ScriptEvaluator

java.lang.Object
- org.jmol.script.ScriptEvaluator

All Implemented Interfaces:: JmolScriptEvaluator

public class ScriptEvaluator
extends Object
implements JmolScriptEvaluator

Field Summary

Fields
Modifier and Type	Field and Description
`T[][]`	`aatoken`
`boolean`	`allowJSThreads`
`boolean`	`chk`
`int[]`	`colorArgb`
`int`	`commandHistoryLevelMax`
`ScriptCompiler`	`compiler`
`private String`	`contextPath`
`Map<String,SV>`	`contextVariables`
`private boolean`	`coordinatesAreFractional`
`private Thread`	`currentThread`
`private boolean`	`debugScript`
`Map<String,Object>`	`definedAtomSets`
`private boolean`	`error`
`(package private) static int`	`ERROR_axisExpected`
`(package private) static int`	`ERROR_backgroundModelError`
`static int`	`ERROR_badArgumentCount`
`(package private) static int`	`ERROR_badMillerIndices`
`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`
`static int`	`ERROR_endOfStatementUnexpected`
`static int`	`ERROR_expressionExpected`
`static int`	`ERROR_expressionOrIntegerExpected`
`(package private) static int`	`ERROR_filenameExpected`
`static int`	`ERROR_fileNotFoundException`
`static int`	`ERROR_incompatibleArguments`
`static int`	`ERROR_insufficientArguments`
`(package private) static int`	`ERROR_integerExpected`
`(package private) static int`	`ERROR_integerOutOfRange`
`static int`	`ERROR_invalidArgument`
`static int`	`ERROR_invalidParameterOrder`
`static int`	`ERROR_keywordExpected`
`static int`	`ERROR_moCoefficients`
`static int`	`ERROR_moIndex`
`static int`	`ERROR_moModelError`
`static int`	`ERROR_moOccupancy`
`static int`	`ERROR_moOnlyOne`
`static int`	`ERROR_multipleModelsDisplayedNotOK`
`(package private) static int`	`ERROR_multipleModelsNotOK`
`static int`	`ERROR_noData`
`static int`	`ERROR_noPartialCharges`
`(package private) static int`	`ERROR_noUnitCell`
`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`
`static int`	`ERROR_what`
`static int`	`ERROR_writeWhat`
`private String`	`errorMessage`
`protected String`	`errorMessageUntranslated`
`protected String`	`errorType`
`private boolean`	`executing`
`private boolean`	`executionPaused`
`private boolean`	`executionStepping`
`private boolean`	`executionStopped`
`private static String`	`EXPRESSION_KEY`
`Object`	`expressionResult`
`private JmolThread`	`fileLoadThread`
`private boolean`	`forceNoAddHydrogens`
`private javajs.util.P3`	`fractionalPoint`
`String`	`fullCommand`
`String`	`functionName`
`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`
`boolean`	`isJS`
`private boolean`	`isStateScript`
`int`	`iToken`
`private int`	`lineEnd`
`private int[][]`	`lineIndices`
`private short[]`	`lineNumbers`
`private boolean`	`listCommands`
`boolean`	`logMessages`
`private boolean`	`mustResumeEval`
`private javajs.util.SB`	`outputBuffer`
`private JmolParallelProcessor`	`parallelProcessor`
`protected int`	`pc`
`private int`	`pcEnd`
`private String`	`script`
`private JmolThread`	`scriptDelayThread`
`private JmolScriptExtension`	`scriptExt`
`private String`	`scriptExtensions`
`String`	`scriptFileName`
`int`	`scriptLevel`
`private static int`	`scriptLevelMax`
`private int`	`scriptReportingLevel`
`int`	`slen`
`ShapeManager`	`sm`
`T[]`	`st`
`private T[]`	`tempStatement`
`int`	`theTok`
`T`	`theToken`
`String`	`thisCommand`
`ScriptContext`	`thisContext`
`private long`	`timeBeginExecution`
`private long`	`timeEndExecution`
`boolean`	`tQuiet`
`(package private) static int`	`tryPt`
`Viewer`	`viewer`

Constructor Summary

Constructors
Constructor and Description

ScriptEvaluator()

