
(package private) void |
saveModelOrientation() |
void |
saveOrientation(java.lang.String saveName,
float[] pymolView) |
void |
saveScene(java.lang.String saveName,
java.util.Map<java.lang.String,java.lang.Object> scene) |
void |
saveSelection(java.lang.String saveName) |
void |
saveState(java.lang.String saveName) |
void |
saveStructure(java.lang.String saveName) |
float |
scaleToPerspective(int z,
float sizeAngstroms) |
float |
scaleToScreen(int z,
int milliAngstroms) |
java.lang.String |
script(java.lang.String strScript) |
java.lang.Object |
scriptCheck(java.lang.String strScript) |
private java.lang.Object |
scriptCheckRet(java.lang.String strScript,
boolean returnContext) |
void |
scriptEcho(java.lang.String strEcho) |
void |
scriptStatus(java.lang.String strStatus) |
void |
scriptStatusMsg(java.lang.String strStatus,
java.lang.String statusMessage) |
java.lang.String |
scriptWait(java.lang.String strScript) |
java.lang.Object |
scriptWaitStatus(java.lang.String strScript,
java.lang.String statusList) |
void |
select(BS bs,
boolean isGroup,
int addRemove,
boolean isQuiet) |
void |
selectAll() |
void |
selectBonds(BS bs) |
void |
setAnimation(int tok) |
void |
setAnimationDirection(int direction) |
void |
setAnimationFps(int fps) |
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 mode,
boolean TF) |
void |
setAppendNew(boolean value) |
(package private) void |
setApplySymmetryToBonds(boolean TF) |
void |
setAtomCoord(int atomIndex,
float x,
float y,
float z) |
void |
setAtomCoordRelative(int atomIndex,
float x,
float y,
float z) |
void |
setAtomCoords(BS bs,
int tokType,
java.lang.Object xyzValues) |
void |
setAtomCoordsRelative(Tuple3f offset,
BS bs) |
void |
setAtomData(int type,
java.lang.String name,
java.lang.String coordinateData,
boolean isDefault) |
void |
setAtomLabel(java.lang.String value,
int i) |
private void |
setAtomPickingOption(java.lang.String option) |
void |
setAtomProperty(BS bs,
int tok,
int iValue,
float fValue,
java.lang.String sValue,
float[] values,
java.lang.String[] list) |
void |
setAutoBond(boolean TF) |
private void |
setAxesModeMolecular(boolean TF) |
(package private) void |
setAxesModeUnitCell(boolean TF) |
void |
setAxesOrientationRasmol(boolean TF) |
(package private) void |
setAxesScale(float scale) |
void |
setBackgroundImage(java.lang.String fileName,
java.lang.Object image) |
void |
setBackgroundModelIndex(int modelIndex) |
void |
setBondParameters(int modelIndex,
int i,
BS bsBonds,
float rad,
float pymolValence,
int argb,
float trans) |
private void |
setBondPickingOption(java.lang.String option) |
void |
setBondTolerance(float bondTolerance) |
void |
setBooleanProperty(java.lang.String key,
boolean value) |
private void |
setBooleanPropertyTok(java.lang.String key,
int tok,
boolean value) |
void |
setBoundBox(P3 pt1,
P3 pt2,
boolean byCorner,
float scale) |
void |
setCenterAt(java.lang.String relativeTo,
P3 pt) |
void |
setCenterBitSet(BS bsCenter,
boolean doScale) |
void |
setCenterSelected() |
void |
setCentroid(BS bs,
int[] minmax) |
void |
setCGO(JmolList<java.lang.Object> info) |
void |
setColorBackground(java.lang.String colorName) |
BS |
setConformation() |
void |
setCurrentCage(java.lang.String isosurfaceId) |
void |
setCurrentCagePts(P3[] points) |
void |
setCurrentColorRange(float min,
float max) |
void |
setCurrentColorRange(java.lang.String label) |
void |
setCurrentColorRangeData(float[] data,
BS bs) |
void |
setCurrentModelID(java.lang.String id) |
void |
setCurrentModelIndex(int modelIndex) |
void |
setCurrentModelIndexClear(int modelIndex,
boolean clearBackground) |
void |
setCurrentUnitCellOffset(int ijk) |
void |
setCurrentUnitCellOffsetPt(P3 pt) |
void |
setCursor(int cursor) |
void |
setData(java.lang.String type,
java.lang.Object[] data,
int arrayCount,
int matchField,
int matchFieldColumnCount,
int field,
int fieldColumnCount) |
void |
setDebugScript(boolean debugScript) |
private void |
setDefaultColors(boolean isRasmol) |
void |
setDefaultLattice(P3 ptLattice) |
private void |
setDefaults() |
private void |
setDefaultsType(java.lang.String type) |
(package private) void |
setDefaultVdw(java.lang.String type) |
void |
setDihedrals(float[] dihedralList,
BS[] bsBranches,
float rate) |
void |
setDisplay(java.lang.Object canvas) |
(package private) void |
setDynamicMeasurements(boolean TF) |
void |
setEchoStateActive(boolean TF) |
void |
setElementArgb(int elementNumber,
int argb) |
java.lang.String |
setErrorMessage(java.lang.String errMsg,
java.lang.String errMsgUntranslated) |
void |
setFileInfo(java.lang.String[] fileInfo) |
private void |
setFileLoadStatus(EnumFileStatus ptLoad,
java.lang.String fullPathName,
java.lang.String fileName,
java.lang.String modelName,
java.lang.String strError,
java.lang.Boolean isAsync) |
void |
setFloatProperty(java.lang.String key,
float value) |
private void |
setFloatPropertyTok(java.lang.String key,
int tok,
float value) |
void |
setFocus() |
void |
setFormalCharges(int formalCharge) |
void |
setFrame(int i) |
void |
setFrameDelayMs(long millis) |
(package private) void |
setFrameOffset(int modelIndex) |
void |
setFrameOffsets(BS bsAtoms) |
void |
setFrameTitle(int modelIndex,
java.lang.String title) |
void |
setFrameTitleObj(java.lang.Object title) |
(package private) void |
setFrameVariables() |
void |
setFrankOn(boolean TF) |
void |
setHoverLabel(java.lang.String strLabel) |
void |
setInMotion(boolean inMotion) |
void |
setIntProperty(java.lang.String key,
int value) |
private void |
setIntPropertyTok(java.lang.String key,
int tok,
int value) |
void |
setIteratorForAtom(AtomIndexIterator iterator,
int atomIndex,
float distance) |
void |
setIteratorForPoint(AtomIndexIterator iterator,
int modelIndex,
P3 pt,
float distance) |
void |
setJmolCallbackListener(JmolCallbackListener jmolCallbackListener) |
void |
setJmolDataFrame(java.lang.String type,
int modelIndex,
int dataIndex) |
void |
setJmolDefaults() |
void |
setJmolStatusListener(JmolStatusListener jmolStatusListener) |
void |
setLigandModel(java.lang.String id,
java.lang.String data) |
java.lang.Object |
setLoadFormat(java.lang.String name,
char type,
boolean withPrefix)
Jmol will either specify a type or look for it in the first character,
making sure it is found using isDatabaseCode() first.
