public class ScriptEvaluator extends java.lang.Object implements JmolScriptEvaluator
Modifier and Type | Field and Description |
---|---|
private T[][] |
aatoken |
private boolean |
allowJSThreads |
protected boolean |
chk |
private int[] |
colorArgb |
private int |
commandHistoryLevelMax |
protected ScriptCompiler |
compiler |
private java.lang.String |
contextPath |
private java.util.Map<java.lang.String,SV> |
contextVariables |
private boolean |
coordinatesAreFractional |
private java.lang.Thread |
currentThread |
private java.lang.Object[] |
data |
private boolean |
debugScript |
private java.util.Map<java.lang.String,java.lang.Object> |
definedAtomSets |
private boolean |
error |
(package private) static int |
ERROR_axisExpected |
(package private) static int |
ERROR_backgroundModelError |
(package private) static int |
ERROR_badArgumentCount |
(package private) static int |
ERROR_badMillerIndices |
(package private) static int |
ERROR_badRGBColor |
(package private) static int |
ERROR_booleanExpected |
(package private) static int |
ERROR_booleanOrNumberExpected |
(package private) static int |
ERROR_booleanOrWhateverExpected |
(package private) static int |
ERROR_cannotSet |
(package private) static int |
ERROR_colorExpected |
(package private) static int |
ERROR_colorOrPaletteRequired |
(package private) static int |
ERROR_commandExpected |
(package private) static int |
ERROR_coordinateOrNameOrExpressionRequired |
(package private) static int |
ERROR_drawObjectNotDefined |
(package private) static int |
ERROR_endOfStatementUnexpected |
(package private) static int |
ERROR_expressionExpected |
(package private) static int |
ERROR_expressionOrIntegerExpected |
(package private) static int |
ERROR_filenameExpected |
(package private) static int |
ERROR_fileNotFoundException |
(package private) static int |
ERROR_incompatibleArguments |
(package private) static int |
ERROR_insufficientArguments |
(package private) static int |
ERROR_integerExpected |
(package private) static int |
ERROR_integerOutOfRange |
(package private) static int |
ERROR_invalidArgument |
(package private) static int |
ERROR_invalidParameterOrder |
(package private) static int |
ERROR_keywordExpected |
(package private) static int |
ERROR_moCoefficients |
(package private) static int |
ERROR_moIndex |
(package private) static int |
ERROR_moModelError |
(package private) static int |
ERROR_moOccupancy |
(package private) static int |
ERROR_moOnlyOne |
(package private) static int |
ERROR_multipleModelsDisplayedNotOK |
(package private) static int |
ERROR_multipleModelsNotOK |
(package private) static int |
ERROR_noData |
(package private) static int |
ERROR_noPartialCharges |
(package private) static int |
ERROR_noUnitCell |
(package private) static int |
ERROR_numberExpected |
(package private) static int |
ERROR_numberMustBe |
(package private) static int |
ERROR_numberOutOfRange |
(package private) static int |
ERROR_objectNameExpected |
(package private) static int |
ERROR_planeExpected |
(package private) static int |
ERROR_propertyNameExpected |
(package private) static int |
ERROR_spaceGroupNotFound |
(package private) static int |
ERROR_stringExpected |
(package private) static int |
ERROR_stringOrIdentifierExpected |
(package private) static int |
ERROR_tooManyPoints |
(package private) static int |
ERROR_tooManyScriptLevels |
(package private) static int |
ERROR_unrecognizedAtomProperty |
(package private) static int |
ERROR_unrecognizedBondProperty |
(package private) static int |
ERROR_unrecognizedCommand |
(package private) static int |
ERROR_unrecognizedExpression |
(package private) static int |
ERROR_unrecognizedObject |
(package private) static int |
ERROR_unrecognizedParameter |
(package private) static int |
ERROR_unrecognizedParameterWarning |
(package private) static int |
ERROR_unrecognizedShowParameter |
(package private) static int |
ERROR_what |
(package private) static int |
ERROR_writeWhat |
private java.lang.String |
errorMessage |
protected java.lang.String |
errorMessageUntranslated |
protected java.lang.String |
errorType |
private boolean |
executing |
private boolean |
executionPaused |
private boolean |
executionStepping |
private boolean |
executionStopped |
private static java.lang.String |
EXPRESSION_KEY |
private java.lang.Object |
expressionResult |
private boolean |
forceNoAddHydrogens |
private P3 |
fractionalPoint |
private java.lang.String |
fullCommand |
private java.lang.String |
functionName |
private boolean |
historyDisabled |
protected int |
iCommandError |
private boolean |
ignoreError |
(package private) static int |
iProcess |
private boolean |
isBondSet |
private boolean |
isCmdLine_C_Option |
protected boolean |
isCmdLine_c_or_C_Option |
private boolean |
isJS |
private boolean |
isStateScript |
private int |
iToken |
private int |
lineEnd |
private int[][] |
lineIndices |
private short[] |
lineNumbers |
private boolean |
listCommands |
protected boolean |
logMessages |
private boolean |
mustResumeEval |
private SB |
outputBuffer |
private JmolParallelProcessor |
parallelProcessor |
protected int |
pc |
private int |
pcEnd |
private java.lang.String |
script |
private java.lang.String |
scriptExtensions |
private java.lang.String |
scriptFileName |
private int |
scriptLevel |
private static int |
scriptLevelMax |
private int |
scriptReportingLevel |
private int |
slen |
(package private) ShapeManager |
sm |
private T[] |
st |
private T[] |
tempStatement |
private int |
theTok |
private T |
theToken |
private java.lang.String |
thisCommand |
private ScriptContext |
thisContext |
private long |
timeBeginExecution |
private long |
timeEndExecution |
private boolean |
tQuiet |
(package private) static int |
tryPt |
protected Viewer |
viewer |
Constructor and Description |
---|
ScriptEvaluator() |
Modifier and Type | Method and Description |
---|---|
BS |
addHydrogensInline(BS bsAtoms,
JmolList<Atom> vConnections,
P3[] pts) |
private void |
addProcess(JmolList<T[]> vProcess,
int pc,
int pt) |
private void |
addShapeProperty(JmolList<java.lang.Object[]> propertyList,
java.lang.String key,
java.lang.Object value) |
private void |
animation() |
private void |
assign() |
private P3 |
atomCenterOrCoordinateParameter(int i) |
private BS |
atomExpression(T[] code,
int pcStart,
int pcStop,
boolean allowRefresh,
boolean allowUnderflow,
boolean mustBeBitSet,
boolean andNotDeleted) |
private BS |
atomExpressionAt(int index) |
private void |
axes(int index) |
private void |
background(int i) |
private void |
bind() |
(package private) BS |
bitSetForModelFileNumber(int m) |
(package private) JmolList<SV> |
bitsetVariableVector(java.lang.Object v) |
private void |
bondorder() |
private boolean |
booleanParameter(int i) |
private void |
boundbox(int index) |
private void |
breakCmd(int pt) |
private void |
cache() |
private void |
calculate() |
private void |
cd() |
private void |
center(int i) |
private void |
centerAt() |
private P3 |
centerParameter(int i) |
private P3 |
centerParameterForModel(int i,
int modelIndex) |
private void |
cgo() |
private boolean |
changeElementColor(java.lang.String str,
int argb) |
private boolean |
checkContinue()
checks to see if there is a pause condition, during which commands can
still be issued, but with the ! first.
