org.jmol.scriptext

Class MathExt

java.lang.Object

org.jmol.scriptext.MathExt

All Implemented Interfaces:

JmolMathExtension

public class MathExt
extends java.lang.Object
implements JmolMathExtension

Field Summary

Fields

Modifier and Type	Field and Description
private ScriptEval	e
private JmolPatternMatcher	pm
private Viewer	vwr

Constructor Summary

Constructors

Constructor and Description
MathExt()

Method Summary

Modifier and Type	Method and Description
private javajs.util.Lst<SV>	addAllLists(javajs.util.Lst<SV> list, javajs.util.Lst<SV> l)
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	evaluateFormat(ScriptMathProcessor mp, int intValue, SV[] args, boolean isLabel)
private boolean	evaluateGetProperty(ScriptMathProcessor mp, SV[] args, boolean isAtomProperty)
private boolean	evaluateHelix(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateIn(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateList(ScriptMathProcessor mp, int tok, SV[] args)
private boolean	evaluateLoad(ScriptMathProcessor mp, SV[] args, boolean isFile)
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)
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) sort() or sort(n) or count() or count("xxxx")
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, java.lang.String name, SV[] args, int tok, boolean isSelector)
private boolean	evaluateWithin(ScriptMathProcessor mp, SV[] args)
private boolean	evaluateWrite(ScriptMathProcessor mp, SV[] args)
private BS	getAtomsNearSurface(float distance, java.lang.String surfaceId)
private float	getDistance(ScriptMathProcessor mp, SV x1, SV x2, int tok)
private java.lang.Object	getHelixData(BS bs, int tokType)
java.lang.Object	getMinMax(java.lang.Object floatOrSVArray, int tok)
private java.lang.Object	getMinMaxPoint(java.lang.Object pointOrSVArray, int tok) calculates the statistical value for x, y, and z independently
private java.lang.Object	getMinMaxQuaternion(javajs.util.Lst<SV> svData, int tok)
private JmolPatternMatcher	getPatternMatcher()
JmolMathExtension	init(java.lang.Object se)
private T	opTokenFor(int tok)
BS	setContactBitSets(BS bsA, BS bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel)

Methods inherited from class java.lang.Object

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

Field Detail

vwr

private Viewer vwr

e

private ScriptEval e

pm

private JmolPatternMatcher pm

Constructor Detail

MathExt

public MathExt()

Method Detail

init

public JmolMathExtension init(java.lang.Object se)

Specified by:

init in interface JmolMathExtension

evaluate

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

Specified by:

evaluate in interface JmolMathExtension

Throws:

ScriptException

evaluateArray

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

evaluateBin

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

Throws:

ScriptException

evaluateCache

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

evaluateColor

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

evaluateCompare

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

Throws:

ScriptException

evaluateConnected

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

evaluateContact

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

evaluateCross

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

evaluateData

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

evaluateDot

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

Throws:

ScriptException

evaluateHelix

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

Throws:

ScriptException

getHelixData

private java.lang.Object getHelixData(BS bs,
                                      int tokType)

evaluateFind

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

Throws:

ScriptException

evaluateGetProperty

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

Throws:

ScriptException

evaluateFormat

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

Throws:

ScriptException

evaluateList

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

Throws:

ScriptException

addAllLists

private javajs.util.Lst<SV> addAllLists(javajs.util.Lst<SV> list,
                                        javajs.util.Lst<SV> l)

evaluateLoad

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

Throws:

ScriptException

evaluateMath

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

evaluateMeasure

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

Throws:

ScriptException

evaluateModulation

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

evaluateQuaternion

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

Throws:

ScriptException

evaluateRandom

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

evaluateRowCol

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

Throws:

ScriptException

evaluateIn

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

Throws:

ScriptException

evaluateReplace

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

Throws:

ScriptException

evaluateScript

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

Throws:

ScriptException

evaluateSort

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

sort() or sort(n) or count() or count("xxxx")

Parameters:

mp -

args -

tok -

Returns:

true if no error

Throws:

ScriptException

evaluateString

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

Throws:

ScriptException

evaluateSubstructure

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

Throws:

ScriptException

evaluateSymop

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

Throws:

ScriptException

evaluateTensor

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

Throws:

ScriptException

evaluateUserFunction

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

Throws:

ScriptException

evaluateWithin

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

Throws:

ScriptException

evaluateWrite

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

Throws:

ScriptException

getAtomsNearSurface

private BS getAtomsNearSurface(float distance,
                               java.lang.String surfaceId)

getDistance

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

Throws:

ScriptException

getMinMax

public java.lang.Object getMinMax(java.lang.Object floatOrSVArray,
                                  int tok)

Specified by:

getMinMax in interface JmolMathExtension

getMinMaxPoint

private java.lang.Object getMinMaxPoint(java.lang.Object pointOrSVArray,
                                        int tok)

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

Parameters:

pointOrSVArray -

tok -

Returns:

Point3f or "NaN"

getMinMaxQuaternion

private java.lang.Object getMinMaxQuaternion(javajs.util.Lst<SV> svData,
                                             int tok)

getPatternMatcher

private JmolPatternMatcher getPatternMatcher()

opTokenFor

private T opTokenFor(int tok)

setContactBitSets

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

Specified by:

setContactBitSets in interface JmolMathExtension