Constructors
Constructor and Description
`ScriptEvaluator()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`BS`	`addHydrogensInline(BS bsAtoms, javajs.util.List<Atom> vConnections, javajs.util.P3[] pts)`
`private void`	`addProcess(javajs.util.List<T[]> vProcess, int pc, int pt)`
`private void`	`animation()`
`private void`	`assign()`
`private javajs.util.P3`	`atomCenterOrCoordinateParameter(int i)`
`BS`	`atomExpression(T[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted)`
`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) javajs.util.List<SV>`	`bitsetVariableVector(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`	`cd()`
`private void`	`center(int i)`
`private void`	`centerAt()`
`javajs.util.P3`	`centerParameter(int i)`
`private javajs.util.P3`	`centerParameterForModel(int i, int modelIndex)`
`private boolean`	`changeElementColor(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.
`int`	`checkLast(int i)`
`int`	`checkLength(int length)`
`int`	`checkLength23()`
`private int`	`checkLength34()`
`private int`	`checkLengthErrorPt(int length, int errorPt)`
`ScriptContext`	`checkScriptSilent(String script)` a method for just checking a script
`TickInfo`	`checkTicks(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst)`
`private boolean`	`checkToken(int i)`
`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 static boolean`	`compareFloat(int tokOperator, float propertyFloat, float comparisonFloat)`
`private BS`	`compareFloatData(int tokWhat, float[] data, int tokOperator, float comparisonFloat)`
`BS`	`compareInt(int tokWhat, int tokOperator, int comparisonValue)`
`private BS`	`compareString(int tokWhat, int tokOperator, String comparisonString)`
`private boolean`	`compareStringValues(int tokOperator, String propertyValue, String comparisonValue)`
`boolean`	`compileScript(String filename, String strScript, boolean debugCompiler)`
`boolean`	`compileScriptFile(String filename, boolean tQuiet)`
`private boolean`	`compileScriptFileInternal(String filename, String localPath, String remotePath, String scriptPath)`
`boolean`	`compileScriptString(String script, boolean tQuiet)`
`private void`	`connect(int index)`
`private void`	`console()`
`private void`	`define()`
`private void`	`defineAtomSet(String script)`
`private void`	`defineSets()` support for @xxx or define xxx commands
`private void`	`delay()`
`void`	`delayScript(int millis)`
`private void`	`delete()`
`void`	`deleteAtomsInVariables(BS bsDeleted)`
`boolean`	`dispatchCommands(boolean isSpt, boolean fromFunc)`
`private void`	`display(boolean isDisplay)`
`private void`	`doDelay(int millis)`
`private void`	`dots(int iShape)`
`private void`	`echo(int index, String id, boolean isImage)`
`private void`	`ellipsoid()`
`RadiusData`	`encodeRadiusParameter(int index, boolean isOnly, boolean allowAbsolute)`
`void`	`error(int iError)`
`(package private) void`	`errorAt(int iError, int i)`
`(package private) void`	`errorMore(int iError, String value, String more, String more2)`
`(package private) void`	`errorOrWarn(int iError, String value, String more, String more2, boolean warningOnly)`
`void`	`errorStr(int iError, String value)`
`void`	`errorStr2(int iError, String value, String more)`
`(package private) static String`	`errorString(int iError, String value, String more, String more2, boolean translated)`
`void`	`evalError(String message, String strUntranslated)`
`float`	`evalFunctionFloat(Object func, Object params, float[] values)`
`private Object`	`evaluate(Object expr, boolean asVariable)`
`void`	`evaluateCompiledScript(boolean isCmdLine_c_or_C_Option, boolean isCmdLine_C_Option, boolean historyDisabled, boolean listCommands, javajs.util.SB outputBuffer, boolean allowThreads)`
`Object`	`evaluateExpression(Object expr, boolean asVariable)` a general-use method to evaluate a "SET" type expression.
`boolean`	`evaluateParallel(ScriptContext context, ShapeManager shapeManager)`
`private void`	`executeCommands(boolean isTry)`
`private void`	`file()`
`void`	`finalizeObject(int shapeID, int colorArgb, float translucentLevel, int intScale, boolean doSet, Object data, int iptDisplayProperty, BS bs)`
`private void`	`fixed()`
`private String`	`fixScriptPath(String strScript, String filename)`
`float`	`floatParameter(int index)`
`private float`	`floatParameterRange(int i, float min, float max)`
`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, javajs.util.List<T[]> vProcess)`
`private void`	`font(int shapeType, float fontsize)`
`private void`	`frameControl(int i)`
`private void`	`frank(int index)`
`private void`	`function()`
`boolean`	`getAllowJSThreads()`
`int`	`getArgbParam(int index)`
`private int`	`getArgbParamLast(int index, boolean allowNone)`
`private int`	`getArgbParamOrNone(int index, boolean allowNone)`
`private BS`	`getAtomBits(int tokType, Object specInfo)`
`BS`	`getAtomBitSet(Object atomExpression)` a general method to evaluate a string representing an atom set.
`javajs.util.List<Integer>`	`getAtomBitSetVector(int atomCount, Object atomExpression)` just provides a vector list of atoms in a string-based expression
`Object`	`getBitsetProperty(BS bs, int tok, javajs.util.P3 ptRef, javajs.util.P4 planeRef, Object tokenValue, Object opValue, boolean useAtomMap, int index, boolean asVectorIfAll)`
`float[]`	`getBitsetPropertyFloat(BS bs, int tok, float min, float max)`
`private SV`	`getBitsetPropertySelector(int i, boolean mustBeSettable)`
`static int`	`getBondOrderFromString(String s)`
`String`	`getColorRange(int i)`
`float`	`getColorTrans(int i, boolean allowNone)` Checks color, translucent, opaque parameters.
`private int`	`getColorTriad(int i)`
`private String`	`getCommand(int pc, boolean allThisLine, boolean addSemi)` used for recall of commands in the application console
`(package private) static javajs.util.SB`	`getContextTrace(Viewer viewer, ScriptContext sc, javajs.util.SB sb, boolean isTop)`
`SV`	`getContextVariableAsVariable(String var)`
`Map<String,SV>`	`getContextVariables()`
`Map<String,Object>`	`getDefinedAtomSets()`
`private javajs.util.V3`	`getDrawObjectAxis(String axisID, int index)`
`static String`	`getErrorLineMessage(String functionName, String filename, int lineCurrent, int pcCurrent, String lineInfo)`
`String`	`getErrorLineMessage2()`
`String`	`getErrorMessage()`
`String`	`getErrorMessageUntranslated()`
`private int`	`getExecutionWalltime()`
`(package private) JmolScriptExtension`	`getExtension()`
`(package private) static int`	`getFloatEncodedInt(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.
`String`	`getFullPathName()`
`private Map<String,Object>`	`getHash(int i)`
`javajs.util.P4`	`getHklPlane(javajs.util.P3 pt)`
`String`	`getIsosurfaceDataRange(int iShape, String sep)`
`int`	`getLinenumber(ScriptContext c)`
`int`	`getMadParameter()`
`String`	`getNextStatement()` when paused, indicates what statement will be next
`private Object`	`getNumericParameter(String var)`
`private javajs.util.P3[]`	`getObjectBoundingBox(String id)`
`private javajs.util.P3`	`getObjectCenter(String axisID, int index, int modelIndex)`
`Object`	`getParameter(String key, int tokType)`
`(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(String s)`
`javajs.util.P3`	`getPoint3f(int i, boolean allowFractional)`
`javajs.util.P4`	`getPoint4f(int i)`
`javajs.util.P3[]`	`getPointArray(int i, int nPoints)`
`private Object`	`getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim)`
`javajs.util.List<javajs.util.P3>`	`getPointVector(T t, int i)`
`private void`	`getProperty()`
`private Quaternion`	`getQuaternionParameter(int i)`
`String`	`getScript()`
`ScriptContext`	`getScriptContext(String why)`
`private static int`	`getSeqCode(T instruction)`
`private int`	`getSetAxesTypeMad(int index)`
`String`	`getShapeNameParameter(int i)`
`Object`	`getShapeProperty(int shapeType, String propertyName)`
`boolean`	`getShapePropertyData(int shapeType, String propertyName, Object[] data)`
`private int`	`getShapeType(int tok)`
`private Object`	`getStringObjectAsVariable(String s, String key)`
`private String`	`getStringParameter(String var, boolean orReturnName)`
`ScriptContext`	`getThisContext()`
`T`	`getToken(int i)`
`private float`	`getTranslucentLevel(int i)`
`private float`	`getZoom(int ptCenter, int i, BS bs, float currentZoom)`
`private void`	`gotoCmd(String strTo)`
`void`	`haltExecution()`
`private void`	`hbond()`
`private void`	`help()`
`private void`	`history(int pt)`
`javajs.util.P4`	`hklParameter(int i)`
`private void`	`hover()`
`private boolean`	`ifCmd()`
`void`	`integerOutOfRange(int min, int max)`
`int`	`intParameter(int index)`
`int`	`intParameterRange(int i, int min, int max)`
`private int`	`intSetting(int pt)`
`private void`	`invArg()`
`private void`	`invertSelected()`
`boolean`	`isArrayParameter(int i)`
`boolean`	`isCenterParameter(int i)`
`boolean`	`isColorParam(int i)`
`private boolean`	`isCommandDisplayable(int i)` provides support for the script editor
`boolean`	`isExecuting()`
`boolean`	`isFloatParameter(int index)`
`boolean`	`isPaused()`
`boolean`	`isPoint3f(int i)`
`boolean`	`isStepping()`
`boolean`	`isStopped()`
`private void`	`label(int index)`
`javajs.util.List<Object>`	`listParameter(int i, int nMin, int nMax)`
`void`	`load()`
`String`	`loadFileAsync(String prefix, String filename, int i, boolean doClear)` Allows asynchronous file loading from the LOAD or SCRIPT command.
`private void`	`log()`
`private void`	`logDebugScript(int ifLevel)`
`private void`	`logLoadInfo(String msg)`
`BS`	`lookupIdentifierValue(String identifier)`
`private BS`	`lookupValue(String setName, boolean plurals)`
`private void`	`message()`
`private void`	`model(int offset)`
`int`	`modelNumberParameter(int index)`
`private void`	`move()`
`private void`	`moveto()`
`void`	`notifyResumeStatus()`
`private void`	`numberOutOfRange(float min, float max)`
`String`	`objectNameParameter(int index)`
`String`	`optParameterAsString(int i)`
`String`	`parameterAsString(int i)`
`private Object`	`parameterExpression(int pt, int ptMax, String key, boolean ignoreComma, boolean asVector, int ptAtom, boolean isArrayItem, Map<String,SV> localVars, String localVar)` This is the primary driver of the RPN (reverse Polish notation) expression processor.
`private boolean`	`parameterExpressionBoolean(int pt, int ptMax)`
`private javajs.util.List<SV>`	`parameterExpressionList(int pt, int ptAtom, boolean isArrayItem)`
`private String`	`parameterExpressionString(int pt, int ptMax)`
`private SV`	`parameterExpressionToken(int pt)`
`private boolean`	`pause()`
`void`	`pauseExecution(boolean withDelay)`
`private void`	`planeExpected()`
`javajs.util.P4`	`planeParameter(int i)`
`(package private) void`	`popContext(boolean isFlowCommand, boolean statementOnly)`
`private void`	`print()`
`private void`	`processShapeCommand(int tok)`
`private void`	`processTry(Map<String,SV> cv)`
`private void`	`prompt()`
`private void`	`proteinShape(int shapeType)`
`private void`	`pushContext(ContextToken token, String why)`
`private void`	`pushContext2(ContextToken token, String why)`
`void`	`pushContextDown(String why)`
`void`	`refresh()`
`private void`	`reset()`
`private void`	`restore()`
`private void`	`restoreFunction(JmolScriptFunction f, javajs.util.List<SV> params, SV tokenAtom)` note that functions requiring motion cannot be run in JavaScript
`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)`
`SV`	`runFunctionRet(JmolScriptFunction function, String name, javajs.util.List<SV> params, SV tokenAtom, boolean getReturn, boolean setContextPath, boolean allowThreads)`
`void`	`runScript(String script)`
`void`	`runScriptBuffer(String script, javajs.util.SB outputBuffer)` runs a script and sends selected output to a provided StringXBuilder
`private void`	`save()`
`void`	`script(int tok, String filename, String theScript)`
`void`	`scriptStatusOrBuffer(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()`
`void`	`setBooleanProperty(String key, boolean value)`
`void`	`setCompiler()`
`void`	`setCursorWait(boolean TF)`
`void`	`setDebugging()`
`private void`	`setEcho()`
`private void`	`setErrorMessage(String err)`
`void`	`setException(ScriptException sx, String msg, String untranslated)`
`private boolean`	`setFloatProperty(String key, float value)`
`private void`	`setHbond()`
`private boolean`	`setIntProperty(String key, int value)`
`private boolean`	`setLabel(String str)`
`boolean`	`setMeshDisplayProperty(int shape, int i, int tok)`
`private void`	`setMonitor()`
`private void`	`setObjectArgb(String str, int argb)`
`void`	`setObjectMad(int iShape, String name, int mad)`
`String`	`setObjectProp(String id, int tokCommand, int iTok)`
`String`	`setObjectProperty()`
`String`	`setObjectPropSafe(String id, int tokCommand, int iTok)`
`private void`	`setPicking()`
`private void`	`setPickingStyle()`
`private int`	`setScriptExtensions()`
`String`	`setShapeId(int iShape, int i, boolean idSeen)`
`void`	`setShapeProperty(int shapeType, String propertyName, Object propertyValue)`
`void`	`setShapePropertyBs(int iShape, String propertyName, Object propertyValue, BS bs)`
`private void`	`setShapeSize(int shapeType, RadiusData rd)`
`void`	`setShapeSizeBs(int shapeType, int size, BS bs)`
`void`	`setShapeTranslucency(int shapeType, String prefix, String translucency, float translucentLevel, BS bs)`
`private void`	`setSsbond()`
`private boolean`	`setStatement(int pc)` provides support for @x and @{....} in statements.
`private void`	`setStringProperty(String key, String value)`
`private boolean`	`setUnits(String units, int tok)`
`private void`	`setUserColors()`
`private void`	`setVariable(int pt, int ptMax, String key, int setType)`
`JmolScriptEvaluator`	`setViewer(Viewer viewer)`
`private void`	`setZslab()`
`void`	`showString(String str)`
`void`	`showStringPrint(String str, boolean isPrint)`
`private void`	`slab(boolean isDepth)`
`private void`	`ssbond()`
`private void`	`startEval()`
`static String`	`statementAsString(Viewer viewer, T[] statement, int iTok, boolean doLogMessages)`
`void`	`stepPausedExecution()`
`private void`	`stereo()`
`void`	`stopScriptThreads()`
`String`	`stringParameter(int index)`
`String[]`	`stringParameterSet(int i)`
`private String`	`stringSetting(int pt, boolean isJmolSet)`
`private void`	`structure()`
`private void`	`subset()`
`private int`	`switchCmd(ContextToken c, int tok)`
`private void`	`sync()`
`private void`	`timeout(int index)`
`int`	`tokAt(int i)`
`String`	`toString()`
`private void`	`translate(boolean isSelected)`
`private void`	`unbind()`
`private void`	`undoRedoMove()`
`private void`	`unitcell(int index)`
`boolean`	`useThreads()`
`private void`	`vector()`
`private void`	`vibration()`
`private void`	`warning(int iError, String value, String more)`
`private void`	`wireframe()`
`javajs.util.P3`	`xypParameter(int index)`
`private void`	`zap(boolean isZapCommand)`
`private void`	`zoom(boolean isZoomTo)`