|
private java.util.Map<java.lang.String,java.lang.Object> |
setLoadParameters(java.util.Map<java.lang.String,java.lang.Object> htParams,
boolean isAppend) |
private java.lang.String |
setLogFile(java.lang.String value) |
void |
setMarBond(short marBond) |
private void |
setMaximumSize(int x) |
void |
setMenu(java.lang.String fileOrText,
boolean isFile) |
void |
setMeshCreator(java.lang.Object meshCreator)
an external applet or app with class that extends org.jmol.jvxl.MeshCreator
might execute:
org.jmol.viewer.Viewer 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 |
setMotionFixedAtoms(BS bs) |
void |
setMouseEnabled(boolean TF) |
private BS |
setMovableBitSet(BS bsSelected,
boolean checkMolecule) |
void |
setMovie(java.util.Map<java.lang.String,java.lang.Object> info) |
void |
setNavigationDepthPercent(float percent) |
private void |
setNavigationMode(boolean TF) |
void |
setNavOn(boolean navOn) |
void |
setNavXYZ(float x,
float y,
float z) |
void |
setNewRotationCenter(P3 center) |
void |
setNoneSelected(boolean noneSelected) |
void |
setObjectArgb(java.lang.String name,
int argb) |
(package private) void |
setObjectColor(java.lang.String name,
java.lang.String colorName) |
void |
setObjectMad(int iShape,
java.lang.String name,
int mad) |
java.lang.String |
setObjectProp(java.lang.String id,
int tokCommand) |
void |
setObjectVisibility(java.lang.String name,
boolean b) |
private void |
setOptions(java.util.Map<java.lang.String,java.lang.Object> info) |
boolean |
setParallel(boolean TF) |
void |
setPdbConectBonding(boolean isAuto,
boolean isStateScript) |
(package private) void |
setPendingMeasurement(MeasurementPending measurementPending) |
void |
setPercentVdwAtom(int value) |
void |
setPerspectiveDepth(boolean perspectiveDepth) |
void |
setPicked(int iAtom) |
(package private) void |
setPickingMode(java.lang.String strMode,
int pickingMode) |
(package private) void |
setPickingStyle(java.lang.String style,
int pickingStyle) |
void |
setPrivateKeyForShape(int iShape) |
void |
setPropertyColorScheme(java.lang.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) |
(package private) void |
setRotationMatrix(Matrix3f rotationMatrix) |
void |
setRotationRadius(float angstroms,
boolean doAll) |
void |
setRubberbandArgb(int argb) |
void |
setScreenDimension(int width,
int height) |
private void |
setScriptQueue(boolean TF) |
void |
setScriptStatus(java.lang.String strStatus,
java.lang.String statusMessage,
int msWalltime,
java.lang.String strErrorMessageUntranslated) |
void |
setSelectedAtom(int atomIndex,
boolean TF) |
void |
setSelectionHalos(boolean TF) |
void |
setSelectionSet(BS set) |
void |
setSelectionSubset(BS subset) |
void |
setShapeErrorState(int shapeID,
java.lang.String state) |
void |
setShapeProperty(int shapeID,
java.lang.String propertyName,
java.lang.Object value) |
void |
setShapeSize(int shapeID,
int mad,
BS bsSelected) |
void |
setShapeSizeRD(int shapeID,
RadiusData rd,
BS bsAtoms) |
void |
setShowAxes(boolean value) |
void |
setShowBbcage(boolean value) |
void |
setShowHydrogens(boolean TF) |
void |
setShowMeasurements(boolean TF) |
void |
setShowUnitCell(boolean value) |
void |
setSlabDepthInternal(boolean isDepth) |
void |
setSmilesString(java.lang.String s) |
void |
setSpin(java.lang.String key,
int value) |
void |
setSpinOn(boolean spinOn) |
private void |
setStartupBooleans() |
void |
setStateScriptVersion(java.lang.String version) |
void |
setStatusAtomHovered(int atomIndex,
java.lang.String info) |
void |
setStatusAtomPicked(int atomIndex,
java.lang.String info) |
(package private) void |
setStatusFrameChanged(boolean isVib) |
void |
setStatusMeasuring(java.lang.String status,
int intInfo,
java.lang.String strMeasure,
float value) |
void |
setStatusObjectHovered(java.lang.String id,
java.lang.String info,
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(java.lang.String key,
java.lang.String value) |
private void |
setStringPropertyTok(java.lang.String key,
int tok,
java.lang.String value) |
void |
setStructureList(float[] list,
EnumStructure type) |
private void |
setSync() |
(package private) void |
setSyncDriver(int mode) |
private void |
setSyncTarget(int mode,
boolean TF) |
void |
setTainted(boolean TF) |
void |
setTaintedAtoms(BS bs,
byte type) |
void |
setTimeout(java.lang.String name,
int mSec,
java.lang.String script) |
(package private) void |
setTrajectory(int modelIndex) |
void |
setTrajectoryBs(BS bsModels) |
private void |
setTransformManagerDefaults() |
void |
setUnits(java.lang.String units,
boolean isDistance) |
void |
setUserScale(int[] scale) |
SV |
setUserVariable(java.lang.String name,
SV value) |
void |
setVectorScale(float scale) |
void |
setVibrationOff() |
void |
setVibrationPeriod(float period) |
void |
setVibrationScale(float scale) |
void |
setZslabPoint(P3 pt) |
void |
show2D(java.lang.String smiles) |
void |
showConsole(boolean showConsole) |
void |
showMessage(java.lang.String s) |
void |
showNMR(java.lang.String smiles) |
void |
showParameter(java.lang.String key,
boolean ifNotSet,
int nMax) |
void |
showString(java.lang.String str,
boolean isPrint) |
java.lang.String |
showTimeout(java.lang.String name) |
void |
showUrl(java.lang.String urlString) |
(package private) void |
slabByPixels(int pixels) |
(package private) void |
slabDepthByPixels(int pixels) |
void |
slabInternal(P4 plane,
boolean isDepth) |
void |
slabReset() |
void |
slabToPercent(int percentSlab) |
void |
spinXYBy(int xDelta,
int yDelta,
float speed) |
void |
startHoverWatcher(boolean tf) |
void |
startSpinningAxis(P3 pt1,
P3 pt2,
boolean isClockwise) |
(package private) void |
stopMinimization() |
void |
stopMotion() |
private void |
stopScriptDelayThread() |
java.lang.String |
streamFileData(java.lang.String fileName,
java.lang.String type,
java.lang.String type2,
int modelIndex,
java.lang.Object[] parameters) |
void |
syncScript(java.lang.String script,
java.lang.String applet,
int port) |
void |
toCartesian(P3 pt,
boolean asAbsolute)
absolute or relative to origin of UNITCELL {x y z}
|
void |
toFractional(P3 pt,
boolean asAbsolute)
absolute or relative to origin of UNITCELL {x y z}
|
void |
togglePickingLabel(BS bs) |
void |
toUnitCell(P3 pt,
P3 offset)
relative to origin without regard to UNITCELL {x y z}
|
void |
transformPoints(P3[] pointsAngstroms,
P3i[] pointsScreens) |
P3i |
transformPt(P3 pointAngstroms) |
void |
transformPt3f(P3 pointAngstroms,
P3 pointScreen) |
void |
transformPtNoClip(P3 pointAngstroms,
P3 pt) |
void |
transformPtScr(P3 pointAngstroms,
P3i pointScreen) |
P3i |
transformPtVib(P3 pointAngstroms,
Vibration vibrationVector) |
void |
transformVector(V3 vectorAngstroms,
V3 vectorTransformed) |
void |
translate(char xyz,
float x,
char type,
BS bsAtoms) |
void |
translateXYBy(int xDelta,
int yDelta) |
void |
triggerTimeout(java.lang.String name) |
void |
unBindAction(java.lang.String desc,
java.lang.String name) |
(package private) void |
undoClear() |
void |
undoMoveAction(int action,
int n) |
(package private) void |
undoMoveActionClear(int taintedAtom,
int type,
boolean clearRedo) |
float |
unscaleToScreen(float z,
float screenDistance) |
void |
unsetProperty(java.lang.String key) |
void |
unTransformPoint(P3 pointScreen,
P3 pointAngstroms) |
void |
updateJS(int width,
int height)
for JavaScript only
|
private boolean |
updateWindow(int width,
int height) |
boolean |
useMinimizationThread() |
void |
writeTextFile(java.lang.String fileName,
java.lang.String data) |
void |
zap(boolean notify,
boolean resetUndo,
boolean zapModelKit) |
private void |
zapMsg(java.lang.String msg) |
(package private) void |
zoomBy(int pixels) |
(package private) void |
zoomByFactor(float factor,
int x,
int y) |
int |
zValueFromPercent(int zPercent) |
allocateViewer, allocateViewer, checkOption, getFileAdapter, getJmolValueAsString, getJsObjectInfo, mouseEvent, openFileAsync, renderScreenImage, setConsole
public boolean autoExit
public boolean haveDisplay
public boolean isJS
public boolean isWebGL
public boolean isSingleThreaded
public boolean queueOnHold
public java.lang.String fullName
public java.lang.String appletDocumentBase
public java.lang.String appletCodeBase
public static java.lang.String jsDocumentBase
public java.lang.Object compiler
public java.util.Map<java.lang.String,java.lang.Object> definedAtomSets
public ModelSet modelSet
public FileManager fileManager
boolean isApplet
boolean isSyntaxAndFileCheck
boolean isSyntaxCheck
boolean listCommands
boolean mustRender
java.lang.String htmlName
java.lang.String insertedCommand
GData gdata
java.lang.Object applet
ActionManager actionManager
AnimationManager animationManager
ColorManager colorManager
DataManager dataManager
ShapeManager shapeManager
SelectionManager selectionManager
JmolRepaintManager repaintManager
public StateManager.GlobalSettings global
StatusManager statusManager
TransformManager transformManager
private static final java.lang.String strJavaVendor
private static final java.lang.String strOSName
private static final java.lang.String strJavaVersion
private java.lang.String syncId
private java.lang.String logFilePath
private boolean allowScripting
private boolean isPrintOnly
private boolean isSignedApplet
private boolean isSignedAppletLocal
private boolean isSilent
private boolean multiTouch
private boolean noGraphicsAllowed
private boolean useCommandThread
private java.lang.String commandOptions
private java.util.Map<java.lang.String,java.lang.Object> viewerOptions
private java.lang.Object display
private JmolAdapter modelAdapter
private Viewer.ACCESS access
private CommandHistory commandHistory
private SymmetryInterface symmetry
private SmilesMatcherInterface smilesMatcher
private ModelManager modelManager
private StateManager stateManager
private JmolScriptManager scriptManager
JmolScriptEvaluator eval
private TempArray tempArray
private static java.lang.String version_date
private boolean isPreviewOnly
private JmolMouseInterface mouse
private boolean mouseEnabled
private boolean noneSelected
java.util.Map<java.lang.String,java.lang.Object> ligandModels
java.util.Map<java.lang.String,java.lang.Boolean> ligandModelSet
JmolStateCreator sc
BS bsFrameOffsets
P3[] frameOffsets
boolean wasInMotion
int motionEventNumber
private boolean refreshing
