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 JmolScriptEvaluatorpublic JmolScriptEvaluator setViewer(Viewer viewer)
setViewer in interface JmolScriptEvaluatorpublic void setCompiler()
setCompiler in interface JmolScriptEvaluatorpublic boolean compileScriptString(java.lang.String script,
boolean tQuiet)
compileScriptString in interface JmolScriptEvaluatorpublic boolean compileScriptFile(java.lang.String filename,
boolean tQuiet)
compileScriptFile in interface JmolScriptEvaluatorpublic void evaluateCompiledScript(boolean isCmdLine_c_or_C_Option,
boolean isCmdLine_C_Option,
boolean historyDisabled,
boolean listCommands,
SB outputBuffer,
boolean allowThreads)
evaluateCompiledScript in interface JmolScriptEvaluatorprivate 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 JmolScriptEvaluatorsc - public void runScriptBuffer(java.lang.String script,
SB outputBuffer)
throws ScriptException
runScriptBuffer in interface JmolScriptEvaluatorscript - outputBuffer - ScriptExceptionpublic ScriptContext checkScriptSilent(java.lang.String script)
checkScriptSilent in interface JmolScriptEvaluatorscript - static SB getContextTrace(Viewer viewer, ScriptContext sc, SB sb, boolean isTop)
public void setDebugging()
setDebugging in interface JmolScriptEvaluatorprivate int getExecutionWalltime()
public void haltExecution()
haltExecution in interface JmolScriptEvaluatorpublic void pauseExecution(boolean withDelay)
pauseExecution in interface JmolScriptEvaluatorpublic void stepPausedExecution()
stepPausedExecution in interface JmolScriptEvaluatorpublic void resumePausedExecution()
resumePausedExecution in interface JmolScriptEvaluatorpublic boolean isExecuting()
isExecuting in interface JmolScriptEvaluatorpublic boolean isPaused()
isPaused in interface JmolScriptEvaluatorpublic boolean isStepping()
isStepping in interface JmolScriptEvaluatorpublic boolean isStopped()
isStopped in interface JmolScriptEvaluatorpublic java.lang.String getNextStatement()
getNextStatement in interface JmolScriptEvaluatorprivate 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 JmolScriptEvaluatorexpr - asVariable - private java.lang.Object evaluate(java.lang.Object expr,
boolean asVariable)
public boolean evaluateParallel(ScriptContext context, ShapeManager shapeManager)
evaluateParallel in interface JmolScriptEvaluatorcontext - shapeManager - public BS getAtomBitSet(java.lang.Object atomExpression)
getAtomBitSet in interface JmolScriptEvaluatoratomExpression - public JmolList<java.lang.Integer> getAtomBitSetVector(int atomCount, java.lang.Object atomExpression)
getAtomBitSetVector in interface JmolScriptEvaluatoratomCount - atomExpression - private JmolList<SV> parameterExpressionList(int pt, int ptAtom, boolean isArrayItem) throws ScriptException
ScriptExceptionprivate java.lang.String parameterExpressionString(int pt,
int ptMax)
throws ScriptException
ScriptExceptionprivate boolean parameterExpressionBoolean(int pt,
int ptMax)
throws ScriptException
ScriptExceptionprivate SV parameterExpressionToken(int pt) throws ScriptException
ScriptExceptionprivate 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
ScriptExceptionjava.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
ScriptExceptionprivate float[] getBitsetPropertyFloat(BS bs, int tok, float min, float max) throws ScriptException
ScriptExceptionprotected 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
ScriptExceptionprivate void setBitsetProperty(BS bs, int tok, int iValue, float fValue, T tokenValue) throws ScriptException
ScriptExceptionpublic java.util.Map<java.lang.String,java.lang.Object> getDefinedAtomSets()
getDefinedAtomSets in interface JmolScriptEvaluatorpublic java.util.Map<java.lang.String,SV> getContextVariables()
getContextVariables in interface JmolScriptEvaluatorpublic java.lang.String getScript()
