public class ScriptEvaluator
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
(package private) class |
ScriptEvaluator.ScriptException |
Modifier and Type | Field and Description |
---|---|
private Token[][] |
aatoken |
private int |
commandHistoryLevelMax |
protected ScriptCompiler |
compiler |
private java.lang.String |
contextPath |
private java.util.Map<java.lang.String,ScriptVariable> |
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 |
executionPaused |
private boolean |
executionStepping |
private static java.lang.String |
EXPRESSION_KEY |
private java.lang.Object |
expressionResult |
private boolean |
forceNoAddHydrogens |
private javax.vecmath.Point3f |
fractionalPoint |
private java.lang.String |
fullCommand |
private java.lang.String |
functionName |
private boolean |
historyDisabled |
protected int |
iCommandError |
private boolean |
ignoreError |
private boolean |
interruptExecution |
(package private) static int |
iProcess |
private boolean |
isBondSet |
private boolean |
isCmdLine_C_Option |
protected boolean |
isCmdLine_c_or_C_Option |
private boolean |
isExecuting |
private boolean |
isStateScript |
protected boolean |
isSyntaxCheck |
private int |
iToken |
private int |
lineEnd |
private int[][] |
lineIndices |
private short[] |
lineNumbers |
protected boolean |
logMessages |
private java.lang.StringBuffer |
outputBuffer |
private ParallelProcessor |
parallelProcessor |
protected int |
pc |
private int |
pcEnd |
private java.lang.String |
script |
static java.lang.String |
SCRIPT_COMPLETED |
private java.lang.String |
scriptExtensions |
private java.lang.String |
scriptFileName |
(package private) int |
scriptLevel |
private static int |
scriptLevelMax |
private int |
scriptReportingLevel |
(package private) ShapeManager |
shapeManager |
private Token[] |
statement |
private int |
statementLength |
private Token[] |
tempStatement |
private static java.lang.Object |
testData |
private static java.lang.Object |
testData2 |
private int |
theTok |
private Token |
theToken |
private java.lang.String |
thisCommand |
protected ScriptContext |
thisContext |
private long |
timeBeginExecution |
private long |
timeEndExecution |
private boolean |
tQuiet |
protected Viewer |
viewer |
private java.util.List<Token[]> |
vProcess |
Constructor and Description |
---|
ScriptEvaluator(Viewer viewer) |
Modifier and Type | Method and Description |
---|---|
private void |
addProcess(int pc,
int pt,
boolean isStart) |
private void |
addShapeProperty(java.util.List<java.lang.Object[]> propertyList,
java.lang.String key,
java.lang.Object value) |
private void |
animation() |
private void |
animationDirection() |
private void |
animationMode() |
private void |
assign() |
private javax.vecmath.Point3f |
atomCenterOrCoordinateParameter(int i) |
private java.util.BitSet |
atomExpression(int index) |
private java.util.BitSet |
atomExpression(Token[] code,
int pcStart,
int pcStop,
boolean allowRefresh,
boolean allowUnderflow,
boolean mustBeBitSet,
boolean andNotDeleted) |
private void |
axes(int index) |
private void |
background(int i) |
private void |
bind() |
(package private) java.util.BitSet |
bitSetForModelFileNumber(int m) |
(package private) java.util.List<ScriptVariable> |
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 |
calculate() |
private void |
cd() |
private void |
center(int i) |
private void |
centerAt() |
private javax.vecmath.Point3f |
centerParameter(int i) |
private javax.vecmath.Point3f |
centerParameter(int i,
int modelIndex) |
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 |
checkLength(int length,
int errorPt) |
private int |
checkLength23() |
private int |
checkLength34() |
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 |
colorShape(int shapeType,
int typeMask,
int argb,
java.lang.String translucency,
float translucentLevel,
java.util.BitSet bs) |
private void |
compare() |
private java.util.BitSet |
compareFloat(int tokWhat,
float[] data,
int tokOperator,
float comparisonFloat) |
private static boolean |
compareFloat(int tokOperator,
float propertyFloat,
float comparisonFloat) |
protected java.util.BitSet |
compareInt(int tokWhat,
int tokOperator,
int comparisonValue) |
private java.util.BitSet |
compareString(int tokWhat,
int tokOperator,
java.lang.String comparisonString) |
private boolean |
compareString(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 |
delay(long millis) |
private void |
delete() |
void |
deleteAtomsInVariables(java.util.BitSet bsDeleted) |
private void |
dipole() |
private void |
display(boolean isDisplay) |
private void |
dots(int iShape) |
private void |
draw() |
private void |
echo(int index,
boolean isImage) |
private void |
ellipsoid() |
private RadiusData |
encodeRadiusParameter(int index,
boolean isOnly,
boolean allowAbsolute) |
(package private) void |
error(int iError) |
(package private) void |
error(int iError,
int i) |
(package private) void |
error(int iError,
java.lang.String value) |
(package private) void |
error(int iError,
java.lang.String value,
java.lang.String more) |
(package private) void |
error(int iError,
java.lang.String value,
java.lang.String more,
java.lang.String more2) |
(package private) void |
error(int iError,
java.lang.String value,
java.lang.String more,
java.lang.String more2,
boolean warningOnly) |
(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,
java.lang.StringBuffer outputBuffer) |
static boolean |
evaluateContext(Viewer viewer,