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

Field Detail

allowJSThreads
```
public boolean allowJSThreads
```

listCommands
```
private boolean listCommands
```

isJS
```
public boolean isJS
```

tQuiet
```
public boolean tQuiet
```

chk
```
public boolean chk
```

isCmdLine_C_Option
```
private boolean isCmdLine_C_Option
```

isCmdLine_c_or_C_Option

protected boolean isCmdLine_c_or_C_Option

historyDisabled
```
public boolean historyDisabled
```

logMessages
```
public boolean logMessages
```

debugScript
```
private boolean debugScript
```

executionStopped
```
private boolean executionStopped
```

executionPaused
```
private boolean executionPaused
```

executionStepping
```
private boolean executionStepping
```

executing
```
private boolean executing
```

timeBeginExecution
```
private long timeBeginExecution
```

timeEndExecution
```
private long timeEndExecution
```

mustResumeEval
```
private boolean mustResumeEval
```

EXPRESSION_KEY

private static final String EXPRESSION_KEY

See Also:: Constant Field Values

sm
```
public ShapeManager sm
```

scriptLevelMax
```
private static final int scriptLevelMax
```
See Also:

Constant Field Values

currentThread
```
private Thread currentThread
```

viewer
```
public Viewer viewer
```

compiler
```
public ScriptCompiler compiler
```

definedAtomSets

public Map<String,Object> definedAtomSets

outputBuffer
```
private javajs.util.SB outputBuffer
```

contextPath
```
private String contextPath
```

scriptFileName
```
public String scriptFileName
```

functionName
```
public String functionName
```

isStateScript
```
private boolean isStateScript
```

scriptLevel
```
public int scriptLevel
```

scriptReportingLevel
```
private int scriptReportingLevel
```

commandHistoryLevelMax
```
public int commandHistoryLevelMax
```

aatoken
```
public T[][] aatoken
```

lineNumbers
```
private short[] lineNumbers
```

lineIndices
```
private int[][] lineIndices
```

contextVariables
```
public Map<String,SV> contextVariables
```

script
```
private String script
```

pc
```
protected int pc
```

thisCommand
```
public String thisCommand
```

fullCommand
```
public String fullCommand
```

st
```
public T[] st
```

slen
```
public int slen
```

iToken
```
public int iToken
```

lineEnd
```
private int lineEnd
```

pcEnd
```
private int pcEnd
```

scriptExtensions
```
private String scriptExtensions
```

forceNoAddHydrogens
```
private boolean forceNoAddHydrogens
```

parallelProcessor

private JmolParallelProcessor parallelProcessor

tryPt
```
static int tryPt
```

thisContext
```
public ScriptContext thisContext
```

error
```
private boolean error
```

errorMessage
```
private String errorMessage
```

errorMessageUntranslated

protected String errorMessageUntranslated

errorType
```
protected String errorType
```

iCommandError
```
protected int iCommandError
```

ignoreError
```
private boolean ignoreError
```

ERROR_axisExpected
```
static final int ERROR_axisExpected
```
See Also:

Constant Field Values

ERROR_backgroundModelError
```
static final int ERROR_backgroundModelError
```
See Also:

Constant Field Values

ERROR_badArgumentCount
```
public static final int ERROR_badArgumentCount
```
See Also:

Constant Field Values

ERROR_badMillerIndices
```
static final int ERROR_badMillerIndices
```
See Also:

Constant Field Values

ERROR_badRGBColor
```
public static final int ERROR_badRGBColor
```
See Also:

Constant Field Values

ERROR_booleanExpected
```
static final int ERROR_booleanExpected
```
See Also:

Constant Field Values

ERROR_booleanOrNumberExpected
```
static final int ERROR_booleanOrNumberExpected
```
See Also:

Constant Field Values

ERROR_booleanOrWhateverExpected
```
static final int ERROR_booleanOrWhateverExpected
```
See Also:

Constant Field Values

ERROR_colorExpected
```
static final int ERROR_colorExpected
```
See Also:

Constant Field Values

ERROR_colorOrPaletteRequired
```
static final int ERROR_colorOrPaletteRequired
```
See Also:

Constant Field Values

ERROR_commandExpected
```
static final int ERROR_commandExpected
```
See Also:

Constant Field Values

ERROR_coordinateOrNameOrExpressionRequired
```
static final int ERROR_coordinateOrNameOrExpressionRequired
```
See Also:

Constant Field Values

ERROR_drawObjectNotDefined
```
static final int ERROR_drawObjectNotDefined
```
See Also:

Constant Field Values

ERROR_endOfStatementUnexpected
```
public static final int ERROR_endOfStatementUnexpected
```
See Also:

Constant Field Values

ERROR_expressionExpected
```
public static final int ERROR_expressionExpected
```
See Also:

Constant Field Values

ERROR_expressionOrIntegerExpected
```
public static final int ERROR_expressionOrIntegerExpected
```
See Also:

Constant Field Values

ERROR_filenameExpected
```
static final int ERROR_filenameExpected
```
See Also:

Constant Field Values

ERROR_fileNotFoundException
```
public static final int ERROR_fileNotFoundException
```
See Also:

Constant Field Values

ERROR_incompatibleArguments
```
public static final int ERROR_incompatibleArguments
```
See Also:

Constant Field Values

ERROR_insufficientArguments
```
public static final int ERROR_insufficientArguments
```
See Also:

Constant Field Values

ERROR_integerExpected
```
static final int ERROR_integerExpected
```
See Also:

Constant Field Values

ERROR_integerOutOfRange
```
static final int ERROR_integerOutOfRange
```
See Also:

Constant Field Values

ERROR_invalidArgument
```
public static final int ERROR_invalidArgument
```
See Also:

Constant Field Values

ERROR_invalidParameterOrder
```
public static final int ERROR_invalidParameterOrder
```
See Also:

Constant Field Values

ERROR_keywordExpected
```
public static final int ERROR_keywordExpected
```
See Also:

Constant Field Values

ERROR_moCoefficients
```
public static final int ERROR_moCoefficients
```
See Also:

Constant Field Values

ERROR_moIndex
```
public static final int ERROR_moIndex
```
See Also:

Constant Field Values

ERROR_moModelError
```
public static final int ERROR_moModelError
```
See Also:

Constant Field Values

ERROR_moOccupancy
```
public static final int ERROR_moOccupancy
```
See Also:

Constant Field Values

ERROR_moOnlyOne
```
public static final int ERROR_moOnlyOne
```
See Also:

Constant Field Values

ERROR_multipleModelsDisplayedNotOK
```
public static final int ERROR_multipleModelsDisplayedNotOK
```
See Also:

Constant Field Values

ERROR_noData
```
public static final int ERROR_noData
```
See Also:

Constant Field Values

ERROR_noPartialCharges
```
public static final int ERROR_noPartialCharges
```
See Also:

Constant Field Values

ERROR_noUnitCell
```
static final int ERROR_noUnitCell
```
See Also:

Constant Field Values

ERROR_numberExpected
```
public static final int ERROR_numberExpected
```
See Also:

Constant Field Values

ERROR_numberMustBe
```
static final int ERROR_numberMustBe
```
See Also:

Constant Field Values

ERROR_numberOutOfRange
```
static final int ERROR_numberOutOfRange
```
See Also:

Constant Field Values

ERROR_objectNameExpected
```
static final int ERROR_objectNameExpected
```
See Also:

Constant Field Values

ERROR_planeExpected
```
static final int ERROR_planeExpected
```
See Also:

Constant Field Values

ERROR_propertyNameExpected
```
static final int ERROR_propertyNameExpected
```
See Also:

Constant Field Values

ERROR_spaceGroupNotFound
```
static final int ERROR_spaceGroupNotFound
```
See Also:

Constant Field Values

ERROR_stringExpected
```
static final int ERROR_stringExpected
```
See Also:

Constant Field Values

ERROR_stringOrIdentifierExpected
```
static final int ERROR_stringOrIdentifierExpected
```
See Also:

Constant Field Values

ERROR_tooManyPoints
```
static final int ERROR_tooManyPoints
```
See Also:

Constant Field Values

ERROR_tooManyScriptLevels
```
static final int ERROR_tooManyScriptLevels
```
See Also:

Constant Field Values

ERROR_unrecognizedAtomProperty
```
static final int ERROR_unrecognizedAtomProperty
```
See Also:

Constant Field Values

ERROR_unrecognizedBondProperty
```
static final int ERROR_unrecognizedBondProperty
```
See Also:

Constant Field Values

ERROR_unrecognizedCommand
```
static final int ERROR_unrecognizedCommand
```
See Also:

Constant Field Values

ERROR_unrecognizedExpression
```
static final int ERROR_unrecognizedExpression
```
See Also:

Constant Field Values

ERROR_unrecognizedObject
```
static final int ERROR_unrecognizedObject
```
See Also:

Constant Field Values

ERROR_unrecognizedParameter
```
static final int ERROR_unrecognizedParameter
```
See Also:

Constant Field Values

ERROR_unrecognizedParameterWarning
```
static final int ERROR_unrecognizedParameterWarning
```
See Also:

Constant Field Values

ERROR_unrecognizedShowParameter
```
static final int ERROR_unrecognizedShowParameter
```
See Also:

Constant Field Values

ERROR_what
```
public static final int ERROR_what
```
See Also:

Constant Field Values

ERROR_writeWhat
```
public static final int ERROR_writeWhat
```
See Also:

Constant Field Values

ERROR_multipleModelsNotOK
```
static final int ERROR_multipleModelsNotOK
```
See Also:

Constant Field Values

ERROR_cannotSet
```
static final int ERROR_cannotSet
```
See Also:

Constant Field Values

tempStatement
```
private T[] tempStatement
```

isBondSet
```
private boolean isBondSet
```

expressionResult
```
public Object expressionResult
```

theTok
```
public int theTok
```

theToken
```
public T theToken
```

coordinatesAreFractional

private boolean coordinatesAreFractional

fractionalPoint
```
private javajs.util.P3 fractionalPoint
```

scriptExt
```
private JmolScriptExtension scriptExt
```

iProcess
```
static int iProcess
```

colorArgb
```
public int[] colorArgb
```

scriptDelayThread
```
private JmolThread scriptDelayThread
```

fileLoadThread
```
private JmolThread fileLoadThread
```

Constructor Detail
- ScriptEvaluator
```
public ScriptEvaluator()
```

Method Detail

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

getAllowJSThreads in interface JmolScriptEvaluator

setViewer
```
public JmolScriptEvaluator setViewer(Viewer viewer)
```
Specified by:

setViewer in interface JmolScriptEvaluator

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

setCompiler in interface JmolScriptEvaluator

compileScriptString

public boolean compileScriptString(String script,
                                   boolean tQuiet)

Specified by:: compileScriptString in interface JmolScriptEvaluator

compileScriptFile

public boolean compileScriptFile(String filename,
                                 boolean tQuiet)

Specified by:: compileScriptFile in interface JmolScriptEvaluator

evaluateCompiledScript

public void evaluateCompiledScript(boolean isCmdLine_c_or_C_Option,
                                   boolean isCmdLine_C_Option,
                                   boolean historyDisabled,
                                   boolean listCommands,
                                   javajs.util.SB outputBuffer,
                                   boolean allowThreads)

Specified by:: evaluateCompiledScript in interface JmolScriptEvaluator

useThreads
```
public boolean useThreads()
```

startEval
```
private void startEval()
```

executeCommands

private void executeCommands(boolean isTry)

resumeEval
```
public void resumeEval(ScriptContext sc)
```
From dispatchCommands and JmolThread resumeEval. After throwing a ScriptInterruption, all statements following the current one are lost. When a JavaScript timeout returns from a DELAY, MOVE, MOVETO, or other sleep-requiring command, it is the ScriptContext that contains all the required information for restarting that "thread". In Java, we don't have to worry about this, because the current thread is just put to sleep, not stopped, but in JavaScript, where we only have one thread, we need to manage this more carefully. We re-enter the halted script here, using a saved script context. The program counter is incremented to skip the initiating statement, and all parent contexts up the line are set with mustResumeEval = true.

Specified by:

resumeEval in interface JmolScriptEvaluator

Parameters:

sc -

runScript
```
public void runScript(String script)
               throws ScriptException
```
Specified by:

runScript in interface JmolScriptEvaluator

Throws:

ScriptException

runScriptBuffer
```
public void runScriptBuffer(String script,
                            javajs.util.SB outputBuffer)
                     throws ScriptException
```
runs a script and sends selected output to a provided StringXBuilder

Specified by:

runScriptBuffer in interface JmolScriptEvaluator

Parameters:

script -

outputBuffer -

Throws:

ScriptException

checkScriptSilent
```
public ScriptContext checkScriptSilent(String script)
```
a method for just checking a script

Specified by:

checkScriptSilent in interface JmolScriptEvaluator

Parameters:

script -

Returns:

a ScriptContext that indicates errors and provides a tokenized version of the script that has passed all syntax checking, both in the compiler and the evaluator

getContextTrace

static javajs.util.SB getContextTrace(Viewer viewer,
                                      ScriptContext sc,
                                      javajs.util.SB sb,
                                      boolean isTop)

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

setDebugging in interface JmolScriptEvaluator

getExecutionWalltime
```
private int getExecutionWalltime()
```

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

haltExecution in interface JmolScriptEvaluator

pauseExecution
```
public void pauseExecution(boolean withDelay)
```
Specified by:

pauseExecution in interface JmolScriptEvaluator

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

stepPausedExecution in interface JmolScriptEvaluator

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

resumePausedExecution in interface JmolScriptEvaluator

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

isExecuting in interface JmolScriptEvaluator

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

isPaused in interface JmolScriptEvaluator

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

isStepping in interface JmolScriptEvaluator

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

isStopped in interface JmolScriptEvaluator

getNextStatement
```
public String getNextStatement()
```
when paused, indicates what statement will be next

Specified by:

getNextStatement in interface JmolScriptEvaluator

Returns:

a string indicating the statement

getCommand
```
private String getCommand(int pc,
                          boolean allThisLine,
                          boolean addSemi)
```
used for recall of commands in the application console

Parameters:

pc -

allThisLine -

addSemi -

Returns:

a string representation of the command

logDebugScript

private void logDebugScript(int ifLevel)

evaluateExpression
```
public Object evaluateExpression(Object expr,
                                 boolean asVariable)
```
a general-use method to evaluate a "SET" type expression.