private boolean axesAreTainted
final Dimension dimScreen
private int maximumSize
private float imageFontScaling
private boolean antialiasDisplay
int hoverAtomIndex
java.lang.String hoverText
public boolean hoverEnabled
private int currentCursor
int prevFrame
private boolean haveJDX
private JmolJSpecView jsv
private java.lang.String language
private RadiusData rd
private boolean frankOn
public boolean scriptEditorVisible
JmolAppConsoleInterface appConsole
JmolScriptEditorInterface scriptEditor
JmolPopupInterface jmolpopup
private JmolPopupInterface modelkitPopup
private java.lang.Object[] headlessImage
JmolPropertyManager pm
boolean isTainted
private boolean movingSelected
private boolean showSelected
private int rotateBondIndex
private int rotatePrev1
private int rotatePrev2
private BS bsRotateBranch
public boolean creatingImage
public static final java.lang.String SYNC_GRAPHICS_MESSAGE
public static final java.lang.String SYNC_NO_GRAPHICS_MESSAGE
private java.lang.String errorMessage
private java.lang.String errorMessageUntranslated
private int currentShapeID
private java.lang.String currentShapeState
static final java.util.Map<java.lang.String,JmolScriptFunction> staticFunctions
java.util.Map<java.lang.String,JmolScriptFunction> localFunctions
private double privateKey
java.lang.String logFile
boolean isKiosk
private MinimizerInterface minimizer
private java.lang.Object executor
public static int nProcessors
public boolean displayLoadErrors
boolean isParallel
final JmolList<java.lang.String> actionStates
final JmolList<java.lang.String> actionStatesRedo
private int stateScriptVersionInt
private JmolRendererInterface jsExporter3D
java.util.Map<java.lang.String,java.lang.String[][]> htPdbBondInfo
java.util.Map<java.lang.String,java.lang.Object> timeouts
private JmolThread scriptDelayThread
public java.util.Map<java.lang.Object,java.lang.Object> chainMap
public JmolList<java.lang.String> chainList
JmolNMRInterface nmrCalculation
public Viewer(java.util.Map<java.lang.String,java.lang.Object> info)
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"protected void finalize() throws java.lang.Throwable
finalize
in class java.lang.Object
java.lang.Throwable
public static java.lang.String getJmolVersion()
protected static JmolViewer allocateViewer(java.lang.Object display, JmolAdapter modelAdapter, java.lang.String fullName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions, JmolStatusListener statusListener, ApiPlatform implementedPlatform)
display
- modelAdapter
- fullName
- documentBase
- codeBase
- commandOptions
- statusListener
- implementedPlatform
- public StateManager.GlobalSettings getGlobalSettings()
StatusManager getStatusManager()
public boolean isApplet()
isApplet
in class JmolViewer
public boolean isJS()
public boolean isRestricted(Viewer.ACCESS a)
public JmolAdapter getModelAdapter()
getModelAdapter
in class JmolViewer
public SymmetryInterface getSymmetry()
public java.lang.Object getSymmetryInfo(BS bsAtoms, java.lang.String xyz, int op, P3 pt, P3 pt2, java.lang.String id, int type)
public SmilesMatcherInterface getSmilesMatcher()
public BS getSmartsMatch(java.lang.String smarts, BS bsSelected)
getSmartsMatch
in class JmolViewer
public java.util.Map<java.lang.String,java.lang.Object> getViewerOptions()
private void setOptions(java.util.Map<java.lang.String,java.lang.Object> info)
public void setDisplay(java.lang.Object canvas)
private JmolScriptManager getScriptManager()
private boolean checkOption2(java.lang.String key1, java.lang.String key2)
public boolean isPreviewOnly()
public boolean isHeadless()
private void setStartupBooleans()
public boolean noGraphicsAllowed()
public java.lang.String getExportDriverList()
public java.lang.String getHtmlName()
public java.lang.Object getDisplay()
getDisplay
in class JmolViewer
public void clearMouse()
public void disposeMouse()
public boolean handleOldJvm10Event(int id, int x, int y, int modifiers, long time)
handleOldJvm10Event
in class JmolViewer
public void reset(boolean includingSpin)
public void homePosition()
homePosition
in class JmolViewer
java.util.Map<java.lang.String,java.lang.Object> getAppletInfo()
public void initialize(boolean clearUserVariables)
public java.lang.String listSavedStates()
public void saveOrientation(java.lang.String saveName, float[] pymolView)
public void saveScene(java.lang.String saveName, java.util.Map<java.lang.String,java.lang.Object> scene)
public void restoreScene(java.lang.String saveName, float timeSeconds)
public boolean restoreOrientation(java.lang.String saveName, float timeSeconds)
public void restoreRotation(java.lang.String saveName, float timeSeconds)
void saveModelOrientation()
public StateManager.Orientation getOrientation()
void restoreModelOrientation(int modelIndex)
void restoreModelRotation(int modelIndex)
public void saveBonds(java.lang.String saveName)
public boolean restoreBonds(java.lang.String saveName)
public void saveState(java.lang.String saveName)
public void deleteSavedState(java.lang.String saveName)
public java.lang.String getSavedState(java.lang.String saveName)
public void saveStructure(java.lang.String saveName)
public java.lang.String getSavedStructure(java.lang.String saveName)
public void saveCoordinates(java.lang.String saveName, BS bsSelected)
public java.lang.String getSavedCoordinates(java.lang.String saveName)
public void saveSelection(java.lang.String saveName)
public boolean restoreSelection(java.lang.String saveName)
public Matrix4f getMatrixtransform()
public Quaternion getRotationQuaternion()
public void setRotationRadius(float angstroms, boolean doAll)
public P3 getRotationCenter()
public void setCenterAt(java.lang.String relativeTo, P3 pt)
public void setCenterBitSet(BS bsCenter, boolean doScale)
public void setNewRotationCenter(P3 center)
public P3 getNavigationCenter()
public float getNavigationDepthPercent()
void navigate(int keyWhere, int modifiers)
public P3 getNavigationOffset()
float getNavigationOffsetPercent(char XorY)
public boolean isNavigating()
public boolean isInPosition(V3 axis, float degrees)
public void move(JmolScriptEvaluator eval, V3 dRot, float dZoom, V3 dTrans, float dSlab, float floatSecondsTotal, int fps)
public void stopMotion()
void setRotationMatrix(Matrix3f rotationMatrix)
public void moveTo(JmolScriptEvaluator eval, float floatSecondsTotal, P3 center, V3 rotAxis, float degrees, Matrix3f rotationMatrix, float zoom, float xTrans, float yTrans, float rotationRadius, P3 navCenter, float xNav, float yNav, float navDepth, float cameraDepth, float cameraX, float cameraY)
public void moveUpdate(float floatSecondsTotal)
java.lang.String getMoveToText(float timespan)
public void navigateList(JmolScriptEvaluator eval, JmolList<java.lang.Object[]> list)
public void navigatePt(P3 center)
public void navigateAxis(V3 rotAxis, float degrees)
public void navTranslatePercent(float x, float y)
public void setMouseEnabled(boolean TF)
public void processEvent(int groupID, int eventType, int touchID, int iData, P3 pt, long time)
processEvent
in class JmolViewer
void zoomBy(int pixels)
void zoomByFactor(float factor, int x, int y)
void rotateXYBy(float xDelta, float yDelta)
public void spinXYBy(int xDelta, int yDelta, float speed)
public void rotateZBy(int zDelta, int x, int y)
void rotateSelected(float deltaX, float deltaY, BS bsSelected)
public void translateXYBy(int xDelta, int yDelta)
void centerAt(int x, int y, P3 pt)
public void rotateFront()
rotateFront
in class JmolViewer
public void rotateX(float angleRadians)
rotateX
in class JmolViewer
public void rotateY(float angleRadians)
rotateY
in class JmolViewer
public void rotateZ(float angleRadians)
rotateZ
in class JmolViewer
public void rotateXDeg(int angleDegrees)
rotateXDeg
in class JmolViewer
public void rotateYDeg(int angleDegrees)
rotateYDeg
in class JmolViewer
public void translate(char xyz, float x, char type, BS bsAtoms)
public float getTranslationXPercent()
public float getTranslationYPercent()
float getTranslationZPercent()
public java.lang.String getTranslationScript()
public int getZShadeStart()
public boolean isWindowCentered()
public int getZoomPercent()
getZoomPercent
in class JmolViewer
public float getZoomSetting()
public float getZoomPercentFloat()
getZoomPercentFloat
in class JmolViewer
public float getMaxZoomPercent()
public void slabReset()
public boolean getZoomEnabled()
public boolean getSlabEnabled()
void slabByPixels(int pixels)
void depthByPixels(int pixels)
void slabDepthByPixels(int pixels)
public void slabInternal(P4 plane, boolean isDepth)
public void slabToPercent(int percentSlab)
public void depthToPercent(int percentDepth)
public void setSlabDepthInternal(boolean isDepth)
public int zValueFromPercent(int zPercent)
public Matrix4f getUnscaledTransformMatrix()
getUnscaledTransformMatrix
in class JmolViewer
public void finalizeTransformParameters()
public float getScalePixelsPerAngstrom(boolean asAntialiased)
public float scaleToScreen(int z, int milliAngstroms)
public float unscaleToScreen(float z, float screenDistance)
public float scaleToPerspective(int z, float sizeAngstroms)
public void setSpin(java.lang.String key, int value)
public java.lang.String getSpinState()
public void setSpinOn(boolean spinOn)
public boolean getSpinOn()
public void setNavOn(boolean navOn)
public boolean getNavOn()
public void setNavXYZ(float x, float y, float z)
public java.lang.String getOrientationText(int type, java.lang.String name)
java.util.Map<java.lang.String,java.lang.Object> getOrientationInfo()
Matrix3f getMatrixRotate()
public void getAxisAngle(AxisAngle4f axisAngle)
public java.lang.String getTransformText()
void getRotation(Matrix3f matrixRotation)
public float[] getCurrentColorRange()
private void setDefaultColors(boolean isRasmol)
public int getColorArgbOrGray(short colix)
public void setRubberbandArgb(int argb)
public short getColixRubberband()
public void setElementArgb(int elementNumber, int argb)
public void setVectorScale(float scale)
setVectorScale
in class JmolViewer
public boolean isVibrationOn()
public void setVibrationScale(float scale)
setVibrationScale
in class JmolViewer
public void setVibrationOff()
public void setVibrationPeriod(float period)
setVibrationPeriod
in class JmolViewer