ScriptContext context,
ShapeManager shapeManager) |
static java.lang.Object |
evaluateExpression(Viewer viewer,
java.lang.Object expr,
boolean asVariable)
a general-use method to evaluate a "SET" type expression.
|
private void |
file() |
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[][][] |
floatArraySet(int i,
int nX,
int nY,
int nZ) |
private float |
floatParameter(int index) |
private float |
floatParameter(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) |
private void |
font(int shapeType,
float fontsize) |
private void |
frame(int offset) |
private void |
frameControl(int i) |
private void |
frank(int index) |
private void |
function() |
private int |
getArgbParam(int index) |
private int |
getArgbParam(int index,
boolean allowNone) |
private int |
getArgbParamLast(int index,
boolean allowNone) |
private java.util.BitSet |
getAtomBits(int tokType,
java.lang.Object specInfo) |
static java.util.BitSet |
getAtomBitSet(ScriptEvaluator e,
java.lang.Object atomExpression)
a general method to evaluate a string representing an atom set.
|
static java.util.List<java.lang.Integer> |
getAtomBitSetVector(ScriptEvaluator e,
int atomCount,
java.lang.Object atomExpression)
just provides a vector list of atoms in a string-based expression
|
(package private) java.util.BitSet |
getAtomsNearSurface(float distance,
java.lang.String surfaceId) |
(package private) java.lang.Object |
getBitsetIdent(java.util.BitSet bs,
java.lang.String label,
java.lang.Object tokenValue,
boolean useAtomMap,
int index,
boolean isExplicitlyAll) |
protected java.lang.Object |
getBitsetProperty(java.util.BitSet bs,
int tok,
javax.vecmath.Point3f ptRef,
javax.vecmath.Point4f planeRef,
java.lang.Object tokenValue,
java.lang.Object opValue,
boolean useAtomMap,
int index,
boolean asVectorIfAll) |
private float[] |
getBitsetPropertyFloat(java.util.BitSet bs,
int tok,
float min,
float max) |
private ScriptVariable |
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 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) |
private ScriptVariable |
getContextVariableAsVariable(java.lang.String var) |
java.util.Map<java.lang.String,ScriptVariable> |
getContextVariables() |
private javax.vecmath.Vector3f |
getDrawObjectAxis(java.lang.String axisID,
int index) |
java.lang.String |
getErrorMessage() |
java.lang.String |
getErrorMessageUntranslated() |
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 javax.vecmath.Point4f |
getHklPlane(javax.vecmath.Point3f 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 javax.vecmath.Point3f[] |
getObjectBoundingBox(java.lang.String id) |
private javax.vecmath.Point3f |
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 javax.vecmath.Point3f |
getPoint3f(int i,
boolean allowFractional) |
private javax.vecmath.Point4f |
getPoint4f(int i) |
private javax.vecmath.Point3f[] |
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) java.util.List<javax.vecmath.Point3f> |
getPointVector(Token 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(Token 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 java.lang.Object |
getShapeProperty(int shapeType,
java.lang.String propertyName,
int index) |
private boolean |
getShapeProperty(int shapeType,
java.lang.String propertyName,
java.lang.Object[] data) |
private int |
getShapeType(int tok) |
(package private) float |
getSmilesCorrelation(java.util.BitSet bsA,
java.util.BitSet bsB,
java.lang.String smiles,
java.util.List<javax.vecmath.Point3f> ptsA,
java.util.List<javax.vecmath.Point3f> ptsB,
javax.vecmath.Matrix4f m,
java.util.List<java.util.BitSet> vReturn,
boolean isSmarts,
boolean asMap) |
(package private) java.lang.Object |
getSmilesMatches(java.lang.String pattern,
java.lang.String smiles,
java.util.BitSet bsSelected,
java.util.BitSet 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) |
private Token |
getToken(int i) |
private float |
getTranslucentLevel(int i) |
private void |
getWithinDistanceVector(java.util.List<java.lang.Object[]> propertyList,
float distance,
javax.vecmath.Point3f ptc,
java.util.BitSet bs,
boolean isShow) |
private float |
getZoom(int ptCenter,
int i,
java.util.BitSet bs,
float currentZoom) |
private void |
gotoCmd(java.lang.String strTo) |
void |
haltExecution() |
private void |
hbond() |
private void |
help() |
private void |
history(int pt) |
private javax.vecmath.Point4f |
hklParameter(int i) |
private void |
hover() |
private boolean |
ifCmd() |
private java.lang.String |
initIsosurface(int iShape) |
private void |
instructionDispatchLoop(boolean doList)
here we go -- everything else in this class is called by this method or one
of its subsidiary methods.
|
private void |
integerOutOfRange(int min,
int max) |
private int |
intParameter(int index) |
private int |
intParameter(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 |
isExecutionPaused() |
boolean |
isExecutionStepping() |
private boolean |
isFloatParameter(int index) |
private void |
isosurface(int iShape) |
private boolean |
isPoint3f(int i) |
boolean |
isScriptExecuting() |
private void |
label(int index) |
private void |
lcaoCartoon() |
private boolean |
listIsosurface(int iShape) |
private void |
load() |
private void |
log() |
private void |
logDebugScript(int ifLevel) |
private void |
logLoadInfo(java.lang.String msg) |
private java.util.BitSet |
lookupIdentifierValue(java.lang.String identifier) |
private java.util.BitSet |
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 int |