getScript in interface JmolScriptEvaluatorprivate 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 JmolScriptEvaluatorScriptExceptionprivate 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 JmolScriptEvaluatorSV runFunctionRet(JmolScriptFunction function, java.lang.String name, JmolList<SV> params, SV tokenAtom, boolean getReturn, boolean setContextPath, boolean allowThreads) throws ScriptException
ScriptExceptionprivate void processTry(java.util.Map<java.lang.String,SV> cv) throws ScriptException
ScriptExceptionprivate void restoreFunction(JmolScriptFunction f, JmolList<SV> params, SV tokenAtom) throws ScriptException
f - params - tokenAtom - ScriptExceptionprivate void clearDefinedVariableAtomSets()
private void defineSets()
private void defineAtomSet(java.lang.String script)
private BS lookupIdentifierValue(java.lang.String identifier) throws ScriptException
ScriptExceptionprivate BS lookupValue(java.lang.String setName, boolean plurals) throws ScriptException
ScriptExceptionpublic void deleteAtomsInVariables(BS bsDeleted)
deleteAtomsInVariables in interface JmolScriptEvaluatorprivate boolean setStatement(int pc)
throws ScriptException
pc - ScriptExceptionprivate void clearState(boolean tQuiet)
public ScriptContext getThisContext()
getThisContext in interface JmolScriptEvaluatorpublic void pushContextDown()
pushContextDown in interface JmolScriptEvaluatorprivate void pushContext(ContextToken token) throws ScriptException
ScriptExceptionprivate void pushContext2(ContextToken token)
public ScriptContext getScriptContext()
getScriptContext in interface JmolScriptEvaluatorvoid 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 JmolScriptEvaluatorpublic java.lang.String getErrorMessage()
getErrorMessage in interface JmolScriptEvaluatorpublic java.lang.String getErrorMessageUntranslated()
getErrorMessageUntranslated in interface JmolScriptEvaluatorprivate void setErrorMessage(java.lang.String err)
private void planeExpected()
throws ScriptException
ScriptExceptionprivate void integerOutOfRange(int min,
int max)
throws ScriptException
ScriptExceptionprivate void numberOutOfRange(float min,
float max)
throws ScriptException
ScriptExceptionvoid errorAt(int iError,
int i)
throws ScriptException
ScriptExceptionvoid error(int iError)
throws ScriptException
ScriptExceptionvoid errorStr(int iError,
java.lang.String value)
throws ScriptException
ScriptExceptionvoid errorStr2(int iError,
java.lang.String value,
java.lang.String more)
throws ScriptException
ScriptExceptionvoid errorMore(int iError,
java.lang.String value,
java.lang.String more,
java.lang.String more2)
throws ScriptException
ScriptExceptionprivate void warning(int iError,
java.lang.String value,
java.lang.String more)
throws ScriptException
ScriptExceptionvoid errorOrWarn(int iError,
java.lang.String value,
java.lang.String more,
java.lang.String more2,
boolean warningOnly)
throws ScriptException
ScriptExceptionvoid evalError(java.lang.String message,
java.lang.String strUntranslated)
throws ScriptException
ScriptExceptionstatic 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.Objectstatic 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
ScriptExceptionprivate 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 - IGNOREDScriptExceptionprivate 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
ScriptExceptionprotected BS compareInt(int tokWhat, int tokOperator, int comparisonValue)
private boolean compareStringValues(int tokOperator,
java.lang.String propertyValue,
java.lang.String comparisonValue)
throws ScriptException
ScriptExceptionprivate 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
ScriptExceptionprivate int checkLength(int length)
throws ScriptException
ScriptExceptionprivate int checkLengthErrorPt(int length,
int errorPt)
throws ScriptException