void setObjectColor(java.lang.String name, java.lang.String colorName)
public void setObjectVisibility(java.lang.String name, boolean b)
public void setObjectArgb(java.lang.String name, int argb)
public void setBackgroundImage(java.lang.String fileName, java.lang.Object image)
int getObjectArgb(int objId)
public short getObjectColix(int objId)
public java.lang.String getFontState(java.lang.String myType, JmolFont font3d)
public void setColorBackground(java.lang.String colorName)
setColorBackground
in class JmolViewer
public int getBackgroundArgb()
getBackgroundArgb
in class JmolViewer
public void setObjectMad(int iShape, java.lang.String name, int mad)
public int getObjectMad(int objId)
public void setPropertyColorScheme(java.lang.String scheme, boolean isTranslucent, boolean isOverloaded)
public java.lang.String getPropertyColorScheme()
public short getColixBackgroundContrast()
public java.lang.String getSpecularState()
public short getColixAtomPalette(Atom atom, byte pid)
public short getColixBondPalette(Bond bond, int pid)
public java.lang.String getColorSchemeList(java.lang.String colorScheme)
public void setUserScale(int[] scale)
public short getColixForPropertyValue(float val)
public P3 getColorPointForPropertyValue(float val)
public void select(BS bs, boolean isGroup, int addRemove, boolean isQuiet)
public void setSelectionSet(BS set)
setSelectionSet
in class JmolViewer
public void selectBonds(BS bs)
public void displayAtoms(BS bs, boolean isDisplay, boolean isGroup, int addRemove, boolean isQuiet)
public BS getHiddenSet()
public boolean isSelected(int atomIndex)
boolean isInSelectionSubset(int atomIndex)
void reportSelection(java.lang.String msg)
private void clearAtomSets()
public BS getDefinedAtomSet(java.lang.String name)
public void selectAll()
selectAll
in class JmolViewer
public void setNoneSelected(boolean noneSelected)
public java.lang.Boolean getNoneSelected()
public void clearSelection()
clearSelection
in class JmolViewer
public void setSelectionSubset(BS subset)
public BS getSelectionSubset()
public void invertSelection()
public BS getSelectionSet(boolean includeDeleted)
public void setSelectedAtom(int atomIndex, boolean TF)
public boolean isAtomSelected(int atomIndex)
public int getSelectionCount()
getSelectionCount
in class JmolViewer
public void setFormalCharges(int formalCharge)
public void addSelectionListener(JmolSelectionListener listener)
addSelectionListener
in class JmolViewer
public void removeSelectionListener(JmolSelectionListener listener)
removeSelectionListener
in class JmolViewer
BS getAtomBitSetEval(JmolScriptEvaluator eval, java.lang.Object atomExpression)
public void setModeMouse(int modeMouse)
setModeMouse
in class JmolViewer
public Rectangle getRubberBandSelection()
public boolean isBound(int action, int gesture)
public int getCursorX()
public int getCursorY()
java.lang.String getDefaultDirectory()
public java.io.BufferedInputStream getBufferedInputStream(java.lang.String fullPathName)
getBufferedInputStream
in interface AtomDataServer
public java.lang.Object getBufferedReaderOrErrorMessageFromName(java.lang.String name, java.lang.String[] fullPathNameReturn, boolean isBinary)
private java.util.Map<java.lang.String,java.lang.Object> setLoadParameters(java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)
public void openFileAsyncPDB(java.lang.String fileName, boolean pdbCartoons)
openFileAsyncPDB
in class JmolViewer
fileName
- public java.lang.String openFile(java.lang.String fileName)
openFile
in class JmolViewer
fileName
- public java.lang.String openFiles(java.lang.String[] fileNames)
openFiles
in class JmolViewer
fileNames
- public java.lang.String openReader(java.lang.String fullPathName, java.lang.String fileName, java.io.Reader reader)
openReader
in class JmolViewer
fullPathName
- fileName
- reader
- public java.lang.String openDOM(java.lang.Object DOMNode)
openDOM
in class JmolViewer
DOMNode
- public java.lang.String loadModelFromFile(java.lang.String fullPathName, java.lang.String fileName, java.lang.String[] fileNames, java.lang.Object reader, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams, SB loadScript, int tokType)
fullPathName
- TODOfileName
- fileNames
- reader
- TODOisAppend
- htParams
- loadScript
- tokType
- public void setLigandModel(java.lang.String id, java.lang.String data)
public java.lang.Object getLigandModel(java.lang.String id)
id
- if null, clear "bad" entries from the set.private java.lang.Object openFileFull(java.lang.String fileName, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams, SB loadScript)
fileName
- isAppend
- htParams
- loadScript
- only necessary for string readingpublic java.lang.String openStringInline(java.lang.String strModel)
openStringInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String strModel)
loadInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String strModel, char newLine)
loadInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String strModel, boolean isAppend)
loadInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String[] arrayModels)
loadInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String[] arrayModels, boolean isAppend)
loadInline
in class JmolViewer
arrayModels
- and array of models, each of which is a Stringpublic java.lang.String loadInline(java.util.List<java.lang.Object> arrayData, boolean isAppend)
loadInline
in class JmolViewer
arrayData
- isAppend
- public java.lang.String loadInlineScript(java.lang.String strModel, char newLine, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams)
public static java.lang.String fixInlineString(java.lang.String strModel, char newLine)
private java.lang.String openStringInlineParams(java.lang.String strModel, java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)
private java.lang.String openStringsInline(java.lang.String[] arrayModels, java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)
public char getInlineChar()
java.lang.String getDataSeparator()
private java.lang.String createModelSetAndReturnError(java.lang.Object atomSetCollection, boolean isAppend, SB loadScript, java.util.Map<java.lang.String,java.lang.Object> htParams)
atomSetCollection
- isAppend
- loadScript
- if null, then some special method like DOM; turn of preserveStatehtParams
- private java.lang.String loadAtomDataAndReturnError(java.lang.Object atomSetCollection, int tokType)
atomSetCollection
- tokType
- public java.lang.String getEmbeddedFileState(java.lang.String filename)
getEmbeddedFileState
in class JmolViewer
public java.lang.Object getFileAsBytes(java.lang.String pathName, java.io.OutputStream os)
getFileAsBytes
in class JmolViewer
public java.lang.String getCurrentFileAsString()
public java.lang.String getFullPathName()
public java.lang.String getFileName()
public java.lang.String[] getFullPathNameOrError(java.lang.String filename)
filename
- public java.lang.String getFileAsString(java.lang.String name)
getFileAsString
in class JmolViewer
public java.lang.String getFileAsString4(java.lang.String name, int nBytesMax, boolean doSpecialLoad, boolean allowBinary)
public boolean getFileAsStringBin(java.lang.String[] data, int nBytesMax, boolean doSpecialLoad)
getFileAsStringBin
in class JmolViewer
private boolean getFileAsStringFM(java.lang.String[] data, int nBytesMax, boolean doSpecialLoad, boolean allowBinary)
public java.lang.String getFilePath(java.lang.String name, boolean asShortName)
public java.lang.String[] getFileInfo()
public void setFileInfo(java.lang.String[] fileInfo)
public void autoCalculate(int tokProperty)
int getSurfaceDistanceMax()
public void calculateStraightness()
public java.util.Map<EnumStructure,float[]> getStructureList()
public void setStructureList(float[] list, EnumStructure type)
public java.lang.String calculateStructures(BS bsAtoms, boolean asDSSP, boolean setStructure)
public AtomIndexIterator getSelectedAtomIterator(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel)
getSelectedAtomIterator
in interface AtomDataServer
public void setIteratorForAtom(AtomIndexIterator iterator, int atomIndex, float distance)
setIteratorForAtom
in interface AtomDataServer
public void setIteratorForPoint(AtomIndexIterator iterator, int modelIndex, P3 pt, float distance)
setIteratorForPoint
in interface AtomDataServer
public void fillAtomData(AtomData atomData, int mode)
fillAtomData
in interface AtomDataServer
public ModelCollection.StateScript addStateScript(java.lang.String script, boolean addFrameNumber, boolean postDefinitions)
public ModelCollection.StateScript addStateScriptRet(java.lang.String script1, BS bsBonds, BS bsAtoms1, BS bsAtoms2, java.lang.String script2, boolean addFrameNumber, boolean postDefinitions)
public boolean getEchoStateActive()
public void setEchoStateActive(boolean TF)
private void clearModelDependentObjects()
public void zap(boolean notify, boolean resetUndo, boolean zapModelKit)
private void zapMsg(java.lang.String msg)
void echoMessage(java.lang.String msg)
private void initializeModel(boolean isAppend)
public void startHoverWatcher(boolean tf)
public java.lang.String getModelSetName()
getModelSetName
in class JmolViewer
public java.lang.String getModelSetFileName()
getModelSetFileName
in class JmolViewer
public java.lang.String getUnitCellInfoText()
public float getUnitCellInfo(int infoType)
public java.util.Map<java.lang.String,java.lang.Object> getSpaceGroupInfo(java.lang.String spaceGroup)
public java.lang.String getModelSetProperty(java.lang.String strProp)
public java.lang.Object getModelSetAuxiliaryInfoValue(java.lang.String strKey)
public java.lang.String getModelSetPathName()
getModelSetPathName
in class JmolViewer
public java.lang.String getModelSetTypeName()
public boolean haveFrame()
haveFrame
in class JmolViewer
boolean haveModelSet()
public void clearBfactorRange()
public java.lang.String getHybridizationAndAxes(int atomIndex, V3 z, V3 x, java.lang.String lcaoType)
public BS getMoleculeBitSet(int atomIndex)
public BS getModelUndeletedAtomsBitSet(int modelIndex)
public void excludeAtoms(BS bs, boolean ignoreSubset)
public ModelSet getModelSet()
public java.lang.String getBoundBoxCommand(boolean withOptions)
public P3 getBoundBoxCenter()
getBoundBoxCenter
in class JmolViewer
P3 getAverageAtomPoint()
public void calcBoundBoxDimensions(BS bs, float scale)