modelNumberParameter(int index) |
private int |
moOffset(int index) |
private void |
move() |
private void |
moveto() |
private void |
navigate() |
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 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 java.util.List<ScriptVariable> |
parameterExpressionList(int pt,
int ptAtom,
boolean isArrayItem) |
private java.lang.String |
parameterExpressionString(int pt,
int ptMax) |
private ScriptVariable |
parameterExpressionToken(int pt) |
private boolean |
pause() |
void |
pauseExecution(boolean withDelay) |
private void |
planeExpected() |
private javax.vecmath.Point4f |
planeParameter(int i) |
private java.lang.String |
plot(Token[] 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 |
prompt() |
private void |
proteinShape(int shapeType) |
private void |
pushContext(ContextToken token) |
private void |
refresh() |
private void |
reset() |
private void |
restore() |
private void |
restoreScriptContext(ScriptContext context,
boolean isPopContext,
boolean isFlowCommand,
boolean statementOnly) |
private void |
restrict() |
private void |
restrictSelected(boolean isBond,
boolean doInvert) |
void |
resumePausedExecution() |
private void |
returnCmd(ScriptVariable tv) |
private void |
rotate(boolean isSpin,
boolean isSelected) |
private void |
runFunction(ScriptFunction function,
java.util.List<ScriptVariable> params,
ScriptVariable tokenAtom) |
(package private) ScriptVariable |
runFunction(ScriptFunction function,
java.lang.String name,
java.util.List<ScriptVariable> params,
ScriptVariable tokenAtom,
boolean getReturn,
boolean setContextPath) |
void |
runScript(java.lang.String script) |
void |
runScript(java.lang.String script,
java.lang.StringBuffer outputBuffer)
runs a script and sends selected output to a provided StringBuffer
|
private void |
save() |
private void |
script(int tok,
java.lang.String filename,
boolean listCommands) |
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(java.util.BitSet bs,
int tok,
int iValue,
float fValue,
Token tokenValue) |
private void |
setBondmode() |
private void |
setBooleanProperty(java.lang.String key,
boolean value) |
private java.lang.String |
setColorOptions(java.lang.StringBuffer sb,
int index,
int iShape,
int nAllowed) |
(package private) java.util.BitSet |
setContactBitSets(java.util.BitSet bsA,
java.util.BitSet bsB,
boolean localOnly,
float distance,
RadiusData rd,
boolean warnMultiModel) |
private void |
setCursorWait(boolean TF) |
void |
setDebugging() |
private void |
setEcho() |
(package private) static java.lang.String |
setErrorLineMessage(java.lang.String functionName,
java.lang.String filename,
int lineCurrent,
int pcCurrent,
java.lang.String lineInfo) |
private void |
setErrorMessage(java.lang.String err) |
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(java.util.List<java.lang.Object[]> propertyList,
int moNumber,
float[] linearCombination,
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) |
private java.lang.String |
setObjectProperty() |
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 |
setShapeProperty(int iShape,
java.lang.String propertyName,
java.lang.Object propertyValue,
java.util.BitSet bs) |
private void |
setShapeSize(int shapeType,
int size,
java.util.BitSet bs) |
private void |
setShapeSize(int shapeType,
RadiusData rd) |
private void |
setShapeTranslucency(int shapeType,
java.lang.String prefix,
java.lang.String translucency,
float translucentLevel,
java.util.BitSet 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) |
private void |
setZslab() |
private void |
show() |
private void |
showString(java.lang.String str) |
private void |
showString(java.lang.String str,
boolean isPrint) |
private void |
slab(boolean isDepth) |
private void |
ssbond() |
(package private) static java.lang.String |
statementAsString(Token[] 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 int |
tokAt(int i,
Token[] args) |
private Token |
tokenAt(int i,
Token[] args) |
java.lang.String |
toString() |
private void |
translate(boolean isSelected) |
private void |
unbind() |
private void |
undoRedoMove() |
private void |
unitcell(int index) |
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(Token[] args) |
private javax.vecmath.Point3f |
xypParameter(int index) |
private void |
zap(boolean isZapCommand) |
private void |
zoom(boolean isZoomTo) |
public static final java.lang.String SCRIPT_COMPLETED
private boolean tQuiet
protected boolean isSyntaxCheck
private boolean isCmdLine_C_Option
protected boolean isCmdLine_c_or_C_Option
private boolean historyDisabled
protected boolean logMessages
private boolean debugScript
private boolean interruptExecution
private boolean executionPaused
private boolean executionStepping
private boolean isExecuting
private long timeBeginExecution
private long timeEndExecution
private static final java.lang.String EXPRESSION_KEY
ShapeManager shapeManager
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 java.lang.StringBuffer outputBuffer
private java.lang.String contextPath
private java.lang.String scriptFileName
private java.lang.String functionName
private boolean isStateScript
int scriptLevel
private int scriptReportingLevel
private int commandHistoryLevelMax
private Token[][] aatoken
private short[] lineNumbers
private int[][] lineIndices
private java.util.Map<java.lang.String,ScriptVariable> contextVariables
private java.lang.String script
protected int pc