|
private int |
checkLast(int i) |
private int |
checkLength(int length) |
private int |
checkLength23() |
private int |
checkLength34() |
private int |
checkLengthErrorPt(int length,
int errorPt) |
ScriptContext |
checkScriptSilent(java.lang.String script)
a method for just checking a script
|
private TickInfo |
checkTicks(int index,
boolean allowUnitCell,
boolean allowScale,
boolean allowFirst) |
private boolean |
checkToken(int i) |
private void |
clearDefinedVariableAtomSets() |
private void |
clearState(boolean tQuiet) |
private void |
color() |
private void |
colorShape(int shapeType,
int index,
boolean isBackground) |
private void |
commandLoop(boolean fromFunc) |
private void |
compare() |
private static boolean |
compareFloat(int tokOperator,
float propertyFloat,
float comparisonFloat) |
private BS |
compareFloatData(int tokWhat,
float[] data,
int tokOperator,
float comparisonFloat) |
protected BS |
compareInt(int tokWhat,
int tokOperator,
int comparisonValue) |
private BS |
compareString(int tokWhat,
int tokOperator,
java.lang.String comparisonString) |
private boolean |
compareStringValues(int tokOperator,
java.lang.String propertyValue,
java.lang.String comparisonValue) |
private boolean |
compileScript(java.lang.String filename,
java.lang.String strScript,
boolean debugCompiler) |
boolean |
compileScriptFile(java.lang.String filename,
boolean tQuiet) |
private boolean |
compileScriptFileInternal(java.lang.String filename,
java.lang.String localPath,
java.lang.String remotePath,
java.lang.String scriptPath) |
boolean |
compileScriptString(java.lang.String script,
boolean tQuiet) |
private void |
configuration() |
private void |
connect(int index) |
private void |
console() |
private void |
contact() |
private java.lang.Object[] |
createFunction(java.lang.String fname,
java.lang.String xyz,
java.lang.String ret)
for the ISOSURFACE command
|
private void |
data() |
private void |
define() |
private void |
defineAtomSet(java.lang.String script) |
private void |
defineSets()
support for @xxx or define xxx commands
|
private void |
delay() |
private void |
delete() |
void |
deleteAtomsInVariables(BS bsDeleted) |
private void |
dipole() |
private boolean |
dispatchCommands(boolean isSpt,
boolean fromFunc) |
private void |
display(boolean isDisplay) |
private void |
doDelay(int millis) |
private void |
dots(int iShape) |
private void |
draw() |
private void |
echo(int index,
java.lang.String id,
boolean isImage) |
private void |
ellipsoid() |
private RadiusData |
encodeRadiusParameter(int index,
boolean isOnly,
boolean allowAbsolute) |
(package private) void |
error(int iError) |
(package private) void |
errorAt(int iError,
int i) |
(package private) void |
errorMore(int iError,
java.lang.String value,
java.lang.String more,
java.lang.String more2) |
(package private) void |
errorOrWarn(int iError,
java.lang.String value,
java.lang.String more,
java.lang.String more2,
boolean warningOnly) |
(package private) void |
errorStr(int iError,
java.lang.String value) |
(package private) void |
errorStr2(int iError,
java.lang.String value,
java.lang.String more) |
(package private) static java.lang.String |
errorString(int iError,
java.lang.String value,
java.lang.String more,
java.lang.String more2,
boolean translated) |
(package private) void |
evalError(java.lang.String message,
java.lang.String strUntranslated) |
float |
evalFunctionFloat(java.lang.Object func,
java.lang.Object params,
float[] values) |
private java.lang.Object |
evaluate(java.lang.Object expr,
boolean asVariable) |
void |
evaluateCompiledScript(boolean isCmdLine_c_or_C_Option,
boolean isCmdLine_C_Option,
boolean historyDisabled,
boolean listCommands,
SB outputBuffer,
boolean allowThreads) |
java.lang.Object |
evaluateExpression(java.lang.Object expr,
boolean asVariable)
a general-use method to evaluate a "SET" type expression.
|
boolean |
evaluateParallel(ScriptContext context,
ShapeManager shapeManager)
used for TRY command
|
private void |
executeCommands(boolean isTry) |
private void |
file() |
private void |
finalizeObject(int shapeID,
int colorArgb,
float translucentLevel,
int intScale,
boolean doSet,
java.lang.Object data,
int iptDisplayProperty,
BS bs) |
private void |
fixed() |
private java.lang.String |
fixScriptPath(java.lang.String strScript,
java.lang.String filename) |
private float[][] |
floatArraySet(int i,
int nX,
int nY) |
private float[][][] |
floatArraySetXYZ(int i,
int nX,
int nY,
int nZ) |
private float |
floatParameter(int index) |
private float |
floatParameterRange(int i,
float min,
float max) |
private float[] |
floatParameterSet(int i,
int nMin,
int nMax)
process a general string or set of parameters as an array of floats,
allowing for relatively free form input
|
private float |
floatSetting(int pt) |
private boolean |
flowControl(int tok,
boolean isForCheck,
JmolList<T[]> vProcess) |
private void |
font(int shapeType,
float fontsize) |
private void |
frameControl(int i) |
private void |
frank(int index) |
private void |
function() |
boolean |
getAllowJSThreads() |
private int |
getArgbParam(int index) |
private int |
getArgbParamLast(int index,
boolean allowNone) |
private int |
getArgbParamOrNone(int index,
boolean allowNone) |
private BS |
getAtomBits(int tokType,
java.lang.Object specInfo) |
BS |
getAtomBitSet(java.lang.Object atomExpression)
a general method to evaluate a string representing an atom set.
|
JmolList<java.lang.Integer> |
getAtomBitSetVector(int atomCount,
java.lang.Object atomExpression)
just provides a vector list of atoms in a string-based expression
|
(package private) BS |
getAtomsNearSurface(float distance,
java.lang.String surfaceId) |
(package private) java.lang.Object |
getBitsetIdent(BS bs,
java.lang.String label,
java.lang.Object tokenValue,
boolean useAtomMap,
int index,
boolean isExplicitlyAll) |
protected java.lang.Object |
getBitsetProperty(BS bs,
int tok,
P3 ptRef,
P4 planeRef,
java.lang.Object tokenValue,
java.lang.Object opValue,
boolean useAtomMap,
int index,
boolean asVectorIfAll) |
private float[] |
getBitsetPropertyFloat(BS bs,
int tok,
float min,
float max) |
private SV |
getBitsetPropertySelector(int i,
boolean mustBeSettable) |
(package private) static int |
getBondOrderFromString(java.lang.String s) |
private java.lang.Object |
getCapSlabObject(int i,
boolean isLcaoCartoon) |
private java.lang.String |
getColorRange(int i) |
private float |
getColorTrans(int i,
boolean allowNone)
Checks color, translucent, opaque parameters.
|
private int |
getColorTriad(int i) |
private java.lang.String |
getCommand(int pc,
boolean allThisLine,
boolean addSemi)
used for recall of commands in the application console
|
private java.lang.String |
getContext(boolean withVariables) |
(package private) static SB |
getContextTrace(Viewer viewer,
ScriptContext sc,
SB sb,
boolean isTop) |
private SV |
getContextVariableAsVariable(java.lang.String var) |
java.util.Map<java.lang.String,SV> |
getContextVariables() |
java.util.Map<java.lang.String,java.lang.Object> |
getDefinedAtomSets() |
private V3 |
getDrawObjectAxis(java.lang.String axisID,
int index) |
(package private) static java.lang.String |
getErrorLineMessage(java.lang.String functionName,
java.lang.String filename,
int lineCurrent,
int pcCurrent,
java.lang.String lineInfo) |
java.lang.String |
getErrorMessage() |
java.lang.String |
getErrorMessageUntranslated() |
private int |
getExecutionWalltime() |
(package private) static int |
getFloatEncodedInt(java.lang.String strDecimal)
Encodes a string such as "2.10" as an integer instead of a float
so as to distinguish "2.1" from "2.10"
used for model numbers and partial bond orders.