public float calcRotationRadius(P3 center)
public float calcRotationRadiusBs(BS bs)
public V3 getBoundBoxCornerVector()
getBoundBoxCornerVector
in class JmolViewer
public P3[] getBoundBoxVertices()
java.util.Map<java.lang.String,java.lang.Object> getBoundBoxInfo()
public BS getBoundBoxModels()
public int getBoundBoxCenterX()
public int getBoundBoxCenterY()
public int getModelCount()
getModelCount
in class JmolViewer
public java.lang.String getModelInfoAsString()
public java.lang.String getSymmetryInfoAsString()
public java.lang.String getSymmetryOperation(java.lang.String spaceGroup, int symop, P3 pt1, P3 pt2, boolean labelOnly)
public java.util.Properties getModelSetProperties()
getModelSetProperties
in class JmolViewer
public java.util.Map<java.lang.String,java.lang.Object> getModelSetAuxiliaryInfo()
getModelSetAuxiliaryInfo
in class JmolViewer
public int getModelNumber(int modelIndex)
getModelNumber
in class JmolViewer
public int getModelFileNumber(int modelIndex)
public java.lang.String getModelNumberDotted(int modelIndex)
getModelNumberDotted
in class JmolViewer
public java.lang.String getModelName(int modelIndex)
getModelName
in class JmolViewer
public java.util.Properties getModelProperties(int modelIndex)
getModelProperties
in class JmolViewer
public java.lang.String getModelProperty(int modelIndex, java.lang.String propertyName)
getModelProperty
in class JmolViewer
public java.lang.String getModelFileInfo()
public java.lang.String getModelFileInfoAll()
public java.util.Map<java.lang.String,java.lang.Object> getModelAuxiliaryInfo(int modelIndex)
getModelAuxiliaryInfo
in class JmolViewer
public java.lang.Object getModelAuxiliaryInfoValue(int modelIndex, java.lang.String keyName)
getModelAuxiliaryInfoValue
in class JmolViewer
public int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
boolean modelSetHasVibrationVectors()
public boolean modelHasVibrationVectors(int modelIndex)
modelHasVibrationVectors
in class JmolViewer
public int getChainCount()
getChainCount
in class JmolViewer
public int getChainCountInModel(int modelIndex)
getChainCountInModel
in class JmolViewer
public int getChainCountInModelWater(int modelIndex, boolean countWater)
public int getGroupCount()
getGroupCount
in class JmolViewer
public int getGroupCountInModel(int modelIndex)
getGroupCountInModel
in class JmolViewer
public int getPolymerCount()
getPolymerCount
in class JmolViewer
public int getPolymerCountInModel(int modelIndex)
getPolymerCountInModel
in class JmolViewer
public int getAtomCount()
getAtomCount
in class JmolViewer
public int getAtomCountInModel(int modelIndex)
getAtomCountInModel
in class JmolViewer
public int getBondCount()
getBondCount
in class JmolViewer
public int getBondCountInModel(int modelIndex)
getBondCountInModel
in class JmolViewer
modelIndex
- the model of interest or -1 for allpublic boolean frankClicked(int x, int y)
public boolean frankClickedModelKit(int x, int y)
public int findNearestAtomIndex(int x, int y)
findNearestAtomIndex
in class JmolViewer
public int findNearestAtomIndexMovable(int x, int y, boolean mustBeMovable)
public void toCartesian(P3 pt, boolean asAbsolute)
pt
- asAbsolute
- TODOpublic void toFractional(P3 pt, boolean asAbsolute)
pt
- asAbsolute
- TODOpublic void toUnitCell(P3 pt, P3 offset)
pt
- offset
- public void setCurrentCage(java.lang.String isosurfaceId)
public void setCurrentCagePts(P3[] points)
public void setCurrentUnitCellOffset(int ijk)
public void setCurrentUnitCellOffsetPt(P3 pt)
public void addUnitCellOffset(P3 pt)
public void setAtomData(int type, java.lang.String name, java.lang.String coordinateData, boolean isDefault)
public void setCenterSelected()
setCenterSelected
in class JmolViewer
void setApplySymmetryToBonds(boolean TF)
public void setBondTolerance(float bondTolerance)
setBondTolerance
in class JmolViewer
public void setMinBondDistance(float minBondDistance)
setMinBondDistance
in class JmolViewer
public int[] getAtomIndices(BS bs)
public BS getAtomBits(int tokType, java.lang.Object specInfo)
public BS getAtomsWithinRadius(float distance, BS bs, boolean withinAllModels, RadiusData rd)
public BS getBranchBitSet(int atomIndex, int atomIndexNot, boolean allowCyclic)
public int getAtomIndexFromAtomNumber(int atomNumber)
public BS getElementsPresentBitSet(int modelIndex)
getElementsPresentBitSet
in class JmolViewer
public java.util.Map<java.lang.String,java.lang.String> getHeteroList(int modelIndex)
getHeteroList
in class JmolViewer
public BS getVisibleSet()
public BS getClickableSet()
public void calcSelectedGroupsCount()
public void calcSelectedMonomersCount()
public void calcSelectedMoleculesCount()
java.lang.String getFileHeader()
java.lang.Object getFileData()
public java.util.Map<java.lang.String,java.lang.Object> getCifData(int modelIndex)
public java.lang.String getPDBHeader()
public java.util.Map<java.lang.String,java.lang.Object> getAuxiliaryInfo(java.lang.Object atomExpression)
public java.lang.String getChimeInfo(int tok)
public JmolStateCreator getStateCreator()
public java.lang.Object getWrappedState(java.lang.String fileName, java.lang.String[] scripts, boolean isImage, boolean asJmolZip, int width, int height)
public java.lang.String getStateInfo()
getStateInfo
in class JmolViewer
public java.lang.String getStateInfo3(java.lang.String type, int width, int height)
public java.lang.String getStructureState()
public java.lang.String getProteinStructureState()
public java.lang.String getCoordinateState(BS bsSelected)
public void setCurrentColorRange(java.lang.String label)
public void setCurrentColorRangeData(float[] data, BS bs)
public void setCurrentColorRange(float min, float max)
public void setData(java.lang.String type, java.lang.Object[] data, int arrayCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)
public java.lang.Object[] getData(java.lang.String type)
public float[] getDataFloat(java.lang.String label)
public float[][] getDataFloat2D(java.lang.String label)
public float[][][] getDataFloat3D(java.lang.String label)
public float getDataFloatAt(java.lang.String label, int atomIndex)
public java.lang.String getAltLocListInModel(int modelIndex)
getAltLocListInModel
in class JmolViewer
public BS setConformation()
public BS getConformation(int iModel, int conformationIndex, boolean doSet)
public boolean havePartialCharges()
havePartialCharges
in class JmolViewer
public SymmetryInterface getCurrentUnitCell()
public SymmetryInterface getModelUnitCell(int modelIndex)
public java.lang.String getDefaultMeasurementLabel(int nPoints)
public int getMeasurementCount()
getMeasurementCount
in class JmolViewer
public java.lang.String getMeasurementStringValue(int i)
getMeasurementStringValue
in class JmolViewer
JmolList<java.util.Map<java.lang.String,java.lang.Object>> getMeasurementInfo()
public java.lang.String getMeasurementInfoAsString()
public int[] getMeasurementCountPlusIndices(int i)
getMeasurementCountPlusIndices
in class JmolViewer
void setPendingMeasurement(MeasurementPending measurementPending)
MeasurementPending getPendingMeasurement()
public void clearAllMeasurements()
public void clearMeasurements()
clearMeasurements
in class JmolViewer
public void setAnimation(int tok)
public void setAnimationDirection(int direction)
int getAnimationDirection()
java.util.Map<java.lang.String,java.lang.Object> getAnimationInfo()
public void setAnimationFps(int fps)
setAnimationFps
in class JmolViewer
public void setAnimationReplayMode(EnumAnimationMode replayMode, float firstFrameDelay, float lastFrameDelay)
EnumAnimationMode getAnimationReplayMode()
public void setAnimationOn(boolean animationOn)
public void setAnimationRange(int modelIndex1, int modelIndex2)
public BS getVisibleFramesBitSet()
getVisibleFramesBitSet
in class JmolViewer
boolean isAnimationOn()
public void setMovie(java.util.Map<java.lang.String,java.lang.Object> info)
public void setAnimMorphCount(int n)
public boolean isMovie()
public int getFrameCount()
public void defineAtomSets(java.util.Map<java.lang.String,java.lang.Object> info)
public void morph(float frame)
public void setAnimDisplay(BS bs)
public void setCurrentModelIndex(int modelIndex)
void setTrajectory(int modelIndex)
public void setTrajectoryBs(BS bsModels)
public boolean isTrajectory(int modelIndex)
public BS getBitSetTrajectories()
public java.lang.String getTrajectoryState()
void setFrameOffset(int modelIndex)
public void setFrameOffsets(BS bsAtoms)
public BS getFrameOffsets()
public void setCurrentModelIndexClear(int modelIndex, boolean clearBackground)
public int getCurrentModelIndex()
public int getDisplayModelIndex()
getDisplayModelIndex
in class JmolViewer
public boolean haveFileSet()
public void setBackgroundModelIndex(int modelIndex)
void setFrameVariables()
public int getMotionEventNumber()
getMotionEventNumber
in class JmolViewer
public void setInMotion(boolean inMotion)
setInMotion
in class JmolViewer
public boolean getInMotion(boolean includeAnim)
private void setRefreshing(boolean TF)
public boolean getRefreshing()
public void pushHoldRepaint()
pushHoldRepaint
in class JmolViewer
public void pushHoldRepaintWhy(java.lang.String why)
why
- public void popHoldRepaint()
popHoldRepaint
in class JmolViewer
public void popHoldRepaintWhy(java.lang.String why)
public void refresh(int mode, java.lang.String strWhy)
refresh
in class JmolViewer
mode
- strWhy
- public void requestRepaintAndWait()
public void clearShapeRenderers()
public boolean isRepaintPending()
public void notifyViewerRepaintDone()
notifyViewerRepaintDone
in class JmolViewer
public boolean areAxesTainted()
private void setMaximumSize(int x)
public void setScreenDimension(int width, int height)
setScreenDimension
in class JmolViewer
public float getImageFontScaling()
void resizeImage(int width, int height, boolean isImageWrite, boolean isExport, boolean isReset)
public int getScreenWidth()
getScreenWidth
in class JmolViewer
public int getScreenHeight()
getScreenHeight
in class JmolViewer
public int getScreenDim()
public java.lang.String generateOutputForExport(java.lang.String type, java.lang.String[] fileName, int width, int height)
generateOutputForExport
in class JmolViewer
private void clearRepaintManager(int iShape)