private java.lang.String thisCommand
private java.lang.String fullCommand
private Token[] statement
private int statementLength
private int iToken
private int lineEnd
private int pcEnd
private java.lang.String scriptExtensions
private boolean forceNoAddHydrogens
private ParallelProcessor parallelProcessor
protected 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 Token[] tempStatement
private boolean isBondSet
private java.lang.Object expressionResult
private int theTok
private Token theToken
private boolean coordinatesAreFractional
private javax.vecmath.Point3f fractionalPoint
private java.util.List<Token[]> vProcess
static int iProcess
private java.lang.Object[] data
private static java.lang.Object testData
private static java.lang.Object testData2
public ScriptEvaluator(Viewer viewer)
public boolean compileScriptString(java.lang.String script, boolean tQuiet)
private java.lang.Object[] createFunction(java.lang.String fname, java.lang.String xyz, java.lang.String ret)
fname
- xyz
- ret
- public boolean compileScriptFile(java.lang.String filename, boolean tQuiet)
public void evaluateCompiledScript(boolean isCmdLine_c_or_C_Option, boolean isCmdLine_C_Option, boolean historyDisabled, boolean listCommands, java.lang.StringBuffer outputBuffer)
public void runScript(java.lang.String script, java.lang.StringBuffer outputBuffer) throws ScriptEvaluator.ScriptException
script
- outputBuffer
- ScriptEvaluator.ScriptException
public ScriptContext checkScriptSilent(java.lang.String script)
script
- public void setDebugging()
public int getExecutionWalltime()
public void haltExecution()
public void pauseExecution(boolean withDelay)
public void stepPausedExecution()
public void resumePausedExecution()
public boolean isScriptExecuting()
public boolean isExecutionPaused()
public boolean isExecutionStepping()
public java.lang.String getNextStatement()
private java.lang.String getCommand(int pc, boolean allThisLine, boolean addSemi)
pc
- allThisLine
- addSemi
- private void logDebugScript(int ifLevel)
public static java.lang.Object evaluateExpression(Viewer viewer, java.lang.Object expr, boolean asVariable)
viewer
- expr
- asVariable
- TODOprivate java.lang.Object evaluate(java.lang.Object expr, boolean asVariable)
public static boolean evaluateContext(Viewer viewer, ScriptContext context, ShapeManager shapeManager)
public static java.util.BitSet getAtomBitSet(ScriptEvaluator e, java.lang.Object atomExpression)
e
- atomExpression
- public static java.util.List<java.lang.Integer> getAtomBitSetVector(ScriptEvaluator e, int atomCount, java.lang.Object atomExpression)
e
- atomCount
- atomExpression
- private java.util.List<ScriptVariable> parameterExpressionList(int pt, int ptAtom, boolean isArrayItem) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String parameterExpressionString(int pt, int ptMax) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean parameterExpressionBoolean(int pt, int ptMax) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private ScriptVariable parameterExpressionToken(int pt) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.Object parameterExpression(int pt, int ptMax, java.lang.String key, boolean ignoreComma, boolean asVector, int ptAtom, boolean isArrayItem, java.util.Map localVars, java.lang.String localVar) throws ScriptEvaluator.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() examplesScriptEvaluator.ScriptException
- errors are thrown directly to the Eval error system.private java.util.Map<java.lang.String,java.lang.Object> getHash(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
java.util.List<ScriptVariable> bitsetVariableVector(java.lang.Object v)
java.lang.Object getBitsetIdent(java.util.BitSet bs, java.lang.String label, java.lang.Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)
private ScriptVariable getBitsetPropertySelector(int i, boolean mustBeSettable) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private float[] getBitsetPropertyFloat(java.util.BitSet bs, int tok, float min, float max) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
protected java.lang.Object getBitsetProperty(java.util.BitSet bs, int tok, javax.vecmath.Point3f ptRef, javax.vecmath.Point4f planeRef, java.lang.Object tokenValue, java.lang.Object opValue, boolean useAtomMap, int index, boolean asVectorIfAll) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setBitsetProperty(java.util.BitSet bs, int tok, int iValue, float fValue, Token tokenValue) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
public java.util.Map<java.lang.String,ScriptVariable> getContextVariables()
public java.lang.String getScript()
private boolean compileScript(java.lang.String filename, java.lang.String strScript, boolean debugCompiler)
private java.lang.String fixScriptPath(java.lang.String strScript, java.lang.String filename)
private int setScriptExtensions()
public void runScript(java.lang.String script) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean compileScriptFileInternal(java.lang.String filename, java.lang.String localPath, java.lang.String remotePath, java.lang.String scriptPath)
private java.lang.Object getParameter(java.lang.String key, int tokType)
private java.lang.String getParameterEscaped(java.lang.String var)
private java.lang.String getStringParameter(java.lang.String var, boolean orReturnName)
private java.lang.Object getNumericParameter(java.lang.String var)
