org.jmol.scriptext

Class ScriptExt

java.lang.Object

org.jmol.scriptext.ScriptExt

All Implemented Interfaces:

JmolScriptExtension

public class ScriptExt
extends Object
implements JmolScriptExtension

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	chk
private Object[]	data
(package private) static int	ERROR_invalidArgument
private ScriptEvaluator	eval
private String	fullCommand
private JmolPatternMatcher	pm
private int	slen
private ShapeManager	sm
private T[]	st
private String	thisCommand
private Viewer	viewer

Constructor Summary

Constructors

Constructor and Description
ScriptExt()

Method Summary

Modifier and Type	Method and Description
private void	addShapeProperty(javajs.util.List<Object[]> propertyList, String key, Object value)
private BS	atomExpressionAt(int i)
private void	calculate()
private void	capture()
private javajs.util.P3	centerParameter(int i)
private boolean	cgo()
private void	checkLength(int i)
private void	compare()
private void	configuration()
private boolean	contact()
private Object[]	createFunction(String fname, String xyz, String ret) for the ISOSURFACE command
void	data()
private boolean	dipole()
boolean	dispatch(int iTok, boolean b, T[] st)
private boolean	draw()
private void	error(int err)
boolean	evaluate(ScriptMathProcessor mp, T op, SV[] args, int tok)
private boolean	evaluateArray(ScriptMathProcessor mp, SV[] args, boolean allowMatrix)
private boolean	evaluateBin(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateCache(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateColor(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateCompare(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateConnected(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateContact(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateCross(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateData(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateDot(ScriptMathProcessor mp, SV[] args, int tok, int intValue)
private boolean	evaluateFind(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateGetProperty(ScriptMathProcessor mp, SV[] args, boolean isAtomProperty)
private boolean	evaluateHelix(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateLabel(ScriptMathProcessor mp, int intValue, SV[] args)
private boolean	evaluateList(ScriptMathProcessor mp, int tok, SV[] args) array.add(x) array.add(sep, x) array.sub(x) array.mul(x) array.mul3(x) array.div(x) array.push() array.pop()
private boolean	evaluateLoad(ScriptMathProcessor mp, SV[] args, int tok)
private boolean	evaluateMath(ScriptMathProcessor mp, SV[] args, int tok)
private boolean	evaluateMeasure(ScriptMathProcessor mp, SV[] args, int tok)
private boolean	evaluateModulation(ScriptMathProcessor mp, SV[] args)
boolean	evaluateParallel(ScriptContext context, ShapeManager shapeManager) used for TRY command
private boolean	evaluatePlane(ScriptMathProcessor mp, SV[] args, int tok)
private boolean	evaluatePoint(ScriptMathProcessor mp, SV[] args)
private boolean	evaluatePrompt(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateQuaternion(ScriptMathProcessor mp, SV[] args, int tok)
private boolean	evaluateRandom(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateReplace(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateRowCol(ScriptMathProcessor mp, SV[] args, int tok)
private boolean	evaluateScript(ScriptMathProcessor mp, SV[] args, int tok)
private boolean	evaluateSort(ScriptMathProcessor mp, SV[] args, int tok)
private boolean	evaluateString(ScriptMathProcessor mp, int tok, SV[] args)
private boolean	evaluateSubstructure(ScriptMathProcessor mp, SV[] args, int tok)
private boolean	evaluateSymop(ScriptMathProcessor mp, SV[] args, boolean haveBitSet)
private boolean	evaluateTensor(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateUserFunction(ScriptMathProcessor mp, String name, SV[] args, int tok, boolean isSelector)
private boolean	evaluateWithin(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateWrite(ScriptMathProcessor mp, SV[] args)
private float[][]	floatArraySet(int i, int nX, int nY)