|
private java.lang.String |
getFullPathName() |
private java.util.Map<java.lang.String,java.lang.Object> |
getHash(int i) |
protected P4 |
getHklPlane(P3 pt) |
private java.lang.String |
getIsosurfaceDataRange(int iShape,
java.lang.String sep) |
private java.lang.String |
getIsosurfaceJvxl(boolean asMesh,
int iShape) |
private int |
getLinenumber(ScriptContext c) |
private int |
getMadParameter() |
private static float |
getMinMax(float[] data,
boolean isMax,
int tok) |
private java.lang.String |
getMoJvxl(int ptMO) |
private java.lang.String |
getNextComment() |
java.lang.String |
getNextStatement()
when paused, indicates what statement will be next
|
private java.lang.Object |
getNumericParameter(java.lang.String var) |
private P3[] |
getObjectBoundingBox(java.lang.String id) |
private P3 |
getObjectCenter(java.lang.String axisID,
int index,
int modelIndex) |
private java.lang.Object |
getParameter(java.lang.String key,
int tokType) |
private java.lang.String |
getParameterEscaped(java.lang.String var) |
(package private) static int |
getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger)
reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5
+ (m % 0x1F)
|
private static int |
getPartialBondOrderFromString(java.lang.String s) |
private P3 |
getPoint3f(int i,
boolean allowFractional) |
private P4 |
getPoint4f(int i) |
private P3[] |
getPointArray(int i,
int nPoints) |
private java.lang.Object |
getPointOrPlane(int index,
boolean integerOnly,
boolean allowFractional,
boolean doConvert,
boolean implicitFractional,
int minDim,
int maxDim) |
(package private) JmolList<P3> |
getPointVector(T t,
int i) |
private void |
getProperty() |
private Quaternion |
getQuaternionParameter(int i) |
java.lang.String |
getScript() |
ScriptContext |
getScriptContext() |
private java.lang.String |
getScriptID(ScriptContext context) |
private static int |
getSeqCode(T instruction) |
private int |
getSetAxesTypeMad(int index) |
private java.lang.String |
getShapeNameParameter(int i) |
private java.lang.Object |
getShapeProperty(int shapeType,
java.lang.String propertyName) |
private boolean |
getShapePropertyData(int shapeType,
java.lang.String propertyName,
java.lang.Object[] data) |
private java.lang.Object |
getShapePropertyIndex(int shapeType,
java.lang.String propertyName,
int index) |
private int |
getShapeType(int tok) |
(package private) float |
getSmilesCorrelation(BS bsA,
BS bsB,
java.lang.String smiles,
JmolList<P3> ptsA,
JmolList<P3> ptsB,
Matrix4f m4,
JmolList<BS> vReturn,
boolean isSmarts,
boolean asMap,
int[][] mapSet,
P3 center) |
(package private) java.lang.Object |
getSmilesMatches(java.lang.String pattern,
java.lang.String smiles,
BS bsSelected,
BS bsMatch3D,
boolean isSmarts,
boolean asOneBitset) |
private java.lang.Object |
getStringObjectAsVariable(java.lang.String s,
java.lang.String key) |
private java.lang.String |
getStringParameter(java.lang.String var,
boolean orReturnName) |
ScriptContext |
getThisContext() |
private T |
getToken(int i) |
private float |
getTranslucentLevel(int i) |
private void |
getWithinDistanceVector(JmolList<java.lang.Object[]> propertyList,
float distance,
P3 ptc,
BS bs,
boolean isShow) |
private float |
getZoom(int ptCenter,
int i,
BS bs,
float currentZoom) |
private void |
gotoCmd(java.lang.String strTo) |
void |
haltExecution() |
private void |
hbond() |
private void |
help() |
private void |
history(int pt) |
private P4 |
hklParameter(int i) |
private void |
hover() |
private boolean |
ifCmd() |
private java.lang.String |
initIsosurface(int iShape) |
private void |
integerOutOfRange(int min,
int max) |
private int |
intParameter(int index) |
private int |
intParameterRange(int i,
int min,
int max) |
private int |
intSetting(int pt) |
private void |
invertSelected() |
private boolean |
isArrayParameter(int i) |
private boolean |
isCenterParameter(int i) |
private boolean |
isColorParam(int i) |
private boolean |
isCommandDisplayable(int i)
provides support for the script editor
|
boolean |
isExecuting() |
private boolean |
isFloatParameter(int index) |
private void |
isosurface(int iShape) |
boolean |
isPaused() |
private boolean |
isPoint3f(int i) |
boolean |
isStepping() |
boolean |
isStopped() |
private void |
label(int index) |
private void |
lcaoCartoon() |
private boolean |
listIsosurface(int iShape) |
private JmolList<java.lang.Object> |
listParameter(int i,
int nMin,
int nMax) |
private void |
load() |
private void |
log() |
private void |
logDebugScript(int ifLevel) |
private void |
logLoadInfo(java.lang.String msg) |
private BS |
lookupIdentifierValue(java.lang.String identifier) |
private BS |
lookupValue(java.lang.String setName,
boolean plurals) |
private void |
mapProperty() |
private void |
measure() |
private void |
message() |
private void |
minimize() |
private boolean |
mo(boolean isInitOnly) |
private float[] |
moCombo(JmolList<java.lang.Object[]> propertyList) |
private void |
model(int offset) |
private int |
modelNumberParameter(int index) |
private int |
moOffset(int index) |
private void |
move() |
private void |
moveto() |
private void |
navigate() |
void |
notifyResumeStatus() |
private void |
numberOutOfRange(float min,
float max) |
private java.lang.String |
objectNameParameter(int index) |
private java.lang.String |
optParameterAsString(int i) |
private java.lang.String |
parameterAsString(int i) |
private java.lang.Object |
parameterExpression(int pt,
int ptMax,
java.lang.String key,
boolean ignoreComma,
boolean asVector,
int ptAtom,
boolean isArrayItem,
java.util.Map<java.lang.String,SV> localVars,
java.lang.String localVar)
This is the primary driver of the RPN (reverse Polish notation) expression
processor.
|
private boolean |
parameterExpressionBoolean(int pt,
int ptMax) |
private JmolList<SV> |
parameterExpressionList(int pt,
int ptAtom,
boolean isArrayItem) |
private java.lang.String |
parameterExpressionString(int pt,
int ptMax) |
private SV |
parameterExpressionToken(int pt) |
private boolean |
pause() |
void |
pauseExecution(boolean withDelay) |
private void |
planeExpected() |
private P4 |
planeParameter(int i) |
private java.lang.String |
plot(T[] args) |
private void |
pointGroup() |
private void |
polyhedra() |
(package private) void |
popContext(boolean isFlowCommand,
boolean statementOnly) |
private void |
print() |
private void |
processShapeCommand(int tok) |
private void |
processTry(java.util.Map<java.lang.String,SV> cv) |
private void |
prompt() |
private void |
proteinShape(int shapeType) |
private void |
pushContext(ContextToken token) |
private void |
pushContext2(ContextToken token) |
void |
pushContextDown() |
private void |
refresh() |
private void |
reset() |
private void |
restore() |
private void |
restoreFunction(JmolScriptFunction f,
JmolList<SV> params,
SV tokenAtom)
note that functions requiring motion cannot be run
in JavaScript
|
private void |
restoreScriptContext(ScriptContext context,
boolean isPopContext,
boolean isFlowCommand,
boolean statementOnly) |
private void |
restrict() |
private void |
restrictSelected(boolean isBond,
boolean doInvert) |
void |
resumeEval(ScriptContext sc)
From dispatchCommands and JmolThread resumeEval.