private ScriptVariable 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)
ScriptVariable runFunction(ScriptFunction function, java.lang.String name, java.util.List<ScriptVariable> params, ScriptVariable tokenAtom, boolean getReturn, boolean setContextPath) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void runFunction(ScriptFunction function, java.util.List<ScriptVariable> params, ScriptVariable tokenAtom) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void clearDefinedVariableAtomSets()
private void defineSets()
private void defineAtomSet(java.lang.String script)
private java.util.BitSet lookupIdentifierValue(java.lang.String identifier) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.util.BitSet lookupValue(java.lang.String setName, boolean plurals) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
public void deleteAtomsInVariables(java.util.BitSet bsDeleted)
private boolean setStatement(int pc) throws ScriptEvaluator.ScriptException
pc
- ScriptEvaluator.ScriptException
private void clearState(boolean tQuiet)
private void pushContext(ContextToken token) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
public ScriptContext getScriptContext()
void popContext(boolean isFlowCommand, boolean statementOnly)
private void restoreScriptContext(ScriptContext context, boolean isPopContext, boolean isFlowCommand, boolean statementOnly)
private java.lang.String getContext(boolean withVariables)
private int getLinenumber(ScriptContext c)
private java.lang.String getScriptID(ScriptContext context)
public java.lang.String getErrorMessage()
public java.lang.String getErrorMessageUntranslated()
private void setErrorMessage(java.lang.String err)
private void planeExpected() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void integerOutOfRange(int min, int max) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void numberOutOfRange(float min, float max) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
void error(int iError, int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
void error(int iError) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
void error(int iError, java.lang.String value) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
void error(int iError, java.lang.String value, java.lang.String more) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
void error(int iError, java.lang.String value, java.lang.String more, java.lang.String more2) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void warning(int iError, java.lang.String value, java.lang.String more) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
void error(int iError, java.lang.String value, java.lang.String more, java.lang.String more2, boolean warningOnly) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
void evalError(java.lang.String message, java.lang.String strUntranslated) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
static java.lang.String errorString(int iError, java.lang.String value, java.lang.String more, java.lang.String more2, boolean translated)
iError
- value
- more
- more2
- translated
- static java.lang.String setErrorLineMessage(java.lang.String functionName, java.lang.String filename, int lineCurrent, int pcCurrent, java.lang.String lineInfo)
public java.lang.String toString()
toString
in class java.lang.Object
static java.lang.String statementAsString(Token[] statement, int iTok, boolean doLogMessages)
private java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName)
private boolean getShapeProperty(int shapeType, java.lang.String propertyName, java.lang.Object[] data)
private java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName, int index)
private void addShapeProperty(java.util.List<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 setShapeProperty(int iShape, java.lang.String propertyName, java.lang.Object propertyValue, java.util.BitSet bs)
private void setShapeSize(int shapeType, int size, java.util.BitSet 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 showString(java.lang.String str, boolean isPrint)
private void scriptStatusOrBuffer(java.lang.String s)
private java.util.BitSet atomExpression(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.util.BitSet atomExpression(Token[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted) throws ScriptEvaluator.ScriptException
code
- pcStart
- pcStop
- allowRefresh
- allowUnderflow
- mustBeBitSet
- andNotDeleted
- IGNOREDScriptEvaluator.ScriptException
private java.util.BitSet compareFloat(int tokWhat, float[] data, int tokOperator, float comparisonFloat)
private java.util.BitSet compareString(int tokWhat, int tokOperator, java.lang.String comparisonString) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
protected java.util.BitSet compareInt(int tokWhat, int tokOperator, int comparisonValue)
private boolean compareString(int tokOperator, java.lang.String propertyValue, java.lang.String comparisonValue) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private static boolean compareFloat(int tokOperator, float propertyFloat, float comparisonFloat)
private java.util.BitSet getAtomBits(int tokType, java.lang.Object specInfo)
private static int getSeqCode(Token instruction)
private int checkLast(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int checkLength(int length) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int checkLength(int length, int errorPt) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int checkLength23() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int checkLength34() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private Token getToken(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int tokAt(int i)