public void renderScreenImageStereo(java.lang.Object gLeft, java.lang.Object gRight, int width, int height)
JmolViewer
renderScreenImageStereo
in class JmolViewer
public void updateJS(int width, int height)
width
- height
- private boolean updateWindow(int width, int height)
public void renderScreenImage(java.lang.Object g, int width, int height)
renderScreenImage
in class JmolViewer
private java.lang.Object getImage(boolean isDouble, boolean isImageWrite)
isDouble
- isImageWrite
- TODOprivate void beginRendering(boolean isDouble, boolean isImageWrite)
public boolean isAntialiased()
private void render()
private void render1(java.lang.Object graphic, java.lang.Object img, int x, int y)
public java.lang.Object getScreenImageBuffer(java.lang.Object graphic, boolean isImageWrite)
getScreenImageBuffer
in class JmolViewer
public java.lang.Object getImageAs(java.lang.String type, int quality, int width, int height, java.lang.String fileName, java.io.OutputStream os)
getImageAs
in class JmolViewer
type
- "PNG", "JPG", "JPEG", "JPG64", "PPM", "GIF"public java.lang.Object getImageAsWithComment(java.lang.String type, int quality, int width, int height, java.lang.String fileName, java.lang.String[] scripts, java.io.OutputStream os, java.lang.String comment)
type
- "PNG", "PNGJ", "JPG", "JPEG", "JPG64", "PPM", "GIF"quality
- width
- height
- fileName
- scripts
- os
- comment
- public void releaseScreenImage()
releaseScreenImage
in class JmolViewer
public java.lang.String evalFile(java.lang.String strFilename)
evalFile
in class JmolViewer
public java.lang.String getInsertedCommand()
public java.lang.String script(java.lang.String strScript)
script
in class JmolViewer
public java.lang.String evalString(java.lang.String strScript)
evalString
in class JmolViewer
public java.lang.String evalStringQuiet(java.lang.String strScript)
evalStringQuiet
in class JmolViewer
java.lang.String evalStringQuietSync(java.lang.String strScript, boolean isQuiet, boolean allowSyncScript)
public void clearScriptQueue()
private void setScriptQueue(boolean TF)
public boolean checkHalt(java.lang.String str, boolean isInsert)
checkHalt
in class JmolViewer
public java.lang.String scriptWait(java.lang.String strScript)
scriptWait
in class JmolViewer
public java.lang.Object scriptWaitStatus(java.lang.String strScript, java.lang.String statusList)
scriptWaitStatus
in class JmolViewer
private java.lang.Object evalWait(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList)
public java.lang.Object evalStringWaitStatusQueued(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)
public void exitJmol()
private java.lang.Object scriptCheckRet(java.lang.String strScript, boolean returnContext)
public java.lang.Object scriptCheck(java.lang.String strScript)
scriptCheck
in class JmolViewer
public boolean isScriptExecuting()
isScriptExecuting
in class JmolViewer
public void haltScriptExecution()
haltScriptExecution
in class JmolViewer
public void pauseScriptExecution()
public java.lang.String getDefaultLoadFilter()
public java.lang.String getDefaultLoadScript()
java.lang.String resolveDatabaseFormat(java.lang.String fileName)
public static boolean isDatabaseCode(char ch)
public static boolean hasDatabasePrefix(java.lang.String fileName)
public java.lang.Object setLoadFormat(java.lang.String name, char type, boolean withPrefix)
name
- type
- withPrefix
- public java.lang.String[] getElectronDensityLoadInfo()
public java.lang.String getStandardLabelFormat(int type)
public P3[] getAdditionalHydrogens(BS bsAtoms, boolean doAll, boolean justCarbon, JmolList<Atom> vConnections)
public void setMarBond(short marBond)
setMarBond
in class JmolViewer
public void setHoverLabel(java.lang.String strLabel)
void hoverOn(int atomIndex, int action)
public void hoverOnPt(int x, int y, java.lang.String text, java.lang.String id, P3 pt)
void hoverOff()
public int getBfactor100Hi()
short getColix(java.lang.Object object)
public void setDebugScript(boolean debugScript)
setDebugScript
in class JmolViewer
void clearClickCount()
public int getCursor()
public void setCursor(int cursor)
void setPickingMode(java.lang.String strMode, int pickingMode)
public int getPickingMode()
void setPickingStyle(java.lang.String style, int pickingStyle)
public boolean getDrawHover()
public java.lang.String getAtomInfo(int atomOrPointIndex)
getAtomInfo
in class JmolViewer
public java.lang.String getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
private void setSync()
public void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
setJmolCallbackListener
in class JmolViewer
public void setJmolStatusListener(JmolStatusListener jmolStatusListener)
setJmolStatusListener
in class JmolViewer
public java.util.Map<java.lang.String,JmolList<JmolList<java.lang.Object>>> getMessageQueue()
JmolList<JmolList<JmolList<java.lang.Object>>> getStatusChanged(java.lang.String statusNameList)
public boolean menuEnabled()
void popupMenu(int x, int y, char type)
public java.lang.String getMenu(java.lang.String type)
private java.lang.Object getPopupMenu()
public void setMenu(java.lang.String fileOrText, boolean isFile)
void setStatusFrameChanged(boolean isVib)
private boolean doHaveJDX()
private JmolJSpecView getJSV()
public int getJDXBaseModelIndex(int modelIndex)
modelIndex
- public java.lang.Object getJspecViewProperties(java.lang.Object myParam)
public void scriptEcho(java.lang.String strEcho)
private boolean isScriptQueued()
public void notifyError(java.lang.String errType, java.lang.String errMsg, java.lang.String errMsgUntranslated)
public java.lang.String jsEval(java.lang.String strEval)
public void setStatusAtomHovered(int atomIndex, java.lang.String info)
public void setStatusObjectHovered(java.lang.String id, java.lang.String info, P3 pt)
private void setFileLoadStatus(EnumFileStatus ptLoad, java.lang.String fullPathName, java.lang.String fileName, java.lang.String modelName, java.lang.String strError, java.lang.Boolean isAsync)
public java.lang.String getZapName()
public void setStatusMeasuring(java.lang.String status, int intInfo, java.lang.String strMeasure, float value)
public void notifyMinimizationStatus()
public void setStatusAtomPicked(int atomIndex, java.lang.String info)
public void setStatusResized(int width, int height)
public void scriptStatus(java.lang.String strStatus)
public void scriptStatusMsg(java.lang.String strStatus, java.lang.String statusMessage)
public void setScriptStatus(java.lang.String strStatus, java.lang.String statusMessage, int msWalltime, java.lang.String strErrorMessageUntranslated)
private java.lang.String getModelTitle(int modelIndex)
public java.lang.String getModelFileName(int modelIndex)
getModelFileName
in class JmolViewer
java.lang.String dialogAsk(java.lang.String type, java.lang.String fileName)
public void showUrl(java.lang.String urlString)
showUrl
in class JmolViewer
public void setMeshCreator(java.lang.Object meshCreator)
meshCreator
- public void showConsole(boolean showConsole)
public void clearConsole()
public java.lang.Object getParameterEscaped(java.lang.String key)
public java.lang.Object getParameter(java.lang.String key)
getParameter
in class JmolViewer
public SV getOrSetNewVariable(java.lang.String key, boolean doSet)
public void unsetProperty(java.lang.String key)
public java.lang.String getVariableList()
public boolean getBooleanProperty(java.lang.String key)
getBooleanProperty
in class JmolViewer
public int getInt(int tok)
getInt
in class JmolViewer
public int getDelayMaximumMs()
public int getHermiteLevel()
public int getHoverDelay()
public boolean getBoolean(int tok)
getBoolean
in class JmolViewer
public boolean allowEmbeddedScripts()
boolean getDragSelected()
boolean getBondPicking()
public boolean useMinimizationThread()
public float getFloat(int tok)
getFloat
in class JmolViewer
public void setStringProperty(java.lang.String key, java.lang.String value)
setStringProperty
in class JmolViewer
private void setStringPropertyTok(java.lang.String key, int tok, java.lang.String value)
public void setFloatProperty(java.lang.String key, float value)
setFloatProperty
in class JmolViewer
private void setFloatPropertyTok(java.lang.String key, int tok, float value)
public void setIntProperty(java.lang.String key, int value)
setIntProperty
in class JmolViewer
private void setIntPropertyTok(java.lang.String key, int tok, int value)
private static int checkIntRange(int value, int min, int max)
private static float checkFloatRange(float value, float min, float max)
public void setBooleanProperty(java.lang.String key, boolean value)
setBooleanProperty
in class JmolViewer
private void setBooleanPropertyTok(java.lang.String key, int tok, boolean value)
private void setModelKitMode(boolean value)
public java.lang.String getLanguage()
public void setSmilesString(java.lang.String s)
public void removeUserVariable(java.lang.String key)
public boolean isJmolVariable(java.lang.String key)
private void jmolTest()
public void showParameter(java.lang.String key, boolean ifNotSet, int nMax)
public void showString(java.lang.String str, boolean isPrint)
public java.lang.String getAllSettings(java.lang.String prefix)
public java.lang.String getBindingInfo(java.lang.String qualifiers)
public int getIsosurfacePropertySmoothing(boolean asPower)
public void setNavigationDepthPercent(float percent)
public boolean getShowNavigationPoint()
public float getCurrentSolventProbeRadius()
public boolean getTestFlag(int i)
public void setPerspectiveDepth(boolean perspectiveDepth)
setPerspectiveDepth
in class JmolViewer
public void setAxesOrientationRasmol(boolean TF)
setAxesOrientationRasmol
in class JmolViewer
void setAxesScale(float scale)
public P3[] getAxisPoints()
public void resetError()
private void setAxesModeMolecular(boolean TF)
void setAxesModeUnitCell(boolean TF)
public EnumAxesMode getAxesMode()
public boolean getPerspectiveDepth()
getPerspectiveDepth
in class JmolViewer
public void setSelectionHalos(boolean TF)
setSelectionHalos
in class JmolViewer
public boolean getSelectionHaloEnabled(boolean isRenderer)
private void setStrandCount(int type, int value)
public int getStrandCount(int type)
private void setNavigationMode(boolean TF)
private void setTransformManagerDefaults()
public P3[] getCameraFactors()
public float getCameraDepth()