|
void |
resumePausedExecution() |
private void |
returnCmd(SV tv) |
private void |
rotate(boolean isSpin,
boolean isSelected) |
(package private) SV |
runFunctionRet(JmolScriptFunction function,
java.lang.String name,
JmolList<SV> params,
SV tokenAtom,
boolean getReturn,
boolean setContextPath,
boolean allowThreads) |
void |
runScript(java.lang.String script) |
void |
runScriptBuffer(java.lang.String script,
SB outputBuffer)
runs a script and sends selected output to a provided StringXBuilder
|
private void |
save() |
private void |
script(int tok,
java.lang.String filename) |
private void |
scriptStatusOrBuffer(java.lang.String s) |
private void |
select(int i) |
private void |
selectionHalo(int pt) |
private void |
set() |
private void |
setAtomShapeSize(int shape,
float scale) |
private void |
setBitsetProperty(BS bs,
int tok,
int iValue,
float fValue,
T tokenValue) |
private void |
setBondmode() |
private void |
setBooleanProperty(java.lang.String key,
boolean value) |
private java.lang.String |
setColorOptions(SB sb,
int index,
int iShape,
int nAllowed) |
void |
setCompiler() |
(package private) BS |
setContactBitSets(BS bsA,
BS bsB,
boolean localOnly,
float distance,
RadiusData rd,
boolean warnMultiModel) |
private void |
setCursorWait(boolean TF) |
void |
setDebugging() |
private void |
setEcho() |
private void |
setErrorMessage(java.lang.String err) |
void |
setException(ScriptException sx,
java.lang.String msg,
java.lang.String untranslated) |
private boolean |
setFloatProperty(java.lang.String key,
float value) |
private void |
setHbond() |
private boolean |
setIntProperty(java.lang.String key,
int value) |
private boolean |
setLabel(java.lang.String str) |
private boolean |
setMeshDisplayProperty(int shape,
int i,
int tok) |
private void |
setMoData(JmolList<java.lang.Object[]> propertyList,
int moNumber,
float[] lc,
int offset,
boolean isNegOffset,
int modelIndex,
java.lang.String title) |
private void |
setMonitor() |
private void |
setObjectArgb(java.lang.String str,
int argb) |
private void |
setObjectMad(int iShape,
java.lang.String name,
int mad) |
java.lang.String |
setObjectProp(java.lang.String id,
int tokCommand,
int iTok) |
private java.lang.String |
setObjectProperty() |
java.lang.String |
setObjectPropSafe(java.lang.String id,
int tokCommand,
int iTok) |
private void |
setPicking() |
private void |
setPickingStyle() |
private int |
setScriptExtensions() |
private java.lang.String |
setShapeId(int iShape,
int i,
boolean idSeen) |
private void |
setShapeProperty(int shapeType,
java.lang.String propertyName,
java.lang.Object propertyValue) |
private void |
setShapePropertyBs(int iShape,
java.lang.String propertyName,
java.lang.Object propertyValue,
BS bs) |
private void |
setShapeSize(int shapeType,
RadiusData rd) |
private void |
setShapeSizeBs(int shapeType,
int size,
BS bs) |
private void |
setShapeTranslucency(int shapeType,
java.lang.String prefix,
java.lang.String translucency,
float translucentLevel,
BS bs) |
private void |
setSsbond() |
private boolean |
setStatement(int pc)
provides support for @x and @{....} in statements.
|
private void |
setStringProperty(java.lang.String key,
java.lang.String value) |
private boolean |
setUnits(java.lang.String units,
int tok) |
private void |
setUserColors() |
private void |
setVariable(int pt,
int ptMax,
java.lang.String key,
int setType) |
JmolScriptEvaluator |
setViewer(Viewer viewer) |
private void |
setZslab() |
private void |
show() |
private void |
showString(java.lang.String str) |
private void |
showStringPrint(java.lang.String str,
boolean isPrint) |
private void |
slab(boolean isDepth) |
private void |
ssbond() |
private void |
startEval() |
(package private) static java.lang.String |
statementAsString(Viewer viewer,
T[] statement,
int iTok,
boolean doLogMessages) |
void |
stepPausedExecution() |
private void |
stereo() |
private java.lang.String |
stringParameter(int index) |
private java.lang.String[] |
stringParameterSet(int i) |
private java.lang.String |
stringSetting(int pt,
boolean isJmolSet) |
private void |
structure() |
private void |
struts() |
private void |
subset() |
private int |
switchCmd(ContextToken c,
int tok) |
private void |
sync() |
private void |
timeout(int index) |
private int |
tokAt(int i) |
private static int |
tokAtArray(int i,
T[] args) |
private T |
tokenAt(int i,
T[] args) |
java.lang.String |
toString() |
private void |
translate(boolean isSelected) |
private void |
unbind() |
private void |
undoRedoMove() |
private void |
unitcell(int index) |
private boolean |
useThreads() |
private void |
vector() |
private void |
vibration() |
private void |
warning(int iError,
java.lang.String value,
java.lang.String more) |
private void |
wireframe() |
(package private) java.lang.String |
write(T[] args) |
private P3 |
xypParameter(int index) |
private void |
zap(boolean isZapCommand) |
private void |
zoom(boolean isZoomTo) |
private boolean allowJSThreads
private boolean listCommands
private boolean isJS
private boolean tQuiet
protected boolean chk
private boolean isCmdLine_C_Option
protected boolean isCmdLine_c_or_C_Option
private boolean historyDisabled
protected boolean logMessages
private boolean debugScript
private boolean executionStopped
private boolean executionPaused
private boolean executionStepping
private boolean executing
private long timeBeginExecution
private long timeEndExecution
private boolean mustResumeEval
private static final java.lang.String EXPRESSION_KEY
ShapeManager sm
private static final int scriptLevelMax
private java.lang.Thread currentThread
protected Viewer viewer
protected ScriptCompiler compiler
private java.util.Map<java.lang.String,java.lang.Object> definedAtomSets
private SB outputBuffer
private java.lang.String contextPath
private java.lang.String scriptFileName
private java.lang.String functionName
private boolean isStateScript
private int scriptLevel
private int scriptReportingLevel
private int commandHistoryLevelMax
private T[][] aatoken
private short[] lineNumbers
private int[][] lineIndices
private java.util.Map<java.lang.String,SV> contextVariables
private java.lang.String script
protected int pc
private java.lang.String thisCommand
private java.lang.String fullCommand
private T[] st
private int slen
private int iToken
private int lineEnd
private int pcEnd
private java.lang.String scriptExtensions
private boolean forceNoAddHydrogens
private JmolParallelProcessor parallelProcessor
static int tryPt
private ScriptContext thisContext
private boolean error
private java.lang.String errorMessage
protected java.lang.String errorMessageUntranslated
protected java.lang.String errorType
protected int iCommandError
private boolean ignoreError
static final int ERROR_axisExpected
static final int ERROR_backgroundModelError
static final int ERROR_badArgumentCount