private float[][][]	floatArraySetXYZ(int i, int nX, int nY, int nZ)
private float	floatParameter(int i)
private float[]	getAtomicPotentials(BS bsSelected, BS bsIgnore, String fileName)
private BS	getAtomsNearSurface(float distance, String surfaceId)
Object	getBitsetIdent(BS bs, String label, Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)
private Object	getCapSlabObject(int i, boolean isLcaoCartoon)
private String	getContext(boolean withVariables)
private float	getDistance(ScriptMathProcessor mp, SV x1, SV x2, int tok)
private float[]	getFlexFitList(BS bs1, BS bs2, String smiles1, boolean isSmarts)
private String	getIsosurfaceJvxl(boolean asMesh, int iShape)
Object	getMinMax(Object floatOrSVArray, int tok)
private Object	getMinMaxPoint(Object pointOrSVArray, int tok) calculates the statistical value for x, y, and z independently
private Object	getMinMaxQuaternion(javajs.util.List<SV> svData, int tok)
private String	getMoJvxl(int ptMO)
private String	getParameterEscaped(String var)
private JmolPatternMatcher	getPatternMatcher()
private float	getPlotMinMax(float[] data, boolean isMax, int tok)
private javajs.util.P3	getPoint3f(int i, boolean allowFractional)
private javajs.util.P4	getPoint4f(int i)
private Quaternion[]	getQuaternionArray(Object quaternionOrSVData, int itype)
private String	getScriptID(ScriptContext context)
private Object	getShapeProperty(int shapeType, String propertyName)
private Object	getShapePropertyIndex(int shapeType, String propertyName, int index)
private float	getSmilesCorrelation(BS bsA, BS bsB, String smiles, javajs.util.List<javajs.util.P3> ptsA, javajs.util.List<javajs.util.P3> ptsB, javajs.util.M4 m4, javajs.util.List<BS> vReturn, boolean isSmarts, boolean asMap, int[][] mapSet, javajs.util.P3 center)
Object	getSmilesMatches(String pattern, String smiles, BS bsSelected, BS bsMatch3D, boolean isSmarts, boolean asOneBitset)
private T	getToken(int i)
private static void	getTorsions(Atom[] atoms, int[][] bondMap, float[][] diff, int pt)
private void	getWithinDistanceVector(javajs.util.List<Object[]> propertyList, float distance, javajs.util.P3 ptc, BS bs, boolean isShow)
JmolScriptExtension	init(Object se)
private String	initIsosurface(int iShape)
private int	intParameter(int index)
private void	invArg()
private void	invPO()
private boolean	isFloatParameter(int index)
private boolean	isosurface(int iShape)
private boolean	lcaoCartoon()
private boolean	listIsosurface(int iShape)
private void	mapProperty()
private void	measure()
private void	minimize()
private boolean	mo(boolean isInitOnly)
private float[]	moCombo(javajs.util.List<Object[]> propertyList)
private void	modulation() Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).
private int	moOffset(int index)
void	navigate()
private MeasurementData	newMeasurementData(String id, javajs.util.List<Object> points)
private T	opTokenFor(int tok)
private String	parameterAsString(int i)
String	plot(T[] args)
private void	pointGroup()
private boolean	polyhedra()
private String	setColorOptions(javajs.util.SB sb, int index, int iShape, int nAllowed)
private BS	setContactBitSets(BS bsA, BS bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel)
private void	setMoData(javajs.util.List<Object[]> propertyList, int moNumber, float[] lc, int offset, boolean isNegOffset, int modelIndex, String title)
private String	setShapeId(int iShape, int i, boolean idSeen)
private void	setShapeProperty(int shapeType, String propertyName, Object propertyValue)
private void	show()
private void	showString(String s)
private String	stringParameter(int index)
private boolean	struts()
private int	tokAt(int i)
private static int	tokAtArray(int i, T[] args)
private T	tokenAt(int i, T[] args)
String	write(T[] args)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

viewer

private Viewer viewer

eval

private ScriptEvaluator eval

sm

private ShapeManager sm

chk

private boolean chk

fullCommand

private String fullCommand

thisCommand

private String thisCommand

st

private T[] st

slen

private int slen

ERROR_invalidArgument

static final int ERROR_invalidArgument

See Also:

Constant Field Values

data

private Object[] data

pm

private JmolPatternMatcher pm

Constructor Detail

ScriptExt

public ScriptExt()

Method Detail

init

public JmolScriptExtension init(Object se)

Specified by:

init in interface JmolScriptExtension

dispatch

public boolean dispatch(int iTok,
                        boolean b,
                        T[] st)
                 throws ScriptException

Specified by:

dispatch in interface JmolScriptExtension

Throws:

ScriptException

atomExpressionAt

private BS atomExpressionAt(int i)
                     throws ScriptException

Throws:

ScriptException

error

private void error(int err)
            throws ScriptException

Throws:

ScriptException

invArg

private void invArg()
             throws ScriptException

Throws:

ScriptException

invPO

private void invPO()
            throws ScriptException

Throws:

ScriptException

getShapeProperty

private Object getShapeProperty(int shapeType,
                                String propertyName)

parameterAsString

private String parameterAsString(int i)
                          throws ScriptException

Throws:

ScriptException

centerParameter

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

Throws:

ScriptException

floatParameter

private float floatParameter(int i)
                      throws ScriptException

Throws:

ScriptException

getPoint3f

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

Throws:

ScriptException

getPoint4f

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

Throws:

ScriptException

intParameter

private int intParameter(int index)
                  throws ScriptException

Throws:

ScriptException

isFloatParameter

private boolean isFloatParameter(int index)

setShapeId

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

Throws:

ScriptException

setShapeProperty

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

stringParameter

private String stringParameter(int index)
                        throws ScriptException

Throws:

ScriptException

getToken

private T getToken(int i)
            throws ScriptException

Throws:

ScriptException

tokAt

private int tokAt(int i)

cgo

private boolean cgo()
             throws ScriptException

Throws:

ScriptException

contact

private boolean contact()
                 throws ScriptException

Throws:

ScriptException

dipole

private boolean dipole()
                throws ScriptException

Throws:

ScriptException

draw

private boolean draw()
              throws ScriptException

Throws:

ScriptException

isosurface

private boolean isosurface(int iShape)
                    throws ScriptException

Throws:

ScriptException

getAtomicPotentials

private float[] getAtomicPotentials(BS bsSelected,
                                    BS bsIgnore,
                                    String fileName)

Parameters:

bsSelected -

bsIgnore -

fileName -

Returns:

calculated atom potentials

lcaoCartoon

private boolean lcaoCartoon()
                     throws ScriptException

Throws:

ScriptException

getCapSlabObject

private Object getCapSlabObject(int i,
                                boolean isLcaoCartoon)
                         throws ScriptException

Throws:

ScriptException

mo

private boolean mo(boolean isInitOnly)
            throws ScriptException

Throws:

ScriptException

moCombo

private float[] moCombo(javajs.util.List<Object[]> propertyList)

moOffset

private int moOffset(int index)
              throws ScriptException

Throws:

ScriptException

setMoData

private void setMoData(javajs.util.List<Object[]> propertyList,
                       int moNumber,
                       float[] lc,
                       int offset,
                       boolean isNegOffset,
                       int modelIndex,
                       String title)
                throws ScriptException

Throws:

ScriptException

plot

public String plot(T[] args)
            throws ScriptException

Specified by:

plot in interface JmolScriptExtension

Throws:

ScriptException

getPlotMinMax

private float getPlotMinMax(float[] data,
                            boolean isMax,
                            int tok)

polyhedra

private boolean polyhedra()
                   throws ScriptException

Throws:

ScriptException

struts

private boolean struts()
                throws ScriptException

Throws:

ScriptException

initIsosurface

private String initIsosurface(int iShape)
                       throws ScriptException

Throws:

ScriptException

getWithinDistanceVector

private void getWithinDistanceVector(javajs.util.List<Object[]> propertyList,
                                     float distance,
                                     javajs.util.P3 ptc,
                                     BS bs,
                                     boolean isShow)

setColorOptions

private String setColorOptions(javajs.util.SB sb,
                               int index,
                               int iShape,
                               int nAllowed)
                        throws ScriptException

Throws:

ScriptException

addShapeProperty

private void addShapeProperty(javajs.util.List<Object[]> propertyList,
                              String key,
                              Object value)

createFunction

private Object[] createFunction(String fname,
                                String xyz,
                                String ret)

for the ISOSURFACE command

Parameters:

fname -

xyz -

ret -

Returns:

[ ScriptFunction, Params ]

floatArraySet

private float[][] floatArraySet(int i,
                                int nX,
                                int nY)
                         throws ScriptException

Throws:

ScriptException

floatArraySetXYZ

private float[][][] floatArraySetXYZ(int i,
                                     int nX,
                                     int nY,
                                     int nZ)
                              throws ScriptException

Throws:

ScriptException

listIsosurface

private boolean listIsosurface(int iShape)
                        throws ScriptException

Throws:

ScriptException

getBitsetIdent

public Object getBitsetIdent(BS bs,
                             String label,
                             Object tokenValue,
                             boolean useAtomMap,
                             int index,
                             boolean isExplicitlyAll)

Specified by:

getBitsetIdent in interface JmolScriptExtension

data

public void data()
          throws ScriptException

Throws:

ScriptException

navigate

public void navigate()
              throws ScriptException

Throws:

ScriptException

evaluateParallel

public boolean evaluateParallel(ScriptContext context,
                                ShapeManager shapeManager)

used for TRY command

Specified by:

evaluateParallel in interface JmolScriptExtension

Parameters:

context -

shapeManager -

Returns:

true if successful; false if not

write

public String write(T[] args)
             throws ScriptException

Specified by:

write in interface JmolScriptExtension

Throws:

ScriptException

show

private void show()
           throws ScriptException

Throws:

ScriptException

showString

private void showString(String s)

checkLength

private void checkLength(int i)
                  throws ScriptException

Throws:

ScriptException

getIsosurfaceJvxl

private String getIsosurfaceJvxl(boolean asMesh,
                                 int iShape)

getMoJvxl

private String getMoJvxl(int ptMO)
                  throws ScriptException

Throws:

ScriptException

getParameterEscaped

private String getParameterEscaped(String var)

getContext

private String getContext(boolean withVariables)

getScriptID

private String getScriptID(ScriptContext context)

getShapePropertyIndex

private Object getShapePropertyIndex(int shapeType,
                                     String propertyName,
                                     int index)

tokenAt

private T tokenAt(int i,
                  T[] args)

tokAtArray

private static int tokAtArray(int i,
                              T[] args)

calculate

private void calculate()
                throws ScriptException

Throws:

ScriptException

pointGroup

private void pointGroup()
                 throws ScriptException

Throws:

ScriptException

mapProperty

private void mapProperty()
                  throws ScriptException

Throws:

ScriptException

minimize

private void minimize()
               throws ScriptException

Throws:

ScriptException

modulation

private void modulation()
                 throws ScriptException

Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).

Throws:

ScriptException

setContactBitSets

private BS setContactBitSets(BS bsA,
                             BS bsB,
                             boolean localOnly,
                             float distance,
                             RadiusData rd,
                             boolean warnMultiModel)

compare

private void compare()
              throws ScriptException

Throws:

ScriptException

configuration

private void configuration()
                    throws ScriptException

Throws:

ScriptException

measure

private void measure()
              throws ScriptException

Throws:

ScriptException

getFlexFitList

private float[] getFlexFitList(BS bs1,
                               BS bs2,
                               String smiles1,
                               boolean isSmarts)
                        throws ScriptException

Throws:

ScriptException

getTorsions

private static void getTorsions(Atom[] atoms,
                                int[][] bondMap,
                                float[][] diff,
                                int pt)

getSmilesCorrelation

private float getSmilesCorrelation(BS bsA,
                                   BS bsB,
                                   String smiles,
                                   javajs.util.List<javajs.util.P3> ptsA,
                                   javajs.util.List<javajs.util.P3> ptsB,
                                   javajs.util.M4 m4,
                                   javajs.util.List<BS> vReturn,
                                   boolean isSmarts,
                                   boolean asMap,
                                   int[][] mapSet,
                                   javajs.util.P3 center)
                            throws ScriptException

Throws:

ScriptException

getSmilesMatches

public Object getSmilesMatches(String pattern,
                               String smiles,
                               BS bsSelected,
                               BS bsMatch3D,
                               boolean isSmarts,
                               boolean asOneBitset)
                        throws ScriptException

Specified by:

getSmilesMatches in interface JmolScriptExtension

Throws:

ScriptException

evaluate

public boolean evaluate(ScriptMathProcessor mp,
                        T op,
                        SV[] args,
                        int tok)
                 throws ScriptException

Specified by:

evaluate in interface JmolScriptExtension

Throws:

ScriptException

evaluateModulation

private boolean evaluateModulation(ScriptMathProcessor mp,
                                   SV[] args)
                            throws ScriptException

Throws:

ScriptException

evaluateTensor

private boolean evaluateTensor(ScriptMathProcessor mp,
                               SV[] args)
                        throws ScriptException

Throws:

ScriptException

evaluateCache

private boolean evaluateCache(ScriptMathProcessor mp,
                              SV[] args)

evaluateCompare

private boolean evaluateCompare(ScriptMathProcessor mp,
                                SV[] args)
                         throws ScriptException

Throws:

ScriptException

evaluateContact

private boolean evaluateContact(ScriptMathProcessor mp,
                                SV[] args)

evaluateSort

private boolean evaluateSort(ScriptMathProcessor mp,
                             SV[] args,
                             int tok)
                      throws ScriptException

Throws:

ScriptException

evaluateSymop

private boolean evaluateSymop(ScriptMathProcessor mp,
                              SV[] args,
                              boolean haveBitSet)
                       throws ScriptException

Throws:

ScriptException

evaluateBin

private boolean evaluateBin(ScriptMathProcessor mp,
                            SV[] args)
                     throws ScriptException

Throws:

ScriptException

evaluateHelix

private boolean evaluateHelix(ScriptMathProcessor mp,
                              SV[] args)
                       throws ScriptException

Throws:

ScriptException

evaluateDot

private boolean evaluateDot(ScriptMathProcessor mp,
                            SV[] args,
                            int tok,
                            int intValue)
                     throws ScriptException

Throws:

ScriptException

getDistance

private float getDistance(ScriptMathProcessor mp,
                          SV x1,
                          SV x2,
                          int tok)
                   throws ScriptException

Throws:

ScriptException

evaluateMeasure

private boolean evaluateMeasure(ScriptMathProcessor mp,
                                SV[] args,
                                int tok)
                         throws ScriptException

Throws:

ScriptException

newMeasurementData

private MeasurementData newMeasurementData(String id,
                                           javajs.util.List<Object> points)

evaluateUserFunction

private boolean evaluateUserFunction(ScriptMathProcessor mp,
                                     String name,
                                     SV[] args,
                                     int tok,
                                     boolean isSelector)
                              throws ScriptException

Throws:

ScriptException

evaluateFind

private boolean evaluateFind(ScriptMathProcessor mp,
                             SV[] args)
                      throws ScriptException

Throws:

ScriptException

getPatternMatcher

private JmolPatternMatcher getPatternMatcher()

evaluateGetProperty

private boolean evaluateGetProperty(ScriptMathProcessor mp,
                                    SV[] args,
                                    boolean isAtomProperty)
                             throws ScriptException

Throws:

ScriptException

evaluatePlane

private boolean evaluatePlane(ScriptMathProcessor mp,
                              SV[] args,
                              int tok)
                       throws ScriptException

Throws:

ScriptException

evaluatePoint

private boolean evaluatePoint(ScriptMathProcessor mp,
                              SV[] args)

evaluatePrompt

private boolean evaluatePrompt(ScriptMathProcessor mp,
                               SV[] args)

evaluateReplace

private boolean evaluateReplace(ScriptMathProcessor mp,
                                SV[] args)
                         throws ScriptException

Throws:

ScriptException

evaluateString

private boolean evaluateString(ScriptMathProcessor mp,
                               int tok,
                               SV[] args)
                        throws ScriptException

Throws:

ScriptException

evaluateList

private boolean evaluateList(ScriptMathProcessor mp,
                             int tok,
                             SV[] args)
                      throws ScriptException

array.add(x) array.add(sep, x) array.sub(x) array.mul(x) array.mul3(x) array.div(x) array.push() array.pop()

Parameters:

mp -

tok -

args -

Returns:

T/F

Throws:

ScriptException

opTokenFor

private T opTokenFor(int tok)

evaluateRowCol

private boolean evaluateRowCol(ScriptMathProcessor mp,
                               SV[] args,
                               int tok)
                        throws ScriptException

Throws:

ScriptException

evaluateArray

private boolean evaluateArray(ScriptMathProcessor mp,
                              SV[] args,
                              boolean allowMatrix)

evaluateMath

private boolean evaluateMath(ScriptMathProcessor mp,
                             SV[] args,
                             int tok)

evaluateQuaternion

private boolean evaluateQuaternion(ScriptMathProcessor mp,
                                   SV[] args,
                                   int tok)
                            throws ScriptException

Throws:

ScriptException

evaluateRandom

private boolean evaluateRandom(ScriptMathProcessor mp,
                               SV[] args)

evaluateCross

private boolean evaluateCross(ScriptMathProcessor mp,
                              SV[] args)

evaluateLoad

private boolean evaluateLoad(ScriptMathProcessor mp,
                             SV[] args,
                             int tok)
                      throws ScriptException

Throws:

ScriptException

evaluateWrite

private boolean evaluateWrite(ScriptMathProcessor mp,
                              SV[] args)
                       throws ScriptException

Throws:

ScriptException

evaluateScript

private boolean evaluateScript(ScriptMathProcessor mp,
                               SV[] args,
                               int tok)
                        throws ScriptException

Throws:

ScriptException

evaluateData

private boolean evaluateData(ScriptMathProcessor mp,
                             SV[] args)

evaluateLabel

private boolean evaluateLabel(ScriptMathProcessor mp,
                              int intValue,
                              SV[] args)
                       throws ScriptException

Throws:

ScriptException

evaluateWithin

private boolean evaluateWithin(ScriptMathProcessor mp,
                               SV[] args)
                        throws ScriptException

Throws:

ScriptException

getAtomsNearSurface

private BS getAtomsNearSurface(float distance,
                               String surfaceId)

evaluateColor

private boolean evaluateColor(ScriptMathProcessor mp,
                              SV[] args)

evaluateConnected

private boolean evaluateConnected(ScriptMathProcessor mp,
                                  SV[] args)

evaluateSubstructure

private boolean evaluateSubstructure(ScriptMathProcessor mp,
                                     SV[] args,
                                     int tok)
                              throws ScriptException

Throws:

ScriptException

getMinMaxPoint

private Object getMinMaxPoint(Object pointOrSVArray,
                              int tok)

calculates the statistical value for x, y, and z independently

Parameters:

pointOrSVArray -

tok -

Returns:

Point3f or "NaN"

getMinMaxQuaternion

private Object getMinMaxQuaternion(javajs.util.List<SV> svData,
                                   int tok)

getQuaternionArray

private Quaternion[] getQuaternionArray(Object quaternionOrSVData,
                                        int itype)

getMinMax

public Object getMinMax(Object floatOrSVArray,
                        int tok)

Specified by:

getMinMax in interface JmolScriptExtension

capture

private void capture()
              throws ScriptException

Throws:

ScriptException