java.lang.String getLoadState(java.util.Map<java.lang.String,java.lang.Object> htParams)
public void setAutoBond(boolean TF)
setAutoBond
in class JmolViewer
public int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy)
public void rebond()
rebond
in class JmolViewer
public void rebondState(boolean isStateScript)
public void setPdbConectBonding(boolean isAuto, boolean isStateScript)
public void setPercentVdwAtom(int value)
setPercentVdwAtom
in class JmolViewer
public RadiusData getDefaultRadiusData()
public short getMadBond()
getMadBond
in class JmolViewer
public short getMarBond()
public byte getModeMultipleBond()
public void setShowHydrogens(boolean TF)
setShowHydrogens
in class JmolViewer
public void setShowBbcage(boolean value)
setShowBbcage
in class JmolViewer
public boolean getShowBbcage()
getShowBbcage
in class JmolViewer
public void setShowUnitCell(boolean value)
public boolean getShowUnitCell()
public void setShowAxes(boolean value)
setShowAxes
in class JmolViewer
public boolean getShowAxes()
getShowAxes
in class JmolViewer
public void setFrankOn(boolean TF)
setFrankOn
in class JmolViewer
public boolean getShowFrank()
public boolean isSignedApplet()
public void setShowMeasurements(boolean TF)
setShowMeasurements
in class JmolViewer
public void setUnits(java.lang.String units, boolean isDistance)
public java.lang.String getMeasureDistanceUnits()
public java.lang.String getEnergyUnits()
public void setAppendNew(boolean value)
public void setRasmolDefaults()
setRasmolDefaults
in class JmolViewer
public void setJmolDefaults()
setJmolDefaults
in class JmolViewer
private void setDefaultsType(java.lang.String type)
private void setDefaults()
private void setAntialias(int mode, boolean TF)
public P3[] allocTempPoints(int size)
public void freeTempPoints(P3[] tempPoints)
public P3i[] allocTempScreens(int size)
public void freeTempScreens(P3i[] tempScreens)
public EnumStructure[] allocTempEnum(int size)
public void freeTempEnum(EnumStructure[] temp)
public JmolFont getFont3D(java.lang.String fontFace, java.lang.String fontStyle, float fontSize)
public java.lang.String formatText(java.lang.String text0)
java.lang.String getElementSymbol(int i)
int getElementNumber(int i)
public java.lang.String getAtomName(int i)
getAtomName
in class JmolViewer
public int getAtomNumber(int i)
getAtomNumber
in class JmolViewer
public Quaternion[] getAtomGroupQuaternions(BS bsAtoms, int nMax)
public Quaternion getAtomQuaternion(int i)
public P3 getAtomPoint3f(int i)
getAtomPoint3f
in class JmolViewer
public float getAtomRadius(int i)
getAtomRadius
in class JmolViewer
public int getAtomArgb(int i)
getAtomArgb
in class JmolViewer
public int getAtomModelIndex(int i)
getAtomModelIndex
in class JmolViewer
public float getBondRadius(int i)
getBondRadius
in class JmolViewer
public int getBondOrder(int i)
getBondOrder
in class JmolViewer
public void assignAromaticBonds()
public void resetAromatic()
public int getBondArgb1(int i)
getBondArgb1
in class JmolViewer
public int getBondModelIndex(int i)
getBondModelIndex
in class JmolViewer
public int getBondArgb2(int i)
getBondArgb2
in class JmolViewer
public P3[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
getPolymerLeadMidPoints
in class JmolViewer
public void setStereoMode(int[] twoColors, EnumStereoMode stereoMode, float degrees)
boolean isStereoDouble()
public java.lang.String getOperatingSystemName()
getOperatingSystemName
in class JmolViewer
public java.lang.String getJavaVendor()
getJavaVendor
in class JmolViewer
public java.lang.String getJavaVersion()
getJavaVersion
in class JmolViewer
public GData getGraphicsData()
public java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
getProperty
in class JmolViewer
returnType
- "JSON", "string", "readable", and anything else returns the Java object.private JmolPropertyManager getPropertyManager()
public java.lang.String getModelExtract(java.lang.Object atomExpression, boolean doTransform, boolean isModelKit, java.lang.String type)
public void setTainted(boolean TF)
public int notifyMouseClicked(int x, int y, int action, int mode)
java.util.Map<java.lang.String,java.lang.Object> checkObjectClicked(int x, int y, int modifiers)
public boolean checkObjectHovered(int x, int y)
void checkObjectDragged(int prevX, int prevY, int x, int y, int action)
public boolean rotateAxisAngleAtCenter(JmolScriptEvaluator eval, P3 rotCenter, V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected)
public boolean rotateAboutPointsInternal(JmolScriptEvaluator eval, P3 point1, P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected, V3 translation, JmolList<P3> finalPoints, float[] dihedralList)
public V3 getModelDipole()
public V3 calculateMolecularDipole()
public void getAtomIdentityInfo(int atomIndex, java.util.Map<java.lang.String,java.lang.Object> info)
public void setDefaultLattice(P3 ptLattice)
public P3 getDefaultLattice()
public BS getTaintedAtoms(byte type)
public void setTaintedAtoms(BS bs, byte type)
public java.lang.String getData(java.lang.String atomExpression, java.lang.String type)
getData
in class JmolViewer
public java.lang.String getModelCml(BS bs, int nAtomsMax, boolean addBonds)
public java.lang.Object getHelixData(BS bs, int tokType)
public java.lang.String getPdbData(BS bs, OutputStringBuilder sb)
public boolean isJmolDataFrameForModel(int modelIndex)
public boolean isJmolDataFrame()
public int getJmolDataFrameIndex(int modelIndex, java.lang.String type)
public void setJmolDataFrame(java.lang.String type, int modelIndex, int dataIndex)
public void setFrameTitle(int modelIndex, java.lang.String title)
public void setFrameTitleObj(java.lang.Object title)
public java.lang.String getFrameTitle()
java.lang.String getJmolFrameType(int modelIndex)
public int getJmolDataSourceFrame(int modelIndex)
public void setAtomProperty(BS bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
public void checkCoordinatesChanged()
public void setAtomCoord(int atomIndex, float x, float y, float z)
public void setAtomCoordRelative(int atomIndex, float x, float y, float z)
public void setAtomCoords(BS bs, int tokType, java.lang.Object xyzValues)
public void moveAtoms(Matrix3f mNew, Matrix3f matrixRotate, V3 translation, P3 center, boolean isInternal, BS bsAtoms)
public void moveSelected(int deltaX, int deltaY, int deltaZ, int x, int y, BS bsSelected, boolean isTranslation, boolean asAtoms)
public void highlightBond(int index, boolean isHover)
public void highlight(BS bs)
void setRotateBondIndex(int index)
int getRotateBondIndex()
void actionRotateBond(int deltaX, int deltaY, int x, int y)
public void refreshMeasures(boolean andStopMinimization)
void setDynamicMeasurements(boolean TF)
public float[][] functionXY(java.lang.String functionName, int nX, int nY)
functionName
- nX
- nY
- public float[][][] functionXYZ(java.lang.String functionName, int nX, int nY, int nZ)
public void showNMR(java.lang.String smiles)
public void getHelp(java.lang.String what)
public void show2D(java.lang.String smiles)
public java.lang.String getChemicalInfo(java.lang.String smiles, char type, java.lang.String info)
public void addCommand(java.lang.String command)
command
- the command to addpublic java.lang.String removeCommand()
public java.lang.String getSetHistory(int howFarBack)
getSetHistory
in class JmolViewer
howFarBack
- number of lines (-1 for next line)public java.io.OutputStream getOutputStream(java.lang.String localName, java.lang.String[] fullPath)
public void writeTextFile(java.lang.String fileName, java.lang.String data)
writeTextFile
in class JmolViewer
public java.lang.String clipImage(java.lang.String text)
clipImage
in class JmolViewer
text
- null here clips image; String clips textpublic java.lang.String createImageSet(java.lang.String fileName, java.lang.String type, java.lang.String text, byte[] bytes, java.lang.String[] scripts, int quality, int width, int height, BS bsFrames, int nVibes, java.lang.String[] fullPath)
fileName
- type
- text
- bytes
- scripts
- quality
- width
- height
- bsFrames
- nVibes
- fullPath
- public java.lang.Object createZip(java.lang.String fileName, java.lang.String type, java.lang.String stateInfo, java.lang.String[] scripts)
public java.lang.Object createImage(java.lang.String fileName, java.lang.String type, java.lang.Object text_or_bytes, int quality, int width, int height)
createImage
in class JmolViewer
public java.lang.Object createImage(java.lang.String fileName, java.lang.String type, java.lang.String text, byte[] bytes, int quality, int width, int height)
JmolImageCreatorInterface getImageCreator()
private void setSyncTarget(int mode, boolean TF)
public void syncScript(java.lang.String script, java.lang.String applet, int port)
syncScript
in class JmolViewer
public int getModelIndexFromId(java.lang.String id)
void setSyncDriver(int mode)
public float[] getPartialCharges()
public float[] getAtomicPotentials(boolean isMep, BS bsSelected, BS bsIgnore, java.lang.String fileName)
isMep
- bsSelected
- bsIgnore
- fileName
- public void setProteinType(EnumStructure type, BS bs)
public P3 getBondPoint3f1(int i)
getBondPoint3f1
in class JmolViewer
public P3 getBondPoint3f2(int i)
getBondPoint3f2
in class JmolViewer
public Vibration getVibration(int atomIndex)
public int getVanderwaalsMar(int i)
public int getVanderwaalsMarType(int atomicAndIsotopeNumber, EnumVdw type)
void setDefaultVdw(java.lang.String type)
public java.lang.String getDefaultVdwTypeNameOrData(int iMode, EnumVdw vType)
public int deleteAtoms(BS bs, boolean fullModels)
public void deleteBonds(BS bsDeleted)
public void deleteModelAtoms(int firstAtomIndex, int nAtoms, BS bsDeleted)
public BS getDeletedAtoms()
public char getQuaternionFrame()
public java.lang.String calculatePointGroup()
public java.util.Map<java.lang.String,java.lang.Object> getPointGroupInfo(java.lang.Object atomExpression)
public java.lang.String getPointGroupAsString(boolean asDraw, java.lang.String type, int index, float scale)
public void loadImage(java.lang.String pathName, java.lang.String echoName)
void loadImageData(java.lang.Object image, java.lang.String nameOrError, java.lang.String echoName, ScriptContext sc)
public java.lang.String cd(java.lang.String dir)
public java.lang.String setErrorMessage(java.lang.String errMsg, java.lang.String errMsgUntranslated)