static final int ERROR_badMillerIndices
static final int ERROR_badRGBColor
static final int ERROR_booleanExpected
static final int ERROR_booleanOrNumberExpected
static final int ERROR_booleanOrWhateverExpected
static final int ERROR_colorExpected
static final int ERROR_colorOrPaletteRequired
static final int ERROR_commandExpected
static final int ERROR_coordinateOrNameOrExpressionRequired
static final int ERROR_drawObjectNotDefined
static final int ERROR_endOfStatementUnexpected
static final int ERROR_expressionExpected
static final int ERROR_expressionOrIntegerExpected
static final int ERROR_filenameExpected
static final int ERROR_fileNotFoundException
static final int ERROR_incompatibleArguments
static final int ERROR_insufficientArguments
static final int ERROR_integerExpected
static final int ERROR_integerOutOfRange
static final int ERROR_invalidArgument
static final int ERROR_invalidParameterOrder
static final int ERROR_keywordExpected
static final int ERROR_moCoefficients
static final int ERROR_moIndex
static final int ERROR_moModelError
static final int ERROR_moOccupancy
static final int ERROR_moOnlyOne
static final int ERROR_multipleModelsDisplayedNotOK
static final int ERROR_noData
static final int ERROR_noPartialCharges
static final int ERROR_noUnitCell
static final int ERROR_numberExpected
static final int ERROR_numberMustBe
static final int ERROR_numberOutOfRange
static final int ERROR_objectNameExpected
static final int ERROR_planeExpected
static final int ERROR_propertyNameExpected
static final int ERROR_spaceGroupNotFound
static final int ERROR_stringExpected
static final int ERROR_stringOrIdentifierExpected
static final int ERROR_tooManyPoints
static final int ERROR_tooManyScriptLevels
static final int ERROR_unrecognizedAtomProperty
static final int ERROR_unrecognizedBondProperty
static final int ERROR_unrecognizedCommand
static final int ERROR_unrecognizedExpression
static final int ERROR_unrecognizedObject
static final int ERROR_unrecognizedParameter
static final int ERROR_unrecognizedParameterWarning
static final int ERROR_unrecognizedShowParameter
static final int ERROR_what
static final int ERROR_writeWhat
static final int ERROR_multipleModelsNotOK
static final int ERROR_cannotSet
private T[] tempStatement
private boolean isBondSet
private java.lang.Object expressionResult
private int theTok
private T theToken
private boolean coordinatesAreFractional
private P3 fractionalPoint
static int iProcess
private java.lang.Object[] data
private int[] colorArgb
public boolean getAllowJSThreads()
getAllowJSThreads
in interface JmolScriptEvaluator
public JmolScriptEvaluator setViewer(Viewer viewer)
setViewer
in interface JmolScriptEvaluator
public void setCompiler()
setCompiler
in interface JmolScriptEvaluator
public boolean compileScriptString(java.lang.String script, boolean tQuiet)
compileScriptString
in interface JmolScriptEvaluator
public boolean compileScriptFile(java.lang.String filename, boolean tQuiet)
compileScriptFile
in interface JmolScriptEvaluator
public void evaluateCompiledScript(boolean isCmdLine_c_or_C_Option, boolean isCmdLine_C_Option, boolean historyDisabled, boolean listCommands, SB outputBuffer, boolean allowThreads)
evaluateCompiledScript
in interface JmolScriptEvaluator
private java.lang.Object[] createFunction(java.lang.String fname, java.lang.String xyz, java.lang.String ret)
fname
- xyz
- ret
- private boolean useThreads()
private void startEval()
private void executeCommands(boolean isTry)
public void resumeEval(ScriptContext sc)
resumeEval
in interface JmolScriptEvaluator
sc
- public void runScriptBuffer(java.lang.String script, SB outputBuffer) throws ScriptException
runScriptBuffer
in interface JmolScriptEvaluator
script
- outputBuffer
- ScriptException
public ScriptContext checkScriptSilent(java.lang.String script)
checkScriptSilent
in interface JmolScriptEvaluator
script
- static SB getContextTrace(Viewer viewer, ScriptContext sc, SB sb, boolean isTop)
public void setDebugging()
setDebugging
in interface JmolScriptEvaluator
private int getExecutionWalltime()
public void haltExecution()
haltExecution
in interface JmolScriptEvaluator
public void pauseExecution(boolean withDelay)
pauseExecution
in interface JmolScriptEvaluator
public void stepPausedExecution()
stepPausedExecution
in interface JmolScriptEvaluator
public void resumePausedExecution()
resumePausedExecution
in interface JmolScriptEvaluator
public boolean isExecuting()
isExecuting
in interface JmolScriptEvaluator
public boolean isPaused()
isPaused
in interface JmolScriptEvaluator
public boolean isStepping()
isStepping
in interface JmolScriptEvaluator
public boolean isStopped()
isStopped
in interface JmolScriptEvaluator
public java.lang.String getNextStatement()
getNextStatement
in interface JmolScriptEvaluator
private java.lang.String getCommand(int pc, boolean allThisLine, boolean addSemi)
pc
- allThisLine
- addSemi
- private void logDebugScript(int ifLevel)
public java.lang.Object evaluateExpression(java.lang.Object expr, boolean asVariable)
evaluateExpression
in interface JmolScriptEvaluator
expr
- asVariable
- private java.lang.Object evaluate(java.lang.Object expr, boolean asVariable)
public boolean evaluateParallel(ScriptContext context, ShapeManager shapeManager)
evaluateParallel
in interface JmolScriptEvaluator
context
- shapeManager
- public BS getAtomBitSet(java.lang.Object atomExpression)
getAtomBitSet
in interface JmolScriptEvaluator
atomExpression
- public JmolList<java.lang.Integer> getAtomBitSetVector(int atomCount, java.lang.Object atomExpression)
getAtomBitSetVector
in interface JmolScriptEvaluator
atomCount
- atomExpression
- private JmolList<SV> parameterExpressionList(int pt, int ptAtom, boolean isArrayItem) throws ScriptException
ScriptException
private java.lang.String parameterExpressionString(int pt, int ptMax) throws ScriptException
ScriptException
private boolean parameterExpressionBoolean(int pt, int ptMax) throws ScriptException
ScriptException
private SV parameterExpressionToken(int pt) throws ScriptException
ScriptException
private java.lang.Object parameterExpression(int pt, int ptMax, java.lang.String key, boolean ignoreComma, boolean asVector, int ptAtom, boolean isArrayItem, java.util.Map<java.lang.String,SV> localVars, java.lang.String localVar) throws ScriptException
pt
- token index in statement start of expressionptMax
- token index in statement end of expressionkey
- variable name for debugging reference only -- null indicates return
Boolean -- "" indicates return StringignoreComma
- TODOasVector
- a flag passed on to RPN;ptAtom
- this is a for() or select() function with a specific atom selectedisArrayItem
- we are storing A[x] = ... so we need to deliver "x" as welllocalVars
- see below -- lists all nested for(x, {exp}, select(y, {ex},...))