ScriptExceptionprivate int checkLength23()
throws ScriptException
ScriptExceptionprivate int checkLength34()
throws ScriptException
ScriptExceptionprivate T getToken(int i) throws ScriptException
ScriptExceptionprivate int tokAt(int i)
private static int tokAtArray(int i,
T[] args)
private boolean checkToken(int i)
private int modelNumberParameter(int index)
throws ScriptException
ScriptExceptionprivate java.lang.String optParameterAsString(int i)
throws ScriptException
ScriptExceptionprivate java.lang.String parameterAsString(int i)
throws ScriptException
ScriptExceptionprivate int intParameter(int index)
throws ScriptException
ScriptExceptionprivate int intParameterRange(int i,
int min,
int max)
throws ScriptException
ScriptExceptionprivate boolean isFloatParameter(int index)
private float floatParameterRange(int i,
float min,
float max)
throws ScriptException
ScriptExceptionprivate float floatParameter(int index)
throws ScriptException
ScriptExceptionprivate JmolList<java.lang.Object> listParameter(int i, int nMin, int nMax) throws ScriptException
ScriptExceptionprivate float[] floatParameterSet(int i,
int nMin,
int nMax)
throws ScriptException
i - nMin - nMax - ScriptExceptionprivate boolean isArrayParameter(int i)
private P3[] getPointArray(int i, int nPoints) throws ScriptException
ScriptExceptionprivate float[][] floatArraySet(int i,
int nX,
int nY)
throws ScriptException
ScriptExceptionprivate float[][][] floatArraySetXYZ(int i,
int nX,
int nY,
int nZ)
throws ScriptException
ScriptExceptionprivate java.lang.String stringParameter(int index)
throws ScriptException
ScriptExceptionprivate java.lang.String[] stringParameterSet(int i)
throws ScriptException
ScriptExceptionprivate java.lang.String objectNameParameter(int index)
throws ScriptException
ScriptExceptionprivate boolean booleanParameter(int i)
throws ScriptException
ScriptExceptionprivate P3 atomCenterOrCoordinateParameter(int i) throws ScriptException
ScriptExceptionprivate boolean isCenterParameter(int i)
private P3 centerParameter(int i) throws ScriptException
ScriptExceptionprivate P3 centerParameterForModel(int i, int modelIndex) throws ScriptException
ScriptExceptionprivate P4 planeParameter(int i) throws ScriptException
ScriptExceptionprivate P4 hklParameter(int i) throws ScriptException
ScriptExceptionprivate int getMadParameter()
throws ScriptException
ScriptExceptionprivate int getSetAxesTypeMad(int index)
throws ScriptException
ScriptExceptionprivate boolean isColorParam(int i)
private int getArgbParam(int index)
throws ScriptException
ScriptExceptionprivate int getArgbParamLast(int index,
boolean allowNone)
throws ScriptException
ScriptExceptionprivate int getArgbParamOrNone(int index,
boolean allowNone)
throws ScriptException
ScriptExceptionprivate int getColorTriad(int i)
throws ScriptException
ScriptExceptionprivate boolean isPoint3f(int i)
private P3 getPoint3f(int i, boolean allowFractional) throws ScriptException
ScriptExceptionprivate P4 getPoint4f(int i) throws ScriptException
ScriptExceptionprivate java.lang.Object getPointOrPlane(int index,
boolean integerOnly,
boolean allowFractional,
boolean doConvert,
boolean implicitFractional,
int minDim,
int maxDim)
throws ScriptException
ScriptExceptionprivate P3 xypParameter(int index) throws ScriptException
ScriptExceptionprivate boolean isCommandDisplayable(int i)
i - private boolean checkContinue()
throws ScriptException
ScriptExceptionpublic void notifyResumeStatus()
notifyResumeStatus in interface JmolScriptEvaluatorprivate void doDelay(int millis)
throws ScriptException
millis - negative here bypasses max checkScriptExceptionprivate boolean dispatchCommands(boolean isSpt,
boolean fromFunc)
throws ScriptException
isSpt - fromFunc - TODOScriptExceptionprivate void commandLoop(boolean fromFunc)
throws ScriptException
ScriptExceptionprivate void cache()