public java.lang.String getErrorMessage()
getErrorMessage
in class JmolViewer
public java.lang.String getErrorMessageUn()
getErrorMessageUn
in class JmolViewer
public void setShapeErrorState(int shapeID, java.lang.String state)
public java.lang.String getShapeErrorState()
public void handleError(java.lang.Error er, boolean doClear)
public float[] getAtomicCharges()
public java.util.Map<java.lang.String,JmolScriptFunction> getFunctions(boolean isStatic)
public void removeFunction(java.lang.String name)
public JmolScriptFunction getFunction(java.lang.String name)
private static boolean isStaticFunction(java.lang.String name)
public boolean isFunction(java.lang.String name)
public void clearFunctions()
public void addFunction(JmolScriptFunction function)
public java.lang.String getFunctionCalls(java.lang.String selectedFunction)
public void showMessage(java.lang.String s)
public java.lang.String getMoInfo(int modelIndex)
public boolean checkPrivateKey(double privateKey)
checkPrivateKey
in class JmolViewer
privateKey
- public void bindAction(java.lang.String desc, java.lang.String name, P3 range1, P3 range2)
public void unBindAction(java.lang.String desc, java.lang.String name)
public java.lang.Object getMouseInfo()
public int getFrontPlane()
public JmolList<java.lang.Object> getPlaneIntersection(int type, P4 plane, float scale, int flags)
public boolean getPreserveState()
public java.lang.String getLogFile()
private java.lang.String setLogFile(java.lang.String value)
public void log(java.lang.String data)
log
in interface AtomDataServer
boolean isKiosk()
public boolean hasFocus()
public void setFocus()
public MinimizerInterface getMinimizer(boolean createNew)
void stopMinimization()
void clearMinimization()
public java.lang.String getMinimizationInfo()
private void checkMinimization()
public void minimize(int steps, float crit, BS bsSelected, BS bsFixed, float rangeFixed, boolean addHydrogen, boolean isSilent, boolean isLoad2D)
steps
- Integer.MAX_VALUE --> use defaultscrit
- -1 --> use defaultsbsSelected
- bsFixed
- TODOrangeFixed
- addHydrogen
- isSilent
- isLoad2D
- public void setMotionFixedAtoms(BS bs)
public BS getMotionFixedAtoms()
void rotateArcBall(int x, int y, float factor)
void getAtomicPropertyState(SB commands, byte type, BS bs, java.lang.String name, float[] data)
public java.lang.String streamFileData(java.lang.String fileName, java.lang.String type, java.lang.String type2, int modelIndex, java.lang.Object[] parameters)
public java.lang.String getPdbData(int modelIndex, java.lang.String type, java.lang.Object[] parameters)
public java.lang.Object getExecutor()
public java.util.Map<java.lang.String,java.lang.Object> getShapeInfo()
public void togglePickingLabel(BS bs)
public void loadShape(int shapeID)
public void setShapeSize(int shapeID, int mad, BS bsSelected)
public void setShapeSizeRD(int shapeID, RadiusData rd, BS bsAtoms)
public void setShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object value)
public java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName)
public boolean getShapePropertyData(int shapeType, java.lang.String propertyName, java.lang.Object[] data)
public java.lang.Object getShapePropertyIndex(int shapeType, java.lang.String propertyName, int index)
private int getShapePropertyAsInt(int shapeID, java.lang.String propertyName)
public void setModelVisibility()
public void resetShapes(boolean andCreateNew)
public void setAtomLabel(java.lang.String value, int i)
public void deleteShapeAtoms(java.lang.Object[] value, BS bs)
public void resetBioshapes(BS bsAllAtoms)
public float getAtomShapeValue(int tok, Group group, int atomIndex)
public void mergeShapes(Shape[] newShapes)
public ShapeManager getShapeManager()
public boolean setParallel(boolean TF)
public boolean isParallel()
public BS getRenderableBitSet()
private void setAtomPickingOption(java.lang.String option)
private void setBondPickingOption(java.lang.String option)
void undoClear()
public void undoMoveAction(int action, int n)
action
- Token.undo or Token.redon
- number of steps to go back/forward; 0 for all; -1 for clear; -2 for
clear BOTHvoid undoMoveActionClear(int taintedAtom, int type, boolean clearRedo)
public void assignBond(int bondIndex, char type)
public void assignAtom(int atomIndex, P3 pt, java.lang.String type)
public void assignConnect(int index, int index2)
protected void moveAtomWithHydrogens(int atomIndex, int deltaX, int deltaY, int deltaZ, BS bsAtoms)
public static void getInlineData(SB loadScript, java.lang.String strModel, boolean isAppend)
public boolean isAtomPDB(int i)
public boolean isModelPDB(int i)
boolean isAtomAssignable(int i)
public void deleteMeasurement(int i)
deleteMeasurement
in class JmolViewer
boolean haveModelKit()
public java.lang.String getSmiles(int index1, int index2, BS bsSelected, boolean isBioSmiles, boolean allowUnmatchedRings, boolean addCrossLinks, boolean addComment)
index1
- index2
- bsSelected
- isBioSmiles
- allowUnmatchedRings
- TODOaddCrossLinks
- TODOaddComment
- public void connect(float[][] connections)
public java.lang.String prompt(java.lang.String label, java.lang.String data, java.lang.String[] list, boolean asButtons)
public ColorEncoder getColorEncoder(java.lang.String colorScheme)
public void displayBonds(Bond.BondSet bs, boolean isDisplay)
public java.lang.String getModelAtomProperty(Atom atom, java.lang.String text)
public void setStateScriptVersion(java.lang.String version)
public JmolRendererInterface initializeExporter(java.lang.String type, java.lang.String fileName)
public void setPrivateKeyForShape(int iShape)
public boolean getMouseEnabled()
public void setZslabPoint(P3 pt)
public void calcAtomsMinMax(BS bs, BoxInfo boxInfo)
calcAtomsMinMax
in class JmolViewer
public void getObjectMap(java.util.Map<java.lang.String,?> map, char c)
map
- c
- public java.lang.String[][] getPdbBondInfo(java.lang.String group3)
public void setPicked(int iAtom)
public java.lang.String runScript(java.lang.String script)
JmolViewer
runScript
in class JmolViewer
public boolean allowSpecAtom()
public void setFrameDelayMs(long millis)
public long getFrameDelayMs(int i)
public BS getBaseModelBitSet()
public java.util.Map<java.lang.String,java.lang.Object> getTimeouts()
public void clearTimeouts()
public void setTimeout(java.lang.String name, int mSec, java.lang.String script)
public void triggerTimeout(java.lang.String name)
public void clearTimeout(java.lang.String name)
public java.lang.String showTimeout(java.lang.String name)
public void calculatePartialCharges(BS bsSelected)
public void cachePut(java.lang.String key, java.lang.Object data)
public java.lang.Object cacheGet(java.lang.String key)
public void cacheClear()
public void setCurrentModelID(java.lang.String id)
public void setCentroid(BS bs, int[] minmax)
public java.lang.String getPathForAllFiles()
public void cacheFile(java.lang.String fileName, byte[] bytes)
cacheFile
in class JmolViewer
fileName
- public int cacheFileByName(java.lang.String fileName, boolean isAdd)
public java.util.Map<java.lang.String,java.lang.Integer> cacheList()
private void stopScriptDelayThread()
public void delayScript(JmolScriptEvaluator eval, int millis)
void clearThreads()
public ScriptContext getEvalContextAndHoldQueue(JmolScriptEvaluator jse)
public void checkInheritedShapes()
public Dimension resizeInnerPanel(int width, int height)
resizeInnerPanel
in class JmolViewer
public java.lang.String getFontLineShapeState(java.lang.String s, java.lang.String myType, TickInfo[] tickInfos)
public void getShapeSetState(AtomShape atomShape, Shape shape, int monomerCount, Group[] monomers, BS bsSizeDefault, java.util.Map<java.lang.String,BS> temp, java.util.Map<java.lang.String,BS> temp2)
public java.lang.String getMeasurementState(Measures measures, JmolList<Measurement> mList, int measurementCount, JmolFont font3d, TickInfo ti)
public java.lang.String getShapeState(Shape shape)
public java.lang.String getAtomShapeState(AtomShape shape)
public java.lang.String getDefaultPropertyParam(int propertyID)
public int getPropertyNumber(java.lang.String name)
public boolean checkPropertyParameter(java.lang.String name)
public java.lang.Object extractProperty(java.lang.Object property, SV[] args, int pt)
private BS addHydrogensInline(BS bsAtoms, JmolList<Atom> vConnections, P3[] pts) throws java.lang.Exception
java.lang.Exception
public float evalFunctionFloat(java.lang.Object func, java.lang.Object params, float[] values)
evalFunctionFloat
in interface AtomDataServer
public boolean evalParallel(ScriptContext context, ShapeManager shapeManager)
public java.lang.Object evaluateExpression(java.lang.Object stringOrTokens)
evaluateExpression
in class JmolViewer
public SV evaluateExpressionAsVariable(java.lang.Object stringOrTokens)
public BS getAtomBitSet(java.lang.Object atomExpression)
JmolList<java.lang.Integer> getAtomBitSetVector(java.lang.Object atomExpression)
public java.util.Map<java.lang.String,SV> getContextVariables()
public ScriptContext getScriptContext()
public java.lang.String getAtomDefs(java.util.Map<java.lang.String,java.lang.Object> names)
getAtomDefs
in class JmolViewer
public void createModels(int n)
public void setCGO(JmolList<java.lang.Object> info)
public void setFrame(int i)
public boolean movePyMOL(JmolScriptEvaluator eval, float floatSecondsTotal, float[] pymolView)
public P3 getCamera()
public void setModelSet(ModelSet modelSet)
public java.lang.String setObjectProp(java.lang.String id, int tokCommand)
public java.lang.String[] getSceneList()
public void setBondParameters(int modelIndex, int i, BS bsBonds, float rad, float pymolValence, int argb, float trans)
public int[][] getDihedralMap(int[] atoms)
public void setDihedrals(float[] dihedralList, BS[] bsBranches, float rate)
public BS[] getBsBranches(float[] dihedralList)
public int getChainID(java.lang.String id)
id
- < 256 is just the character of a single-character
chain id; >= 256 indicates a list pointer into
chainList.public java.lang.String getChainIDStr(int id)
public java.lang.Boolean getScriptQueueInfo()
public JmolNMRInterface getNMRCalculation()
public java.lang.String getDistanceUnits(java.lang.String s)
public int calculateFormalCharges(BS bs)
public boolean cachePngFiles()