Specified by:

evaluateExpression in interface JmolScriptEvaluator

Parameters:

expr -

asVariable -

Returns:

an object of one of the following types: Boolean, Integer, Float, String, Point3f, BitSet

evaluate

private Object evaluate(Object expr,
                        boolean asVariable)

getAtomBitSet
```
public BS getAtomBitSet(Object atomExpression)
```
a general method to evaluate a string representing an atom set.

Specified by:

getAtomBitSet in interface JmolScriptEvaluator

Parameters:

atomExpression -

Returns:

is a bitset indicating the selected atoms

getAtomBitSetVector
```
public javajs.util.List<Integer> getAtomBitSetVector(int atomCount,
                                                     Object atomExpression)
```
just provides a vector list of atoms in a string-based expression

Specified by:

getAtomBitSetVector in interface JmolScriptEvaluator

Parameters:

atomCount -

atomExpression -

Returns:

vector list of selected atoms

parameterExpressionList

private javajs.util.List<SV> parameterExpressionList(int pt,
                                                     int ptAtom,
                                                     boolean isArrayItem)
                                              throws ScriptException

Throws:: ScriptException

parameterExpressionString

private String parameterExpressionString(int pt,
                                         int ptMax)
                                  throws ScriptException

Throws:: ScriptException

parameterExpressionBoolean

private boolean parameterExpressionBoolean(int pt,
                                           int ptMax)
                                    throws ScriptException

Throws:: ScriptException

parameterExpressionToken

private SV parameterExpressionToken(int pt)
                             throws ScriptException

Throws:: ScriptException

parameterExpression
```
private Object parameterExpression(int pt,
                                   int ptMax,
                                   String key,
                                   boolean ignoreComma,
                                   boolean asVector,
                                   int ptAtom,
                                   boolean isArrayItem,
                                   Map<String,SV> localVars,
                                   String localVar)
                            throws ScriptException
```
This is the primary driver of the RPN (reverse Polish notation) expression processor. It handles all math outside of a "traditional" Jmol SELECT/RESTRICT context. [Object atomExpression() takes care of that, and also uses the RPN class.]

Parameters:

pt - token index in statement start of expression

ptMax - token index in statement end of expression

key - variable name for debugging reference only -- null indicates return Boolean -- "" indicates return String

ignoreComma -

asVector - a flag passed on to RPN;

ptAtom - this is a for() or select() function with a specific atom selected

isArrayItem - we are storing A[x] = ... so we need to deliver "x" as well

localVars - see below -- lists all nested for(x, {exp}, select(y, {ex},...)) variables

localVar - x or y in above for(), select() examples

Returns:

either a vector or a value, caller's choice.

Throws:

ScriptException - errors are thrown directly to the Eval error system.

getHash

private Map<String,Object> getHash(int i)
                            throws ScriptException

Throws:: ScriptException

bitsetVariableVector

javajs.util.List<SV> bitsetVariableVector(Object v)

getBitsetPropertySelector

private SV getBitsetPropertySelector(int i,
                                     boolean mustBeSettable)
                              throws ScriptException

Throws:: ScriptException

getBitsetPropertyFloat

public float[] getBitsetPropertyFloat(BS bs,
                                      int tok,
                                      float min,
                                      float max)
                               throws ScriptException

Throws:: ScriptException

getBitsetProperty

public Object getBitsetProperty(BS bs,
                                int tok,
                                javajs.util.P3 ptRef,
                                javajs.util.P4 planeRef,
                                Object tokenValue,
                                Object opValue,
                                boolean useAtomMap,
                                int index,
                                boolean asVectorIfAll)
                         throws ScriptException

Throws:: ScriptException

setBitsetProperty

private void setBitsetProperty(BS bs,
                               int tok,
                               int iValue,
                               float fValue,
                               T tokenValue)
                        throws ScriptException

Throws:: ScriptException

getDefinedAtomSets
```
public Map<String,Object> getDefinedAtomSets()
```
Specified by:

getDefinedAtomSets in interface JmolScriptEvaluator

getContextVariables
```
public Map<String,SV> getContextVariables()
```
Specified by:

getContextVariables in interface JmolScriptEvaluator

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

getScript in interface JmolScriptEvaluator

compileScript

public boolean compileScript(String filename,
                             String strScript,
                             boolean debugCompiler)

fixScriptPath

private String fixScriptPath(String strScript,
                             String filename)

setScriptExtensions
```
private int setScriptExtensions()
```

compileScriptFileInternal

private boolean compileScriptFileInternal(String filename,
                                          String localPath,
                                          String remotePath,
                                          String scriptPath)

getParameter

public Object getParameter(String key,
                           int tokType)

getStringParameter

private String getStringParameter(String var,
                                  boolean orReturnName)

getNumericParameter

private Object getNumericParameter(String var)

getContextVariableAsVariable

public SV getContextVariableAsVariable(String var)

getStringObjectAsVariable

private Object getStringObjectAsVariable(String s,
                                         String key)

evalFunctionFloat

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

Specified by:: evalFunctionFloat in interface JmolScriptEvaluator

runFunctionRet

public SV runFunctionRet(JmolScriptFunction function,
                         String name,
                         javajs.util.List<SV> params,
                         SV tokenAtom,
                         boolean getReturn,
                         boolean setContextPath,
                         boolean allowThreads)
                  throws ScriptException

Throws:: ScriptException

processTry

private void processTry(Map<String,SV> cv)
                 throws ScriptException

Throws:: ScriptException

restoreFunction

private void restoreFunction(JmolScriptFunction f,
                             javajs.util.List<SV> params,
                             SV tokenAtom)
                      throws ScriptException

note that functions requiring motion cannot be run in JavaScript

Parameters:: f -; params -; tokenAtom -
Throws:: ScriptException

clearDefinedVariableAtomSets

public void clearDefinedVariableAtomSets()

defineSets
```
private void defineSets()
```
support for @xxx or define xxx commands

defineAtomSet

private void defineAtomSet(String script)

lookupIdentifierValue

public BS lookupIdentifierValue(String identifier)
                         throws ScriptException

Throws:: ScriptException

lookupValue

private BS lookupValue(String setName,
                       boolean plurals)
                throws ScriptException

Throws:: ScriptException

deleteAtomsInVariables
```
public void deleteAtomsInVariables(BS bsDeleted)
```
Specified by:

deleteAtomsInVariables in interface JmolScriptEvaluator

setStatement
```
private boolean setStatement(int pc)
                      throws ScriptException
```
provides support for @x and @{....} in statements. The compiler passes on these, because they must be integrated with the statement dynamically.

Parameters:

pc -

Returns:

a fixed token set -- with possible overrun of unused null tokens

Throws:

ScriptException

clearState

private void clearState(boolean tQuiet)

getThisContext
```
public ScriptContext getThisContext()
```
Specified by:

getThisContext in interface JmolScriptEvaluator

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

pushContextDown in interface JmolScriptEvaluator

pushContext

private void pushContext(ContextToken token,
                         String why)
                  throws ScriptException

Throws:: ScriptException

pushContext2

private void pushContext2(ContextToken token,
                          String why)

getScriptContext
```
public ScriptContext getScriptContext(String why)
```
Specified by:

getScriptContext in interface JmolScriptEvaluator

popContext

void popContext(boolean isFlowCommand,
                boolean statementOnly)

restoreScriptContext

public void restoreScriptContext(ScriptContext context,
                                 boolean isPopContext,
                                 boolean isFlowCommand,
                                 boolean statementOnly)

getLinenumber

public int getLinenumber(ScriptContext c)

setException

public void setException(ScriptException sx,
                         String msg,
                         String untranslated)

Specified by:: setException in interface JmolScriptEvaluator

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

getErrorMessage in interface JmolScriptEvaluator

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

getErrorMessageUntranslated in interface JmolScriptEvaluator

setErrorMessage

private void setErrorMessage(String err)

planeExpected

private void planeExpected()
                    throws ScriptException

Throws:: ScriptException

integerOutOfRange

public void integerOutOfRange(int min,
                              int max)
                       throws ScriptException

Throws:: ScriptException

numberOutOfRange

private void numberOutOfRange(float min,
                              float max)
                       throws ScriptException