throws ScriptException
ScriptExceptionprivate void setCursorWait(boolean TF)
private void processShapeCommand(int tok)
throws ScriptException
ScriptExceptionprivate boolean flowControl(int tok,
boolean isForCheck,
JmolList<T[]> vProcess)
throws ScriptException
ScriptExceptionprivate void gotoCmd(java.lang.String strTo)
throws ScriptException
ScriptExceptionprivate void breakCmd(int pt)
private int switchCmd(ContextToken c, int tok) throws ScriptException
ScriptExceptionprivate boolean ifCmd()
throws ScriptException
ScriptExceptionprivate void returnCmd(SV tv) throws ScriptException
ScriptExceptionprivate void help()
throws ScriptException
ScriptExceptionprivate void move()
throws ScriptException
ScriptExceptionprivate void moveto()
throws ScriptException
ScriptExceptionprivate void navigate()
throws ScriptException
ScriptExceptionprivate void bondorder()
throws ScriptException
ScriptExceptionprivate void console()
throws ScriptException
ScriptExceptionprivate void centerAt()
throws ScriptException
ScriptExceptionprivate void stereo()
throws ScriptException
ScriptExceptionprivate void compare()
throws ScriptException
ScriptExceptionfloat 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
ScriptExceptionjava.lang.Object getSmilesMatches(java.lang.String pattern,
java.lang.String smiles,
BS bsSelected,
BS bsMatch3D,
boolean isSmarts,
boolean asOneBitset)
throws ScriptException
ScriptExceptionprivate void connect(int index)
throws ScriptException
index - 0 is this is the hbond commandScriptExceptionprivate float getTranslucentLevel(int i)
throws ScriptException
ScriptExceptionprivate void getProperty()
throws ScriptException
ScriptExceptionprivate void background(int i)
throws ScriptException
ScriptExceptionprivate void center(int i)
throws ScriptException
ScriptExceptionprivate java.lang.String setObjectProperty()
throws ScriptException
ScriptExceptionpublic java.lang.String setObjectPropSafe(java.lang.String id,
int tokCommand,
int iTok)
setObjectPropSafe in interface JmolScriptEvaluatorpublic java.lang.String setObjectProp(java.lang.String id,
int tokCommand,
int iTok)
throws ScriptException
ScriptExceptionprivate void color()
throws ScriptException
ScriptExceptionprivate boolean changeElementColor(java.lang.String str,
int argb)
private void colorShape(int shapeType,
int index,
boolean isBackground)
throws ScriptException
ScriptExceptionprivate void setShapeTranslucency(int shapeType,
java.lang.String prefix,
java.lang.String translucency,
float translucentLevel,
BS bs)
private void cd()
throws ScriptException
ScriptExceptionprivate void mapProperty()
throws ScriptException
ScriptExceptionprivate void data()
throws ScriptException
ScriptExceptionprivate void define()
throws ScriptException
ScriptExceptionprivate void echo(int index,
java.lang.String id,
boolean isImage)
throws ScriptException
ScriptExceptionprivate void message()
throws ScriptException
ScriptExceptionprivate void log()
throws ScriptException
ScriptExceptionprivate void label(int index)
throws ScriptException
ScriptExceptionprivate void hover()
throws ScriptException
ScriptExceptionprivate void load()
throws ScriptException
ScriptExceptionprivate void logLoadInfo(java.lang.String msg)
private java.lang.String getFullPathName()
throws ScriptException
ScriptExceptionprivate void measure()
throws ScriptException
ScriptExceptionprivate java.lang.String plot(T[] args) throws ScriptException
ScriptExceptionprivate static float getMinMax(float[] data,
boolean isMax,
int tok)
private boolean pause()
throws ScriptException
ScriptExceptionprivate void print()
throws ScriptException
ScriptExceptionprivate void prompt()
throws ScriptException
ScriptExceptionprivate void refresh()
private void reset()
throws ScriptException
ScriptExceptionprivate void restrict()
throws ScriptException