private int tokAt(int i, Token[] args)
private boolean checkToken(int i)
private int modelNumberParameter(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String optParameterAsString(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String parameterAsString(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int intParameter(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int intParameter(int i, int min, int max) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean isFloatParameter(int index)
private float floatParameter(int i, float min, float max) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private float floatParameter(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private float[] floatParameterSet(int i, int nMin, int nMax) throws ScriptEvaluator.ScriptException
i
- nMin
- nMax
- ScriptEvaluator.ScriptException
private boolean isArrayParameter(int i)
private javax.vecmath.Point3f[] getPointArray(int i, int nPoints) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private float[][] floatArraySet(int i, int nX, int nY) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private float[][][] floatArraySet(int i, int nX, int nY, int nZ) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String stringParameter(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String[] stringParameterSet(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String objectNameParameter(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean booleanParameter(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private javax.vecmath.Point3f atomCenterOrCoordinateParameter(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean isCenterParameter(int i)
private javax.vecmath.Point3f centerParameter(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private javax.vecmath.Point3f centerParameter(int i, int modelIndex) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private javax.vecmath.Point4f planeParameter(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private javax.vecmath.Point4f hklParameter(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
protected javax.vecmath.Point4f getHklPlane(javax.vecmath.Point3f pt)
private int getMadParameter() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int getSetAxesTypeMad(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean isColorParam(int i)
private int getArgbParam(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int getArgbParamLast(int index, boolean allowNone) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int getArgbParam(int index, boolean allowNone) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int getColorTriad(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean isPoint3f(int i)
private javax.vecmath.Point3f getPoint3f(int i, boolean allowFractional) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private javax.vecmath.Point4f getPoint4f(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.Object getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private javax.vecmath.Point3f xypParameter(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean isCommandDisplayable(int i)
i
- private boolean checkContinue()
private void instructionDispatchLoop(boolean doList) throws ScriptEvaluator.ScriptException
doList
- ScriptEvaluator.ScriptException
private void setCursorWait(boolean TF)
private void processShapeCommand(int tok) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean flowControl(int tok, boolean isForCheck) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void gotoCmd(java.lang.String strTo) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void breakCmd(int pt)
private void addProcess(int pc, int pt, boolean isStart)
private int switchCmd(ContextToken c, int tok) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean ifCmd() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void returnCmd(ScriptVariable tv) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void help() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void move() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void moveto() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void navigate() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void bondorder() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void console() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void centerAt() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void stereo() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void compare() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
float getSmilesCorrelation(java.util.BitSet bsA, java.util.BitSet bsB, java.lang.String smiles, java.util.List<javax.vecmath.Point3f> ptsA, java.util.List<javax.vecmath.Point3f> ptsB, javax.vecmath.Matrix4f m, java.util.List<java.util.BitSet> vReturn, boolean isSmarts, boolean asMap) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