variableslocalVar
- x or y in above for(), select() examplesScriptException
- errors are thrown directly to the Eval error system.private java.util.Map<java.lang.String,java.lang.Object> getHash(int i) throws ScriptException
ScriptException
java.lang.Object getBitsetIdent(BS bs, java.lang.String label, java.lang.Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)
private SV getBitsetPropertySelector(int i, boolean mustBeSettable) throws ScriptException
ScriptException
private float[] getBitsetPropertyFloat(BS bs, int tok, float min, float max) throws ScriptException
ScriptException
protected java.lang.Object getBitsetProperty(BS bs, int tok, P3 ptRef, P4 planeRef, java.lang.Object tokenValue, java.lang.Object opValue, boolean useAtomMap, int index, boolean asVectorIfAll) throws ScriptException
ScriptException
private void setBitsetProperty(BS bs, int tok, int iValue, float fValue, T tokenValue) throws ScriptException
ScriptException
public java.util.Map<java.lang.String,java.lang.Object> getDefinedAtomSets()
getDefinedAtomSets
in interface JmolScriptEvaluator
public java.util.Map<java.lang.String,SV> getContextVariables()
getContextVariables
in interface JmolScriptEvaluator
public java.lang.String getScript()
getScript
in interface JmolScriptEvaluator
private boolean compileScript(java.lang.String filename, java.lang.String strScript, boolean debugCompiler)
private java.lang.String fixScriptPath(java.lang.String strScript, java.lang.String filename)
private int setScriptExtensions()
public void runScript(java.lang.String script) throws ScriptException
runScript
in interface JmolScriptEvaluator
ScriptException
private boolean compileScriptFileInternal(java.lang.String filename, java.lang.String localPath, java.lang.String remotePath, java.lang.String scriptPath)
private java.lang.Object getParameter(java.lang.String key, int tokType)
private java.lang.String getParameterEscaped(java.lang.String var)
private java.lang.String getStringParameter(java.lang.String var, boolean orReturnName)
private java.lang.Object getNumericParameter(java.lang.String var)
private SV getContextVariableAsVariable(java.lang.String var)
private java.lang.Object getStringObjectAsVariable(java.lang.String s, java.lang.String key)
public float evalFunctionFloat(java.lang.Object func, java.lang.Object params, float[] values)
evalFunctionFloat
in interface JmolScriptEvaluator
SV runFunctionRet(JmolScriptFunction function, java.lang.String name, JmolList<SV> params, SV tokenAtom, boolean getReturn, boolean setContextPath, boolean allowThreads) throws ScriptException
ScriptException
private void processTry(java.util.Map<java.lang.String,SV> cv) throws ScriptException
ScriptException
private void restoreFunction(JmolScriptFunction f, JmolList<SV> params, SV tokenAtom) throws ScriptException
f
- params
- tokenAtom
- ScriptException
private void clearDefinedVariableAtomSets()
private void defineSets()
private void defineAtomSet(java.lang.String script)
private BS lookupIdentifierValue(java.lang.String identifier) throws ScriptException
ScriptException
private BS lookupValue(java.lang.String setName, boolean plurals) throws ScriptException
ScriptException
public void deleteAtomsInVariables(BS bsDeleted)
deleteAtomsInVariables
in interface JmolScriptEvaluator
private boolean setStatement(int pc) throws ScriptException
pc
- ScriptException
private void clearState(boolean tQuiet)
public ScriptContext getThisContext()
getThisContext
in interface JmolScriptEvaluator
public void pushContextDown()
pushContextDown
in interface JmolScriptEvaluator
private void pushContext(ContextToken token) throws ScriptException
ScriptException
private void pushContext2(ContextToken token)
public ScriptContext getScriptContext()
getScriptContext
in interface JmolScriptEvaluator
void popContext(boolean isFlowCommand, boolean statementOnly)
private void restoreScriptContext(ScriptContext context, boolean isPopContext, boolean isFlowCommand, boolean statementOnly)
private java.lang.String getContext(boolean withVariables)
private int getLinenumber(ScriptContext c)
private java.lang.String getScriptID(ScriptContext context)
public void setException(ScriptException sx, java.lang.String msg, java.lang.String untranslated)
setException
in interface JmolScriptEvaluator
public java.lang.String getErrorMessage()
getErrorMessage
in interface JmolScriptEvaluator
public java.lang.String getErrorMessageUntranslated()
getErrorMessageUntranslated
in interface JmolScriptEvaluator
private void setErrorMessage(java.lang.String err)
private void planeExpected() throws ScriptException
ScriptException
private void integerOutOfRange(int min, int max) throws ScriptException
ScriptException
private void numberOutOfRange(float min, float max) throws ScriptException
ScriptException
void errorAt(int iError, int i) throws ScriptException
ScriptException
void error(int iError) throws ScriptException
ScriptException
void errorStr(int iError, java.lang.String value) throws ScriptException
ScriptException
void errorStr2(int iError, java.lang.String value, java.lang.String more) throws ScriptException
ScriptException
void errorMore(int iError, java.lang.String value, java.lang.String more, java.lang.String more2) throws ScriptException
ScriptException
private void warning(int iError, java.lang.String value, java.lang.String more) throws ScriptException
ScriptException
void errorOrWarn(int iError, java.lang.String value, java.lang.String more, java.lang.String more2, boolean warningOnly) throws ScriptException
ScriptException
void evalError(java.lang.String message, java.lang.String strUntranslated) throws ScriptException
ScriptException
static java.lang.String errorString(int iError, java.lang.String value, java.lang.String more, java.lang.String more2, boolean translated)
iError
- value
- more
- more2
- translated
- static java.lang.String getErrorLineMessage(java.lang.String functionName, java.lang.String filename, int lineCurrent, int pcCurrent, java.lang.String lineInfo)
public java.lang.String toString()
toString
in class java.lang.Object
static java.lang.String statementAsString(Viewer viewer, T[] statement, int iTok, boolean doLogMessages)
private java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName)
private boolean getShapePropertyData(int shapeType, java.lang.String propertyName, java.lang.Object[] data)
private java.lang.Object getShapePropertyIndex(int shapeType, java.lang.String propertyName, int index)
private void addShapeProperty(JmolList<java.lang.Object[]> propertyList, java.lang.String key, java.lang.Object value)
private void setObjectMad(int iShape, java.lang.String name, int mad)
private void setObjectArgb(java.lang.String str, int argb)
private void setShapeProperty(int shapeType, java.lang.String propertyName, java.lang.Object propertyValue)
private void setShapePropertyBs(int iShape, java.lang.String propertyName, java.lang.Object propertyValue, BS bs)
private void setShapeSizeBs(int shapeType, int size, BS bs)
private void setShapeSize(int shapeType, RadiusData rd)
private void setBooleanProperty(java.lang.String key, boolean value)
private boolean setIntProperty(java.lang.String key, int value)
private boolean setFloatProperty(java.lang.String key, float value)
private void setStringProperty(java.lang.String key, java.lang.String value)
private void showString(java.lang.String str)
private void showStringPrint(java.lang.String str, boolean isPrint)
private void scriptStatusOrBuffer(java.lang.String s)
private BS atomExpressionAt(int index) throws ScriptException
ScriptException
private BS atomExpression(T[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted) throws ScriptException
code
- pcStart
- pcStop
- allowRefresh
- allowUnderflow
- mustBeBitSet
- andNotDeleted
- IGNOREDScriptException
private BS compareFloatData(int tokWhat, float[] data, int tokOperator, float comparisonFloat)
tokWhat
- data
- tokOperator
- comparisonFloat
- private BS compareString(int tokWhat, int tokOperator, java.lang.String comparisonString) throws ScriptException
ScriptException
protected BS compareInt(int tokWhat, int tokOperator, int comparisonValue)
private boolean compareStringValues(int tokOperator, java.lang.String propertyValue, java.lang.String comparisonValue) throws ScriptException
ScriptException
private static boolean compareFloat(int tokOperator, float propertyFloat, float comparisonFloat)