ScriptExceptionprivate void restrictSelected(boolean isBond,
boolean doInvert)
private void rotate(boolean isSpin,
boolean isSelected)
throws ScriptException
ScriptExceptionprivate Quaternion getQuaternionParameter(int i) throws ScriptException
ScriptExceptionJmolList<P3> getPointVector(T t, int i) throws ScriptException
ScriptExceptionprivate 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
ScriptExceptionprivate void function()
throws ScriptException
ScriptExceptionprivate void sync()
throws ScriptException
ScriptExceptionprivate void history(int pt)
throws ScriptException
ScriptExceptionprivate void display(boolean isDisplay)
throws ScriptException
ScriptExceptionprivate void delete()
throws ScriptException
ScriptExceptionprivate void minimize()
throws ScriptException
ScriptExceptionprivate void select(int i)
throws ScriptException
ScriptExceptionprivate void subset()
throws ScriptException
ScriptExceptionprivate void invertSelected()
throws ScriptException
ScriptExceptionprivate void translate(boolean isSelected)
throws ScriptException
ScriptExceptionprivate void zap(boolean isZapCommand)
throws ScriptException
ScriptExceptionprivate void zoom(boolean isZoomTo)
throws ScriptException
ScriptExceptionprivate float getZoom(int ptCenter,
int i,
BS bs,
float currentZoom)
throws ScriptException
ScriptExceptionprivate void delay()
throws ScriptException
ScriptExceptionprivate void slab(boolean isDepth)
throws ScriptException
ScriptExceptionprivate void ellipsoid()
throws ScriptException
ScriptExceptionprivate java.lang.String getShapeNameParameter(int i)
throws ScriptException
ScriptExceptionprivate java.lang.String setShapeId(int iShape,
int i,
boolean idSeen)
throws ScriptException
ScriptExceptionprivate void setAtomShapeSize(int shape,
float scale)
throws ScriptException
ScriptExceptionprivate RadiusData encodeRadiusParameter(int index, boolean isOnly, boolean allowAbsolute) throws ScriptException
ScriptExceptionprivate void structure()
throws ScriptException
ScriptExceptionprivate void wireframe()
throws ScriptException
ScriptExceptionprivate void ssbond()
throws ScriptException
ScriptExceptionprivate void struts()
throws ScriptException
ScriptExceptionprivate void hbond()
throws ScriptException
ScriptExceptionprivate void configuration()
throws ScriptException
ScriptExceptionprivate void vector()
throws ScriptException
ScriptExceptionprivate void dipole()
throws ScriptException
ScriptExceptionprivate void vibration()
throws ScriptException
ScriptExceptionprivate void calculate()
throws ScriptException
ScriptExceptionprivate void pointGroup()
throws ScriptException
ScriptExceptionprivate void dots(int iShape)
throws ScriptException
ScriptExceptionprivate void proteinShape(int shapeType)
throws ScriptException
ScriptExceptionprivate void animation()
throws ScriptException
ScriptExceptionprivate void assign()
throws ScriptException
ScriptExceptionprivate void file()
throws ScriptException
ScriptExceptionprivate void fixed()
throws ScriptException
ScriptExceptionprivate void model(int offset)
throws ScriptException
ScriptExceptionBS bitSetForModelFileNumber(int m)
private void frameControl(int i)
throws ScriptException
ScriptExceptionprivate int getShapeType(int tok)
throws ScriptException
ScriptExceptionprivate void font(int shapeType,
float fontsize)
throws ScriptException
ScriptExceptionprivate void set()
throws ScriptException
ScriptExceptionprivate void setZslab()
throws ScriptException
ScriptExceptionprivate void setBondmode()
throws ScriptException
ScriptExceptionprivate void setEcho()
throws ScriptException
ScriptExceptionprivate int intSetting(int pt)
throws ScriptException
ScriptExceptionprivate float floatSetting(int pt)
throws ScriptException
ScriptExceptionprivate java.lang.String stringSetting(int pt,
boolean isJmolSet)
throws ScriptException
