org.jmol.scriptext

Class CmdExt

java.lang.Object

org.jmol.scriptext.CmdExt

All Implemented Interfaces:

JmolCmdExtension

public class CmdExt
extends java.lang.Object
implements JmolCmdExtension

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	chk
private ScriptEval	e
(package private) static int	ERROR_invalidArgument
private java.lang.String	fullCommand
private java.lang.Object[]	lastData
private int	slen
private ShapeManager	sm
private T[]	st
private java.lang.String	thisCommand
private Viewer	vwr

Constructor Summary

Constructors

Constructor and Description
CmdExt()

Method Summary

Modifier and Type	Method and Description
private void	addShapeProperty(javajs.util.List<java.lang.Object[]> propertyList, java.lang.String key, java.lang.Object value)
private void	assign()
private void	assignAtom(int atomIndex, javajs.util.P3 pt, java.lang.String type)
private void	assignBond(int bondIndex, char type)
private void	assignConnect(int index, int index2)
private BS	atomExpressionAt(int i)
private void	cache()
private void	calculate()
private void	capture()
private void	centerAt()
private javajs.util.P3	centerParameter(int i)
private boolean	cgo()
private void	checkLength(int i)
private void	compare()
private void	configuration()
private void	connect(int index)
private void	console()
private boolean	contact()
private java.lang.Object[]	createFunction(java.lang.String fname, java.lang.String xyz, java.lang.String ret) for the ISOSURFACE command
void	data()
private boolean	dipole()
boolean	dispatch(int iTok, boolean b, T[] st)
private boolean	draw()
private void	ellipsoid()
private void	error(int err)
boolean	evalParallel(ScriptContext context, ShapeManager shapeManager) used for TRY command
private void	finalizeObject(int shapeID, int colorArgb, float translucentLevel, int intScale, boolean doSet, java.lang.Object data, int iptDisplayProperty, BS bs)
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, java.lang.String fileName)
java.lang.Object	getBitsetIdent(BS bs, java.lang.String label, java.lang.Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)
private java.lang.Object	getCapSlabObject(int i, boolean isLcaoCartoon)
private float	getColorTrans(ScriptEval eval, int i, boolean allowNone, int[] ret) Checks color, translucent, opaque parameters.
private java.lang.String	getContext(boolean withVariables)
private java.lang.String	getIsosurfaceJvxl(boolean asMesh, int iShape)
private java.lang.String	getMoJvxl(int ptMO)
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 java.lang.String	getScriptID(ScriptContext context)
private java.lang.Object	getShapeProperty(int shapeType, java.lang.String propertyName)
private java.lang.Object	getShapePropertyIndex(int shapeType, java.lang.String propertyName, int index)
private T	getToken(int i)
private void	getWithinDistanceVector(javajs.util.List<java.lang.Object[]> propertyList, float distance, javajs.util.P3 ptc, BS bs, boolean isShow)
JmolCmdExtension	init(java.lang.Object se)
private java.lang.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<java.lang.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 java.lang.String	paramAsStr(int i)
private java.lang.Object	parseDataArray(java.lang.String str, boolean is3D)
java.lang.String	plot(T[] args)
private boolean	polyhedra()
private java.lang.String	setColorOptions(javajs.util.SB sb, int index, int iShape, int nAllowed)
private void	setMoData(javajs.util.List<java.lang.Object[]> propertyList, int moNumber, float[] lc, int offset, boolean isNegOffset, int modelIndex, java.lang.String title)
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	show()
private void	showString(java.lang.String s)
private void	stereo()
private java.lang.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)
java.lang.String	write(T[] args)

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

sm

private ShapeManager sm

chk

private boolean chk

fullCommand

private java.lang.String fullCommand

thisCommand

private java.lang.String thisCommand

st

private T[] st

slen

private int slen

lastData

private java.lang.Object[] lastData

ERROR_invalidArgument

static final int ERROR_invalidArgument

See Also:

Constant Field Values

Constructor Detail

CmdExt

public CmdExt()

Method Detail

init

public JmolCmdExtension init(java.lang.Object se)

Specified by:

init in interface JmolCmdExtension

dispatch

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

Specified by:

dispatch in interface JmolCmdExtension

Throws:

ScriptException

atomExpressionAt

private BS atomExpressionAt(int i)
                     throws ScriptException

Throws:

ScriptException

checkLength

private void checkLength(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 java.lang.Object getShapeProperty(int shapeType,
                                          java.lang.String propertyName)

paramAsStr

private java.lang.String paramAsStr(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)

setShapeProperty

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

showString

private void showString(java.lang.String s)

stringParameter

private java.lang.String stringParameter(int index)
                                  throws ScriptException

Throws:

ScriptException

getToken

private T getToken(int i)
            throws ScriptException

Throws:

ScriptException

tokAt

private int tokAt(int i)

cache

private void cache()
            throws ScriptException

Throws:

ScriptException

calculate

private void calculate()
                throws ScriptException

Throws:

ScriptException

capture

private void capture()
              throws ScriptException

Throws:

ScriptException

centerAt

private void centerAt()
               throws ScriptException

Throws:

ScriptException

cgo

private boolean cgo()
             throws ScriptException

Throws:

ScriptException

compare

private void compare()
              throws ScriptException

Throws:

ScriptException

configuration

private void configuration()
                    throws ScriptException

Throws:

ScriptException

measure

private void measure()
              throws ScriptException

Throws:

ScriptException

connect

private void connect(int index)
              throws ScriptException

Parameters:

index - 0 indicates hbond command

Throws:

ScriptException

console

private void console()
              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

data

public void data()
          throws ScriptException

Throws:

ScriptException

ellipsoid

private void ellipsoid()
                throws ScriptException

Throws:

ScriptException

isosurface

private boolean isosurface(int iShape)
                    throws ScriptException

Throws:

ScriptException

lcaoCartoon

private boolean lcaoCartoon()
                     throws ScriptException

Throws:

ScriptException

mapProperty

private void mapProperty()
                  throws ScriptException

Throws:

ScriptException

minimize

private void minimize()
               throws ScriptException

Throws:

ScriptException

mo

private boolean mo(boolean isInitOnly)
            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

navigate

public void navigate()
              throws ScriptException

Throws:

ScriptException

plot

public java.lang.String plot(T[] args)
                      throws ScriptException

Specified by:

plot in interface JmolCmdExtension

Throws:

ScriptException

polyhedra

private boolean polyhedra()
                   throws ScriptException

Throws:

ScriptException

evalParallel

public boolean evalParallel(ScriptContext context,
                            ShapeManager shapeManager)

used for TRY command

Specified by:

evalParallel in interface JmolCmdExtension

Parameters:

context -

shapeManager -

Returns:

true if successful; false if not

write

public java.lang.String write(T[] args)
                       throws ScriptException

Specified by:

write in interface JmolCmdExtension

Throws:

ScriptException

show

private void show()
           throws ScriptException

Throws:

ScriptException

stereo

private void stereo()
             throws ScriptException

Throws:

ScriptException

struts

private boolean struts()
                throws ScriptException

Throws:

ScriptException

addShapeProperty

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

assign

private void assign()
             throws ScriptException

Throws:

ScriptException

assignAtom

private void assignAtom(int atomIndex,
                        javajs.util.P3 pt,
                        java.lang.String type)

assignBond

private void assignBond(int bondIndex,
                        char type)

assignConnect

private void assignConnect(int index,
                           int index2)

getContext

private java.lang.String getContext(boolean withVariables)

getAtomicPotentials

private float[] getAtomicPotentials(BS bsSelected,
                                    BS bsIgnore,
                                    java.lang.String fileName)
                             throws java.lang.Exception

Parameters:

bsSelected -

bsIgnore -

fileName -

Returns:

calculated atom potentials

Throws:

java.lang.Exception

getColorTrans

private float getColorTrans(ScriptEval eval,
                            int i,
                            boolean allowNone,
                            int[] ret)
                     throws ScriptException

Checks color, translucent, opaque parameters.

Parameters:

eval -

i -

allowNone -

ret - returned int argb color

Returns:

translucentLevel and sets iToken and ret[0]

Throws:

ScriptException

getCapSlabObject

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

Throws:

ScriptException

getIsosurfaceJvxl

private java.lang.String getIsosurfaceJvxl(boolean asMesh,
                                           int iShape)

getMoJvxl

private java.lang.String getMoJvxl(int ptMO)
                            throws ScriptException

Throws:

ScriptException

getScriptID

private java.lang.String getScriptID(ScriptContext context)

getShapePropertyIndex

private java.lang.Object getShapePropertyIndex(int shapeType,
                                               java.lang.String propertyName,
                                               int index)

tokenAt

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

tokAtArray

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

finalizeObject

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

Throws:

ScriptException

moCombo

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

moOffset

private int moOffset(int index)
              throws ScriptException

Throws:

ScriptException

setMoData

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

Throws:

ScriptException

getPlotMinMax

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

initIsosurface

private java.lang.String initIsosurface(int iShape)
                                 throws ScriptException

Throws:

ScriptException

getWithinDistanceVector

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

setColorOptions

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

Throws:

ScriptException

createFunction

private java.lang.Object[] createFunction(java.lang.String fname,
                                          java.lang.String xyz,
                                          java.lang.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

getBitsetIdent

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

Specified by:

getBitsetIdent in interface JmolCmdExtension

listIsosurface

private boolean listIsosurface(int iShape)
                        throws ScriptException

Throws:

ScriptException

setShapeId

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

Throws:

ScriptException

parseDataArray

private java.lang.Object parseDataArray(java.lang.String str,
                                        boolean is3D)