private BS getAtomBits(int tokType, java.lang.Object specInfo)
private static int getSeqCode(T instruction)
private int checkLast(int i) throws ScriptException
ScriptException
private int checkLength(int length) throws ScriptException
ScriptException
private int checkLengthErrorPt(int length, int errorPt) throws ScriptException
ScriptException
private int checkLength23() throws ScriptException
ScriptException
private int checkLength34() throws ScriptException
ScriptException
private T getToken(int i) throws ScriptException
ScriptException
private int tokAt(int i)
private static int tokAtArray(int i, T[] args)
private boolean checkToken(int i)
private int modelNumberParameter(int index) throws ScriptException
ScriptException
private java.lang.String optParameterAsString(int i) throws ScriptException
ScriptException
private java.lang.String parameterAsString(int i) throws ScriptException
ScriptException
private int intParameter(int index) throws ScriptException
ScriptException
private int intParameterRange(int i, int min, int max) throws ScriptException
ScriptException
private boolean isFloatParameter(int index)
private float floatParameterRange(int i, float min, float max) throws ScriptException
ScriptException
private float floatParameter(int index) throws ScriptException
ScriptException
private JmolList<java.lang.Object> listParameter(int i, int nMin, int nMax) throws ScriptException
ScriptException
private float[] floatParameterSet(int i, int nMin, int nMax) throws ScriptException
i
- nMin
- nMax
- ScriptException
private boolean isArrayParameter(int i)
private P3[] getPointArray(int i, int nPoints) throws ScriptException
ScriptException
private float[][] floatArraySet(int i, int nX, int nY) throws ScriptException
ScriptException
private float[][][] floatArraySetXYZ(int i, int nX, int nY, int nZ) throws ScriptException
ScriptException
private java.lang.String stringParameter(int index) throws ScriptException
ScriptException
private java.lang.String[] stringParameterSet(int i) throws ScriptException
ScriptException
private java.lang.String objectNameParameter(int index) throws ScriptException
ScriptException
private boolean booleanParameter(int i) throws ScriptException
ScriptException
private P3 atomCenterOrCoordinateParameter(int i) throws ScriptException
ScriptException
private boolean isCenterParameter(int i)
private P3 centerParameter(int i) throws ScriptException
ScriptException
private P3 centerParameterForModel(int i, int modelIndex) throws ScriptException
ScriptException
private P4 planeParameter(int i) throws ScriptException
ScriptException
private P4 hklParameter(int i) throws ScriptException
ScriptException
private int getMadParameter() throws ScriptException
ScriptException
private int getSetAxesTypeMad(int index) throws ScriptException
ScriptException
private boolean isColorParam(int i)
private int getArgbParam(int index) throws ScriptException
ScriptException
private int getArgbParamLast(int index, boolean allowNone) throws ScriptException
ScriptException
private int getArgbParamOrNone(int index, boolean allowNone) throws ScriptException
ScriptException
private int getColorTriad(int i) throws ScriptException
ScriptException
private boolean isPoint3f(int i)
private P3 getPoint3f(int i, boolean allowFractional) throws ScriptException
ScriptException
private P4 getPoint4f(int i) throws ScriptException
ScriptException
private java.lang.Object getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim) throws ScriptException
ScriptException
private P3 xypParameter(int index) throws ScriptException
ScriptException
private boolean isCommandDisplayable(int i)
i
- private boolean checkContinue() throws ScriptException
ScriptException
public void notifyResumeStatus()
notifyResumeStatus
in interface JmolScriptEvaluator
private void doDelay(int millis) throws ScriptException
millis
- negative here bypasses max checkScriptException
private boolean dispatchCommands(boolean isSpt, boolean fromFunc) throws ScriptException
isSpt
- fromFunc
- TODOScriptException
private void commandLoop(boolean fromFunc) throws ScriptException
ScriptException
private void cache() throws ScriptException
ScriptException
private void setCursorWait(boolean TF)
private void processShapeCommand(int tok) throws ScriptException
ScriptException
private boolean flowControl(int tok, boolean isForCheck, JmolList<T[]> vProcess) throws ScriptException
ScriptException
private void gotoCmd(java.lang.String strTo) throws ScriptException
ScriptException
private void breakCmd(int pt)
private int switchCmd(ContextToken c, int tok) throws ScriptException
ScriptException
private boolean ifCmd() throws ScriptException
ScriptException
private void returnCmd(SV tv) throws ScriptException
ScriptException
private void help() throws ScriptException
ScriptException
private void move() throws ScriptException
ScriptException
private void moveto() throws ScriptException
ScriptException
private void navigate() throws ScriptException
ScriptException
private void bondorder() throws ScriptException
ScriptException
private void console() throws ScriptException
ScriptException
private void centerAt() throws ScriptException
ScriptException
private void stereo() throws ScriptException
ScriptException
private void compare() throws ScriptException
ScriptException
float getSmilesCorrelation(BS bsA, BS bsB, java.lang.String smiles, JmolList<P3> ptsA, JmolList<P3> ptsB, Matrix4f m4, JmolList<BS> vReturn, boolean isSmarts, boolean asMap, int[][] mapSet, P3 center) throws ScriptException
ScriptException
java.lang.Object getSmilesMatches(java.lang.String pattern, java.lang.String smiles, BS bsSelected, BS bsMatch3D, boolean isSmarts, boolean asOneBitset) throws ScriptException
ScriptException
private void connect(int index) throws ScriptException
index
- 0 is this is the hbond commandScriptException
private float getTranslucentLevel(int i) throws ScriptException
ScriptException
private void getProperty() throws ScriptException
ScriptException
private void background(int i) throws ScriptException
ScriptException
private void center(int i) throws ScriptException
ScriptException
private java.lang.String setObjectProperty() throws ScriptException
ScriptException
public java.lang.String setObjectPropSafe(java.lang.String id, int tokCommand, int iTok)
setObjectPropSafe
in interface JmolScriptEvaluator
public java.lang.String setObjectProp(java.lang.String id, int tokCommand, int iTok) throws ScriptException
ScriptException
private void color() throws ScriptException
ScriptException
private boolean changeElementColor(java.lang.String str, int argb)
private void colorShape(int shapeType, int index, boolean isBackground) throws ScriptException
ScriptException
private void setShapeTranslucency(int shapeType, java.lang.String prefix, java.lang.String translucency, float translucentLevel, BS bs)
private void cd() throws ScriptException
ScriptException
private void mapProperty() throws ScriptException
ScriptException
private void data() throws ScriptException
ScriptException
private void define() throws ScriptException
ScriptException
private void echo(int index, java.lang.String id, boolean isImage) throws ScriptException
ScriptException
private void message() throws ScriptException
ScriptException
private void log() throws ScriptException
ScriptException
private void label(int index) throws ScriptException
ScriptException
private void hover() throws ScriptException
ScriptException
private void load() throws ScriptException
ScriptException
private void logLoadInfo(java.lang.String msg)
private java.lang.String getFullPathName() throws ScriptException
ScriptException
private void measure() throws ScriptException
ScriptException
private java.lang.String plot(T[] args) throws ScriptException
ScriptException
private static float getMinMax(float[] data, boolean isMax, int tok)
private boolean pause() throws ScriptException
ScriptException
private void print() throws ScriptException
ScriptException
private void prompt() throws ScriptException
ScriptException
private void refresh()
private void reset() throws ScriptException
ScriptException
private void restrict() throws ScriptException
ScriptException
private void restrictSelected(boolean isBond, boolean doInvert)
private void rotate(boolean isSpin, boolean isSelected) throws ScriptException
ScriptException
private Quaternion getQuaternionParameter(int i) throws ScriptException