Throws:: ScriptException

errorAt

void errorAt(int iError,
             int i)
      throws ScriptException

Throws:: ScriptException

invArg

private void invArg()
             throws ScriptException

Throws:: ScriptException

error

public void error(int iError)
           throws ScriptException

Throws:: ScriptException

errorStr

public void errorStr(int iError,
                     String value)
              throws ScriptException

Throws:: ScriptException

errorStr2

public void errorStr2(int iError,
                      String value,
                      String more)
               throws ScriptException

Throws:: ScriptException

errorMore

void errorMore(int iError,
               String value,
               String more,
               String more2)
        throws ScriptException

Throws:: ScriptException

warning

private void warning(int iError,
                     String value,
                     String more)
              throws ScriptException

Throws:: ScriptException

errorOrWarn

void errorOrWarn(int iError,
                 String value,
                 String more,
                 String more2,
                 boolean warningOnly)
          throws ScriptException

Throws:: ScriptException

evalError

public void evalError(String message,
                      String strUntranslated)
               throws ScriptException

Throws:: ScriptException

errorString

static String errorString(int iError,
                          String value,
                          String more,
                          String more2,
                          boolean translated)

Parameters:: iError -; value -; more -; more2 -; translated -
Returns:: constructed error string

getErrorLineMessage

public static String getErrorLineMessage(String functionName,
                                         String filename,
                                         int lineCurrent,
                                         int pcCurrent,
                                         String lineInfo)

toString
```
public String toString()
```
Overrides:

toString in class Object

statementAsString

public static String statementAsString(Viewer viewer,
                                       T[] statement,
                                       int iTok,
                                       boolean doLogMessages)

getShapeProperty

public Object getShapeProperty(int shapeType,
                               String propertyName)

getShapePropertyData

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

setObjectMad

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

setObjectArgb

private void setObjectArgb(String str,
                           int argb)

setShapeProperty

public void setShapeProperty(int shapeType,
                             String propertyName,
                             Object propertyValue)

setShapePropertyBs

public void setShapePropertyBs(int iShape,
                               String propertyName,
                               Object propertyValue,
                               BS bs)

setShapeSizeBs

public void setShapeSizeBs(int shapeType,
                           int size,
                           BS bs)

setShapeSize

private void setShapeSize(int shapeType,
                          RadiusData rd)

setBooleanProperty

public void setBooleanProperty(String key,
                               boolean value)

setIntProperty

private boolean setIntProperty(String key,
                               int value)

setFloatProperty

private boolean setFloatProperty(String key,
                                 float value)

setStringProperty

private void setStringProperty(String key,
                               String value)

showString
```
public void showString(String str)
```

showStringPrint

public void showStringPrint(String str,
                            boolean isPrint)

scriptStatusOrBuffer

public void scriptStatusOrBuffer(String s)

atomExpressionAt

public BS atomExpressionAt(int index)
                    throws ScriptException

Throws:: ScriptException

atomExpression

public BS atomExpression(T[] code,
                         int pcStart,
                         int pcStop,
                         boolean allowRefresh,
                         boolean allowUnderflow,
                         boolean mustBeBitSet,
                         boolean andNotDeleted)
                  throws ScriptException

Parameters:: code -; pcStart -; pcStop -; allowRefresh -; allowUnderflow -; mustBeBitSet -; andNotDeleted - IGNORED
Returns:: atom bitset
Throws:: ScriptException

compareFloatData

private BS compareFloatData(int tokWhat,
                            float[] data,
                            int tokOperator,
                            float comparisonFloat)

Parameters:: tokWhat -; data -; tokOperator -; comparisonFloat -
Returns:: BitSet

compareString

private BS compareString(int tokWhat,
                         int tokOperator,
                         String comparisonString)
                  throws ScriptException

Throws:: ScriptException

compareInt

public BS compareInt(int tokWhat,
                     int tokOperator,
                     int comparisonValue)

compareStringValues

private boolean compareStringValues(int tokOperator,
                                    String propertyValue,
                                    String comparisonValue)
                             throws ScriptException

Throws:: ScriptException

compareFloat

private static boolean compareFloat(int tokOperator,
                                    float propertyFloat,
                                    float comparisonFloat)

getAtomBits

private BS getAtomBits(int tokType,
                       Object specInfo)

getSeqCode

private static int getSeqCode(T instruction)

checkLast

public int checkLast(int i)
              throws ScriptException

Throws:: ScriptException

checkLength

public int checkLength(int length)
                throws ScriptException

Throws:: ScriptException

checkLengthErrorPt

private int checkLengthErrorPt(int length,
                               int errorPt)
                        throws ScriptException

Throws:: ScriptException

checkLength23

public int checkLength23()
                  throws ScriptException

Throws:: ScriptException

checkLength34

private int checkLength34()
                   throws ScriptException

Throws:: ScriptException

getToken

public T getToken(int i)
           throws ScriptException

Throws:: ScriptException

tokAt
```
public int tokAt(int i)
```

checkToken
```
private boolean checkToken(int i)
```

modelNumberParameter

public int modelNumberParameter(int index)
                         throws ScriptException

Throws:: ScriptException

optParameterAsString

public String optParameterAsString(int i)
                            throws ScriptException

Throws:: ScriptException

parameterAsString

public String parameterAsString(int i)
                         throws ScriptException

Throws:: ScriptException

intParameter

public int intParameter(int index)
                 throws ScriptException

Throws:: ScriptException

intParameterRange

public int intParameterRange(int i,
                             int min,
                             int max)
                      throws ScriptException

Throws:: ScriptException

isFloatParameter

public boolean isFloatParameter(int index)

floatParameterRange

private float floatParameterRange(int i,
                                  float min,
                                  float max)
                           throws ScriptException

Throws:: ScriptException

floatParameter

public float floatParameter(int index)
                     throws ScriptException

Throws:: ScriptException

listParameter

public javajs.util.List<Object> listParameter(int i,
                                              int nMin,
                                              int nMax)
                                       throws ScriptException

Throws:: ScriptException

floatParameterSet
```
public float[] floatParameterSet(int i,
                                 int nMin,
                                 int nMax)
                          throws ScriptException
```
process a general string or set of parameters as an array of floats, allowing for relatively free form input

Parameters:

i -

nMin -

nMax -

Returns:

array of floats

Throws:

ScriptException

isArrayParameter

public boolean isArrayParameter(int i)

getPointArray

public javajs.util.P3[] getPointArray(int i,
                                      int nPoints)
                               throws ScriptException

Throws:: ScriptException

stringParameter

public String stringParameter(int index)
                       throws ScriptException

Throws:: ScriptException

stringParameterSet

public String[] stringParameterSet(int i)
                            throws ScriptException

Throws:: ScriptException

objectNameParameter

public String objectNameParameter(int index)
                           throws ScriptException

Throws:: ScriptException

booleanParameter

private boolean booleanParameter(int i)
                          throws ScriptException

Throws:: ScriptException

atomCenterOrCoordinateParameter

private javajs.util.P3 atomCenterOrCoordinateParameter(int i)
                                                throws ScriptException

Throws:: ScriptException

isCenterParameter

public boolean isCenterParameter(int i)

centerParameter

public javajs.util.P3 centerParameter(int i)
                               throws ScriptException

Throws:: ScriptException

centerParameterForModel

private javajs.util.P3 centerParameterForModel(int i,
                                               int modelIndex)
                                        throws ScriptException

Throws:: ScriptException

planeParameter

public javajs.util.P4 planeParameter(int i)
                              throws ScriptException

Throws:: ScriptException

hklParameter

public javajs.util.P4 hklParameter(int i)
                            throws ScriptException

Throws:: ScriptException

getHklPlane

public javajs.util.P4 getHklPlane(javajs.util.P3 pt)

getMadParameter

public int getMadParameter()
                    throws ScriptException

Throws:: ScriptException

getSetAxesTypeMad

private int getSetAxesTypeMad(int index)
                       throws ScriptException

Throws:: ScriptException

isColorParam
```
public boolean isColorParam(int i)
```

getArgbParam

public int getArgbParam(int index)
                 throws ScriptException

Throws:: ScriptException

getArgbParamLast

private int getArgbParamLast(int index,
                             boolean allowNone)
                      throws ScriptException

Throws:: ScriptException

getArgbParamOrNone

private int getArgbParamOrNone(int index,
                               boolean allowNone)
                        throws ScriptException

Throws:: ScriptException

getColorTriad

private int getColorTriad(int i)
                   throws ScriptException

Throws:: ScriptException

isPoint3f
```
public boolean isPoint3f(int i)
```

getPoint3f

public javajs.util.P3 getPoint3f(int i,
                                 boolean allowFractional)
                          throws ScriptException

Throws:: ScriptException

getPoint4f

public javajs.util.P4 getPoint4f(int i)
                          throws ScriptException

Throws:: ScriptException

getPointOrPlane

private Object getPointOrPlane(int index,
                               boolean integerOnly,
                               boolean allowFractional,
                               boolean doConvert,
                               boolean implicitFractional,
                               int minDim,
                               int maxDim)
                        throws ScriptException

Throws:: ScriptException

xypParameter

public javajs.util.P3 xypParameter(int index)
                            throws ScriptException

Throws:: ScriptException

isCommandDisplayable
```
private boolean isCommandDisplayable(int i)
```
provides support for the script editor

Parameters:

i -

Returns:

true if displayable

checkContinue
```
private boolean checkContinue()
                       throws ScriptException
```
checks to see if there is a pause condition, during which commands can still be issued, but with the ! first.