java.lang.Object getSmilesMatches(java.lang.String pattern, java.lang.String smiles, java.util.BitSet bsSelected, java.util.BitSet bsMatch3D, boolean isSmarts, boolean asOneBitset) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void connect(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private float getTranslucentLevel(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void getProperty() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void background(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void center(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String setObjectProperty() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void color() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean changeElementColor(java.lang.String str, int argb)
private void colorShape(int shapeType, int index, boolean isBackground) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void colorShape(int shapeType, int typeMask, int argb, java.lang.String translucency, float translucentLevel, java.util.BitSet bs)
private void setShapeTranslucency(int shapeType, java.lang.String prefix, java.lang.String translucency, float translucentLevel, java.util.BitSet bs)
private void cd() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void mapProperty() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void data() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void define() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void echo(int index, boolean isImage) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void message() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void log() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void label(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void hover() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void load() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void logLoadInfo(java.lang.String msg)
private java.lang.String getFullPathName() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void measure() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String plot(Token[] args) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private static float getMinMax(float[] data, boolean isMax, int tok)
private boolean pause() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void print() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void prompt() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void refresh()
private void reset() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void restrict() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void restrictSelected(boolean isBond, boolean doInvert)
private void rotate(boolean isSpin, boolean isSelected) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private Quaternion getQuaternionParameter(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
java.util.List<javax.vecmath.Point3f> getPointVector(Token t, int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private javax.vecmath.Point3f getObjectCenter(java.lang.String axisID, int index, int modelIndex)
private javax.vecmath.Point3f[] getObjectBoundingBox(java.lang.String id)
private javax.vecmath.Vector3f getDrawObjectAxis(java.lang.String axisID, int index)
private void script(int tok, java.lang.String filename, boolean listCommands) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void function() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void sync() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void history(int pt) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void display(boolean isDisplay) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void delete() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void minimize() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void select(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void subset() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void invertSelected() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void translate(boolean isSelected) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void zap(boolean isZapCommand) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void zoom(boolean isZoomTo) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private float getZoom(int ptCenter, int i, java.util.BitSet bs, float currentZoom) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void delay() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void delay(long millis)
private void slab(boolean isDepth) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void ellipsoid() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String getShapeNameParameter(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String setShapeId(int iShape, int i, boolean idSeen) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setAtomShapeSize(int shape, float scale) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private RadiusData encodeRadiusParameter(int index, boolean isOnly, boolean allowAbsolute) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void structure() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void wireframe() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void ssbond() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void struts() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void hbond() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void configuration() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void vector() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void dipole() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void animationMode() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void vibration() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void animationDirection() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void calculate() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void pointGroup() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void dots(int iShape) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void proteinShape(int shapeType) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void animation() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void assign() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void file() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void fixed() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void frame(int offset) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