ScriptException
JmolList<P3> getPointVector(T t, int i) throws ScriptException
ScriptException
private P3 getObjectCenter(java.lang.String axisID, int index, int modelIndex)
private P3[] getObjectBoundingBox(java.lang.String id)
private V3 getDrawObjectAxis(java.lang.String axisID, int index)
private void script(int tok, java.lang.String filename) throws ScriptException
ScriptException
private void function() throws ScriptException
ScriptException
private void sync() throws ScriptException
ScriptException
private void history(int pt) throws ScriptException
ScriptException
private void display(boolean isDisplay) throws ScriptException
ScriptException
private void delete() throws ScriptException
ScriptException
private void minimize() throws ScriptException
ScriptException
private void select(int i) throws ScriptException
ScriptException
private void subset() throws ScriptException
ScriptException
private void invertSelected() throws ScriptException
ScriptException
private void translate(boolean isSelected) throws ScriptException
ScriptException
private void zap(boolean isZapCommand) throws ScriptException
ScriptException
private void zoom(boolean isZoomTo) throws ScriptException
ScriptException
private float getZoom(int ptCenter, int i, BS bs, float currentZoom) throws ScriptException
ScriptException
private void delay() throws ScriptException
ScriptException
private void slab(boolean isDepth) throws ScriptException
ScriptException
private void ellipsoid() throws ScriptException
ScriptException
private java.lang.String getShapeNameParameter(int i) throws ScriptException
ScriptException
private java.lang.String setShapeId(int iShape, int i, boolean idSeen) throws ScriptException
ScriptException
private void setAtomShapeSize(int shape, float scale) throws ScriptException
ScriptException
private RadiusData encodeRadiusParameter(int index, boolean isOnly, boolean allowAbsolute) throws ScriptException
ScriptException
private void structure() throws ScriptException
ScriptException
private void wireframe() throws ScriptException
ScriptException
private void ssbond() throws ScriptException
ScriptException
private void struts() throws ScriptException
ScriptException
private void hbond() throws ScriptException
ScriptException
private void configuration() throws ScriptException
ScriptException
private void vector() throws ScriptException
ScriptException
private void dipole() throws ScriptException
ScriptException
private void vibration() throws ScriptException
ScriptException
private void calculate() throws ScriptException
ScriptException
private void pointGroup() throws ScriptException
ScriptException
private void dots(int iShape) throws ScriptException
ScriptException
private void proteinShape(int shapeType) throws ScriptException
ScriptException
private void animation() throws ScriptException
ScriptException
private void assign() throws ScriptException
ScriptException
private void file() throws ScriptException
ScriptException
private void fixed() throws ScriptException
ScriptException
private void model(int offset) throws ScriptException
ScriptException
BS bitSetForModelFileNumber(int m)
private void frameControl(int i) throws ScriptException
ScriptException
private int getShapeType(int tok) throws ScriptException
ScriptException
private void font(int shapeType, float fontsize) throws ScriptException
ScriptException
private void set() throws ScriptException
ScriptException
private void setZslab() throws ScriptException
ScriptException
private void setBondmode() throws ScriptException
ScriptException
private void setEcho() throws ScriptException
ScriptException
private int intSetting(int pt) throws ScriptException
ScriptException
private float floatSetting(int pt) throws ScriptException
ScriptException
private java.lang.String stringSetting(int pt, boolean isJmolSet) throws ScriptException
ScriptException
private boolean setLabel(java.lang.String str) throws ScriptException
ScriptException
private void setMonitor() throws ScriptException
ScriptException
private boolean setUnits(java.lang.String units, int tok) throws ScriptException
ScriptException
private void setSsbond() throws ScriptException
ScriptException
private void setHbond() throws ScriptException
ScriptException
private void setPicking() throws ScriptException
ScriptException
private void setPickingStyle() throws ScriptException
ScriptException
private void timeout(int index) throws ScriptException
ScriptException
private void setUserColors() throws ScriptException
ScriptException
private void setVariable(int pt, int ptMax, java.lang.String key, int setType) throws ScriptException
pt
- ptMax
- key
- setType
- ScriptException
private void axes(int index) throws ScriptException
ScriptException
private void boundbox(int index) throws ScriptException
ScriptException
private TickInfo checkTicks(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst) throws ScriptException
index
- allowUnitCell
- IGNOREDallowScale
- allowFirst
- ScriptException
private void unitcell(int index) throws ScriptException
ScriptException
private void frank(int index) throws ScriptException
ScriptException
private void selectionHalo(int pt) throws ScriptException
ScriptException
private void save() throws ScriptException
ScriptException
private void restore() throws ScriptException
ScriptException
java.lang.String write(T[] args) throws ScriptException
ScriptException
private void show() throws ScriptException
ScriptException
private java.lang.String getIsosurfaceJvxl(boolean asMesh, int iShape)
private java.lang.String getMoJvxl(int ptMO) throws ScriptException
ScriptException
private void cgo() throws ScriptException
ScriptException
private float getColorTrans(int i, boolean allowNone) throws ScriptException
i
- allowNone
- TODOScriptException
private void finalizeObject(int shapeID, int colorArgb, float translucentLevel, int intScale, boolean doSet, java.lang.Object data, int iptDisplayProperty, BS bs) throws ScriptException
ScriptException
private void draw() throws ScriptException
ScriptException
private void polyhedra() throws ScriptException
ScriptException
private void contact() throws ScriptException
ScriptException
BS setContactBitSets(BS bsA, BS bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel)
private void lcaoCartoon() throws ScriptException
ScriptException
private java.lang.Object getCapSlabObject(int i, boolean isLcaoCartoon) throws ScriptException
ScriptException
private boolean mo(boolean isInitOnly) throws ScriptException
ScriptException
private float[] moCombo(JmolList<java.lang.Object[]> propertyList)
private int moOffset(int index) throws ScriptException
ScriptException
private void setMoData(JmolList<java.lang.Object[]> propertyList, int moNumber, float[] lc, int offset, boolean isNegOffset, int modelIndex, java.lang.String title) throws ScriptException
ScriptException
private java.lang.String initIsosurface(int iShape) throws ScriptException
ScriptException
private java.lang.String getNextComment()
private boolean listIsosurface(int iShape) throws ScriptException
ScriptException
private void isosurface(int iShape) throws ScriptException
ScriptException
private java.lang.String setColorOptions(SB sb, int index, int iShape, int nAllowed) throws ScriptException
ScriptException
private java.lang.String getColorRange(int i) throws ScriptException
ScriptException
private java.lang.String getIsosurfaceDataRange(int iShape, java.lang.String sep)
private void getWithinDistanceVector(JmolList<java.lang.Object[]> propertyList, float distance, P3 ptc, BS bs, boolean isShow)
private boolean setMeshDisplayProperty(int shape, int i, int tok) throws ScriptException
shape
- i
- tok
- ScriptException
private void bind() throws ScriptException
ScriptException
private void unbind() throws ScriptException
ScriptException
private void undoRedoMove() throws ScriptException
ScriptException
BS getAtomsNearSurface(float distance, java.lang.String surfaceId)
static int getFloatEncodedInt(java.lang.String strDecimal)
strDecimal
- static int getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger)
bondOrderInteger
- static int getBondOrderFromString(java.lang.String s)
private static int getPartialBondOrderFromString(java.lang.String s)
public BS addHydrogensInline(BS bsAtoms, JmolList<Atom> vConnections, P3[] pts) throws java.lang.Exception
addHydrogensInline
in interface JmolScriptEvaluator
java.lang.Exception