Returns:

false if there was a problem

Throws:

ScriptException

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

notifyResumeStatus in interface JmolScriptEvaluator

doDelay
```
private void doDelay(int millis)
              throws ScriptException
```
Parameters:

millis - negative here bypasses max check

Throws:

ScriptException

dispatchCommands

public boolean dispatchCommands(boolean isSpt,
                                boolean fromFunc)
                         throws ScriptException

Parameters:: isSpt -; fromFunc -
Returns:: false only when still working through resumeEval
Throws:: ScriptException

commandLoop

private void commandLoop(boolean fromFunc)
                  throws ScriptException

Throws:: ScriptException

cache

private void cache()
            throws ScriptException

Throws:: ScriptException

setCursorWait

public void setCursorWait(boolean TF)

processShapeCommand

private void processShapeCommand(int tok)
                          throws ScriptException

Throws:: ScriptException

getExtension
```
JmolScriptExtension getExtension()
```

flowControl

private boolean flowControl(int tok,
                            boolean isForCheck,
                            javajs.util.List<T[]> vProcess)
                     throws ScriptException

Throws:: ScriptException

gotoCmd

private void gotoCmd(String strTo)
              throws ScriptException

Throws:: ScriptException

breakCmd
```
private void breakCmd(int pt)
```

addProcess

private void addProcess(javajs.util.List<T[]> vProcess,
                        int pc,
                        int pt)

switchCmd

private int switchCmd(ContextToken c,
                      int tok)
               throws ScriptException

Throws:: ScriptException

ifCmd

private boolean ifCmd()
               throws ScriptException

Throws:: ScriptException

returnCmd

private void returnCmd(SV tv)
                throws ScriptException

Throws:: ScriptException

help

private void help()
           throws ScriptException

Throws:: ScriptException

move

private void move()
           throws ScriptException

Throws:: ScriptException

moveto

private void moveto()
             throws ScriptException

Throws:: ScriptException

bondorder

private void bondorder()
                throws ScriptException

Throws:: ScriptException

console

private void console()
              throws ScriptException

Throws:: ScriptException

centerAt

private void centerAt()
               throws ScriptException

Throws:: ScriptException

stereo

private void stereo()
             throws ScriptException

Throws:: ScriptException

connect
```
private void connect(int index)
              throws ScriptException
```
Parameters:

index - 0 is this is the hbond command

Throws:

ScriptException

getTranslucentLevel

private float getTranslucentLevel(int i)
                           throws ScriptException

Throws:: ScriptException

getProperty

private void getProperty()
                  throws ScriptException

Throws:: ScriptException

background

private void background(int i)
                 throws ScriptException

Throws:: ScriptException

center

private void center(int i)
             throws ScriptException

Throws:: ScriptException

setObjectProperty

public String setObjectProperty()
                         throws ScriptException

Throws:: ScriptException

setObjectPropSafe

public String setObjectPropSafe(String id,
                                int tokCommand,
                                int iTok)

Specified by:: setObjectPropSafe in interface JmolScriptEvaluator

setObjectProp

public String setObjectProp(String id,
                            int tokCommand,
                            int iTok)
                     throws ScriptException

Throws:: ScriptException

color

private void color()
            throws ScriptException

Throws:: ScriptException

changeElementColor

private boolean changeElementColor(String str,
                                   int argb)

colorShape

private void colorShape(int shapeType,
                        int index,
                        boolean isBackground)
                 throws ScriptException

Throws:: ScriptException

setShapeTranslucency

public void setShapeTranslucency(int shapeType,
                                 String prefix,
                                 String translucency,
                                 float translucentLevel,
                                 BS bs)

cd

private void cd()
         throws ScriptException

Throws:: ScriptException

define

private void define()
             throws ScriptException

Throws:: ScriptException

echo

private void echo(int index,
                  String id,
                  boolean isImage)
           throws ScriptException

Throws:: ScriptException

message

private void message()
              throws ScriptException

Throws:: ScriptException

log

private void log()
          throws ScriptException

Throws:: ScriptException

label

private void label(int index)
            throws ScriptException

Throws:: ScriptException

hover

private void hover()
            throws ScriptException

Throws:: ScriptException

load

public void load()
          throws ScriptException

Throws:: ScriptException

loadFileAsync
```
public String loadFileAsync(String prefix,
                            String filename,
                            int i,
                            boolean doClear)
                     throws ScriptException
```
Allows asynchronous file loading from the LOAD or SCRIPT command. Saves the context, initiates a FileLoadThread instance. When the file loading completes, the file data (sans filename) is saved in the FileManager cache under cache://localLoad_xxxxx. Context is resumed at this command in the script, and the file is then retrieved from the cache. Only run from JSmol/HTML5 when viewer.isJS; Incompatibilities: LOAD and SCRIPT commands, load() function only; only one "?" per LOAD command

Parameters:

prefix -

filename - or null if end of LOAD command and now just clearing out cache

i -

doClear - ensures only one file is in the cache for a given type

Returns:

cached file name if it exists

Throws:

ScriptException

logLoadInfo
```
private void logLoadInfo(String msg)
```

getFullPathName

public String getFullPathName()
                       throws ScriptException

Throws:: ScriptException

pause

private boolean pause()
               throws ScriptException

Throws:: ScriptException

print

private void print()
            throws ScriptException

Throws:: ScriptException

prompt

private void prompt()
             throws ScriptException

Throws:: ScriptException

refresh
```
public void refresh()
```

reset

private void reset()
            throws ScriptException

Throws:: ScriptException

restrict

private void restrict()
               throws ScriptException

Throws:: ScriptException

restrictSelected

private void restrictSelected(boolean isBond,
                              boolean doInvert)

rotate

private void rotate(boolean isSpin,
                    boolean isSelected)
             throws ScriptException

Throws:: ScriptException

getQuaternionParameter

private Quaternion getQuaternionParameter(int i)
                                   throws ScriptException

Throws:: ScriptException

getPointVector

public javajs.util.List<javajs.util.P3> getPointVector(T t,
                                                       int i)
                                                throws ScriptException

Throws:: ScriptException

getObjectCenter

private javajs.util.P3 getObjectCenter(String axisID,
                                       int index,
                                       int modelIndex)

getObjectBoundingBox

private javajs.util.P3[] getObjectBoundingBox(String id)

getDrawObjectAxis

private javajs.util.V3 getDrawObjectAxis(String axisID,
                                         int index)

script

public void script(int tok,
                   String filename,
                   String theScript)
            throws ScriptException

Throws:: ScriptException

function

private void function()
               throws ScriptException

Throws:: ScriptException

sync

private void sync()
           throws ScriptException

Throws:: ScriptException

history

private void history(int pt)
              throws ScriptException

Throws:: ScriptException

display

private void display(boolean isDisplay)
              throws ScriptException

Throws:: ScriptException

delete

private void delete()
             throws ScriptException

Throws:: ScriptException

select

private void select(int i)
             throws ScriptException

Throws:: ScriptException

subset

private void subset()
             throws ScriptException

Throws:: ScriptException

invertSelected

private void invertSelected()
                     throws ScriptException

Throws:: ScriptException

translate

private void translate(boolean isSelected)
                throws ScriptException

Throws:: ScriptException

zap

private void zap(boolean isZapCommand)
          throws ScriptException

Throws:: ScriptException

zoom

private void zoom(boolean isZoomTo)
           throws ScriptException

Throws:: ScriptException

getZoom

private float getZoom(int ptCenter,
                      int i,
                      BS bs,
                      float currentZoom)
               throws ScriptException