java.util.BitSet bitSetForModelFileNumber(int m)
private void frameControl(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int getShapeType(int tok) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void font(int shapeType, float fontsize) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void set() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setZslab() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setBondmode() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setEcho() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int intSetting(int pt) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private float floatSetting(int pt) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String stringSetting(int pt, boolean isJmolSet) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean setLabel(java.lang.String str) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setMonitor() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean setUnits(java.lang.String units, int tok) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setSsbond() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setHbond() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setPicking() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setPickingStyle() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void timeout(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setUserColors() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setVariable(int pt, int ptMax, java.lang.String key, int setType) throws ScriptEvaluator.ScriptException
pt
- ptMax
- key
- setType
- ScriptEvaluator.ScriptException
private void axes(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void boundbox(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private TickInfo checkTicks(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst) throws ScriptEvaluator.ScriptException
index
- allowUnitCell
- IGNOREDallowScale
- allowFirst
- ScriptEvaluator.ScriptException
private void unitcell(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void frank(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void selectionHalo(int pt) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void save() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void restore() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
java.lang.String write(Token[] args) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void show() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String getIsosurfaceJvxl(boolean asMesh, int iShape)
private java.lang.String getMoJvxl(int ptMO) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void draw() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void polyhedra() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void contact() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
java.util.BitSet setContactBitSets(java.util.BitSet bsA, java.util.BitSet bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel)
private void lcaoCartoon() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.Object getCapSlabObject(int i, boolean isLcaoCartoon) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private boolean mo(boolean isInitOnly) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String setColorOptions(java.lang.StringBuffer sb, int index, int iShape, int nAllowed) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private int moOffset(int index) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void setMoData(java.util.List<java.lang.Object[]> propertyList, int moNumber, float[] linearCombination, int offset, boolean isNegOffset, int modelIndex, java.lang.String title) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String initIsosurface(int iShape) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String getNextComment()
private boolean listIsosurface(int iShape) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void isosurface(int iShape) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String getColorRange(int i) throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private java.lang.String getIsosurfaceDataRange(int iShape, java.lang.String sep)
private void getWithinDistanceVector(java.util.List<java.lang.Object[]> propertyList, float distance, javax.vecmath.Point3f ptc, java.util.BitSet bs, boolean isShow)
private boolean setMeshDisplayProperty(int shape, int i, int tok) throws ScriptEvaluator.ScriptException
shape
- i
- tok
- ScriptEvaluator.ScriptException
private void bind() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void unbind() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
private void undoRedoMove() throws ScriptEvaluator.ScriptException
ScriptEvaluator.ScriptException
java.util.BitSet 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)