ScriptExceptionprivate boolean setLabel(java.lang.String str)
throws ScriptException
ScriptExceptionprivate void setMonitor()
throws ScriptException
ScriptExceptionprivate boolean setUnits(java.lang.String units,
int tok)
throws ScriptException
ScriptExceptionprivate void setSsbond()
throws ScriptException
ScriptExceptionprivate void setHbond()
throws ScriptException
ScriptExceptionprivate void setPicking()
throws ScriptException
ScriptExceptionprivate void setPickingStyle()
throws ScriptException
ScriptExceptionprivate void timeout(int index)
throws ScriptException
ScriptExceptionprivate void setUserColors()
throws ScriptException
ScriptExceptionprivate void setVariable(int pt,
int ptMax,
java.lang.String key,
int setType)
throws ScriptException
pt - ptMax - key - setType - ScriptExceptionprivate void axes(int index)
throws ScriptException
ScriptExceptionprivate void boundbox(int index)
throws ScriptException
ScriptExceptionprivate TickInfo checkTicks(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst) throws ScriptException
index - allowUnitCell - IGNOREDallowScale - allowFirst - ScriptExceptionprivate void unitcell(int index)
throws ScriptException
ScriptExceptionprivate void frank(int index)
throws ScriptException
ScriptExceptionprivate void selectionHalo(int pt)
throws ScriptException
ScriptExceptionprivate void save()
throws ScriptException
ScriptExceptionprivate void restore()
throws ScriptException
ScriptExceptionjava.lang.String write(T[] args) throws ScriptException
ScriptExceptionprivate void show()
throws ScriptException
ScriptExceptionprivate java.lang.String getIsosurfaceJvxl(boolean asMesh,
int iShape)
private java.lang.String getMoJvxl(int ptMO)
throws ScriptException
ScriptExceptionprivate void cgo()
throws ScriptException
ScriptExceptionprivate float getColorTrans(int i,
boolean allowNone)
throws ScriptException
i - allowNone - TODOScriptExceptionprivate void finalizeObject(int shapeID,
int colorArgb,
float translucentLevel,
int intScale,
boolean doSet,
java.lang.Object data,
int iptDisplayProperty,
BS bs)
throws ScriptException
ScriptExceptionprivate void draw()
throws ScriptException
ScriptExceptionprivate void polyhedra()
throws ScriptException
ScriptExceptionprivate void contact()
throws ScriptException
ScriptExceptionBS setContactBitSets(BS bsA, BS bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel)
private void lcaoCartoon()
throws ScriptException
ScriptExceptionprivate java.lang.Object getCapSlabObject(int i,
boolean isLcaoCartoon)
throws ScriptException
ScriptExceptionprivate boolean mo(boolean isInitOnly)
throws ScriptException
ScriptExceptionprivate float[] moCombo(JmolList<java.lang.Object[]> propertyList)
private int moOffset(int index)
throws ScriptException
ScriptExceptionprivate void setMoData(JmolList<java.lang.Object[]> propertyList, int moNumber, float[] lc, int offset, boolean isNegOffset, int modelIndex, java.lang.String title) throws ScriptException
ScriptExceptionprivate java.lang.String initIsosurface(int iShape)
throws ScriptException
ScriptExceptionprivate java.lang.String getNextComment()
private boolean listIsosurface(int iShape)
throws ScriptException
ScriptExceptionprivate void isosurface(int iShape)
throws ScriptException
ScriptExceptionprivate java.lang.String setColorOptions(SB sb, int index, int iShape, int nAllowed) throws ScriptException
ScriptExceptionprivate java.lang.String getColorRange(int i)
throws ScriptException
ScriptExceptionprivate 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 - ScriptExceptionprivate void bind()
throws ScriptException
ScriptExceptionprivate void unbind()
throws ScriptException
ScriptExceptionprivate void undoRedoMove()
throws ScriptException
ScriptExceptionBS 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 JmolScriptEvaluatorjava.lang.Exception