Throws:: ScriptException

delay

private void delay()
            throws ScriptException

Throws:: ScriptException

slab

private void slab(boolean isDepth)
           throws ScriptException

Throws:: ScriptException

ellipsoid

private void ellipsoid()
                throws ScriptException

Throws:: ScriptException

getShapeNameParameter

public String getShapeNameParameter(int i)
                             throws ScriptException

Throws:: ScriptException

setShapeId

public String setShapeId(int iShape,
                         int i,
                         boolean idSeen)
                  throws ScriptException

Throws:: ScriptException

setAtomShapeSize

private void setAtomShapeSize(int shape,
                              float scale)
                       throws ScriptException

Throws:: ScriptException

encodeRadiusParameter

public RadiusData encodeRadiusParameter(int index,
                                        boolean isOnly,
                                        boolean allowAbsolute)
                                 throws ScriptException

Throws:: ScriptException

structure

private void structure()
                throws ScriptException

Throws:: ScriptException

wireframe

private void wireframe()
                throws ScriptException

Throws:: ScriptException

ssbond

private void ssbond()
             throws ScriptException

Throws:: ScriptException

hbond

private void hbond()
            throws ScriptException

Throws:: ScriptException

vector

private void vector()
             throws ScriptException

Throws:: ScriptException

vibration

private void vibration()
                throws ScriptException

Throws:: ScriptException

dots

private void dots(int iShape)
           throws ScriptException

Throws:: ScriptException

proteinShape

private void proteinShape(int shapeType)
                   throws ScriptException

Throws:: ScriptException

animation

private void animation()
                throws ScriptException

Throws:: ScriptException

assign

private void assign()
             throws ScriptException

Throws:: ScriptException

file

private void file()
           throws ScriptException

Throws:: ScriptException

fixed

private void fixed()
            throws ScriptException

Throws:: ScriptException

model

private void model(int offset)
            throws ScriptException

Throws:: ScriptException

bitSetForModelFileNumber
```
BS bitSetForModelFileNumber(int m)
```

frameControl

private void frameControl(int i)
                   throws ScriptException

Throws:: ScriptException

getShapeType

private int getShapeType(int tok)
                  throws ScriptException

Throws:: ScriptException

font

private void font(int shapeType,
                  float fontsize)
           throws ScriptException

Throws:: ScriptException

set

private void set()
          throws ScriptException

Throws:: ScriptException

setZslab

private void setZslab()
               throws ScriptException

Throws:: ScriptException

setBondmode

private void setBondmode()
                  throws ScriptException

Throws:: ScriptException

setEcho

private void setEcho()
              throws ScriptException

Throws:: ScriptException

intSetting

private int intSetting(int pt)
                throws ScriptException

Throws:: ScriptException

floatSetting

private float floatSetting(int pt)
                    throws ScriptException

Throws:: ScriptException

stringSetting

private String stringSetting(int pt,
                             boolean isJmolSet)
                      throws ScriptException

Throws:: ScriptException

setLabel

private boolean setLabel(String str)
                  throws ScriptException

Throws:: ScriptException

setMonitor

private void setMonitor()
                 throws ScriptException

Throws:: ScriptException

setUnits

private boolean setUnits(String units,
                         int tok)
                  throws ScriptException

Throws:: ScriptException

setSsbond

private void setSsbond()
                throws ScriptException

Throws:: ScriptException

setHbond

private void setHbond()
               throws ScriptException

Throws:: ScriptException

setPicking

private void setPicking()
                 throws ScriptException

Throws:: ScriptException

setPickingStyle

private void setPickingStyle()
                      throws ScriptException

Throws:: ScriptException

timeout

private void timeout(int index)
              throws ScriptException

Throws:: ScriptException

setUserColors

private void setUserColors()
                    throws ScriptException

Throws:: ScriptException

setVariable

private void setVariable(int pt,
                         int ptMax,
                         String key,
                         int setType)
                  throws ScriptException

Parameters:: pt -; ptMax -; key -; setType -
Throws:: ScriptException

axes

private void axes(int index)
           throws ScriptException

Throws:: ScriptException

boundbox

private void boundbox(int index)
               throws ScriptException

Throws:: ScriptException

checkTicks

public TickInfo checkTicks(int index,
                           boolean allowUnitCell,
                           boolean allowScale,
                           boolean allowFirst)
                    throws ScriptException

Parameters:: index -; allowUnitCell - IGNORED; allowScale -; allowFirst -
Returns:: TickInfo
Throws:: ScriptException

unitcell

private void unitcell(int index)
               throws ScriptException

Throws:: ScriptException

frank

private void frank(int index)
            throws ScriptException

Throws:: ScriptException

selectionHalo

private void selectionHalo(int pt)
                    throws ScriptException

Throws:: ScriptException

save

private void save()
           throws ScriptException

Throws:: ScriptException

restore

private void restore()
              throws ScriptException

Throws:: ScriptException

getColorTrans
```
public float getColorTrans(int i,
                           boolean allowNone)
                    throws ScriptException
```
Checks color, translucent, opaque parameters.

Parameters:

i -

allowNone -

Returns:

translucentLevel and sets iToken and colorArgb[0]

Throws:

ScriptException

finalizeObject

public void finalizeObject(int shapeID,
                           int colorArgb,
                           float translucentLevel,
                           int intScale,
                           boolean doSet,
                           Object data,
                           int iptDisplayProperty,
                           BS bs)
                    throws ScriptException

Throws:: ScriptException

getColorRange

public String getColorRange(int i)
                     throws ScriptException

Throws:: ScriptException

getIsosurfaceDataRange

public String getIsosurfaceDataRange(int iShape,
                                     String sep)

setMeshDisplayProperty

public boolean setMeshDisplayProperty(int shape,
                                      int i,
                                      int tok)
                               throws ScriptException

Parameters:: shape -; i -; tok -
Returns:: true if successful
Throws:: ScriptException

bind

private void bind()
           throws ScriptException

Throws:: ScriptException

unbind

private void unbind()
             throws ScriptException

Throws:: ScriptException

undoRedoMove

private void undoRedoMove()
                   throws ScriptException

Throws:: ScriptException

getFloatEncodedInt
```
static int getFloatEncodedInt(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. 2147483647 is maxvalue, so this allows loading simultaneously up to 2147 files, each with 999999 models (or trajectories)

Parameters:

strDecimal -

Returns:

float encoded as an integer

getPartialBondOrderFromFloatEncodedInt
```
static int getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger)
```
reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)

Parameters:

bondOrderInteger -

Returns:

Bond order partial mask

getBondOrderFromString

public static int getBondOrderFromString(String s)

getPartialBondOrderFromString

private static int getPartialBondOrderFromString(String s)

addHydrogensInline

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

Specified by:: addHydrogensInline in interface JmolScriptEvaluator
Throws:: Exception

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

stopScriptThreads in interface JmolScriptEvaluator

delayScript
```
public void delayScript(int millis)
```

getErrorLineMessage2
```
public String getErrorLineMessage2()
```

evaluateParallel

public boolean evaluateParallel(ScriptContext context,
                                ShapeManager shapeManager)

Specified by:: evaluateParallel in interface JmolScriptEvaluator

Class ScriptEvaluator

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

allowJSThreads

listCommands

isJS

tQuiet

chk

isCmdLine_C_Option

isCmdLine_c_or_C_Option

historyDisabled

logMessages

debugScript

executionStopped

executionPaused

executionStepping

executing

timeBeginExecution

timeEndExecution

mustResumeEval

EXPRESSION_KEY

sm

scriptLevelMax

currentThread

viewer

compiler

definedAtomSets

outputBuffer

contextPath

scriptFileName

functionName

isStateScript

scriptLevel

scriptReportingLevel

commandHistoryLevelMax

aatoken

lineNumbers

lineIndices

contextVariables

script

pc

thisCommand

fullCommand

st

slen

iToken

lineEnd

pcEnd

scriptExtensions

forceNoAddHydrogens

parallelProcessor

tryPt

thisContext

error

errorMessage

errorMessageUntranslated

errorType

iCommandError

ignoreError

ERROR_axisExpected

ERROR_backgroundModelError

ERROR_badArgumentCount

ERROR_badMillerIndices

ERROR_badRGBColor

ERROR_booleanExpected

ERROR_booleanOrNumberExpected

ERROR_booleanOrWhateverExpected

ERROR_colorExpected

ERROR_colorOrPaletteRequired

ERROR_commandExpected

ERROR_coordinateOrNameOrExpressionRequired

ERROR_drawObjectNotDefined

ERROR_endOfStatementUnexpected

ERROR_expressionExpected

ERROR_expressionOrIntegerExpected

ERROR_filenameExpected

ERROR_fileNotFoundException