Package org.jmol.scriptext

Class IsoExt

java.lang.Object

org.jmol.scriptext.ScriptExt

org.jmol.scriptext.IsoExt

public class IsoExt
extends ScriptExt

Field Summary

Fields inherited from class org.jmol.scriptext.ScriptExt

chk, e, slen, st, vwr

Constructor Summary

Constructors

Constructor	Description
IsoExt()

Method Summary

Modifier and Type	Method	Description
private void	addShapeProperty(javajs.util.Lst<Object[]> propertyList, String key, Object value)
private boolean	cgo()
private boolean	contact()
private Object[]	createFunction(String fname, String xyz, String ret)	for the ISOSURFACE command
private void	dipole()
String	dispatch(int iTok, boolean b, T[] st)
private void	draw()
private float[][]	floatArraySet(int i, int nX, int nY)
private float[][][]	floatArraySetXYZ(int i, int nX, int nY, int nZ)
private float[]	getAtomicPotentials(javajs.util.BS bsSelected, javajs.util.BS bsIgnore, String fileName)
private Object	getCapSlabObject(int i, boolean isLcaoCartoon)
private javajs.util.Lst<Object>	getPlaneIntersection(int type, javajs.util.P4 plane, SymmetryInterface uc, float scale, int flags)
private javajs.util.P3[]	getWithinDistanceVector(javajs.util.Lst<Object[]> propertyList, float distance, javajs.util.P3 ptc, javajs.util.BS bs, boolean isShow)
private String	initIsosurface(int iShape)
private void	isosurface(int iShape)
private void	lcaoCartoon()
private boolean	listIsosurface(int iShape)
private void	mo(boolean isInitOnly, int iShape)
private float[]	moCombo(javajs.util.Lst<Object[]> propertyList)
private int	moOffset(int index)
private String	setColorOptions(javajs.util.SB sb, int index, int iShape, int nAllowed)
private void	setMoData(javajs.util.Lst<Object[]> propertyList, int moNumber, float[] lc, int offset, boolean isNegOffset, int modelIndex, String title, String nboType, boolean isBeta)
private int	setNBOType(Map<String,Object> moData, String type)

Methods inherited from class org.jmol.scriptext.ScriptExt

atomExpressionAt, centerParameter, checkLength, error, finalizeObject, floatParameter, getAllPoints, getColorTrans, getIntArray2, getPoint3f, getShapeProperty, getToken, init, intParameter, invArg, invPO, isFloatParameter, paramAsStr, setShapeId, setShapeProperty, showString, stringParameter, tokAt

Methods inherited from class java.lang.Object

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

Constructor Detail

IsoExt

public IsoExt()

Method Detail

dispatch

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

Specified by:

dispatch in class ScriptExt

Throws:

ScriptException

dipole

private void dipole()
             throws ScriptException

Throws:

ScriptException

draw

private void draw()
           throws ScriptException

Throws:

ScriptException

mo

private void mo(boolean isInitOnly,
                int iShape)
         throws ScriptException

Throws:

ScriptException

setNBOType

private int setNBOType(Map<String,Object> moData,
                       String type)
                throws ScriptException

Throws:

ScriptException

moCombo

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

moOffset

private int moOffset(int index)
              throws ScriptException

Throws:

ScriptException

setMoData

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

Throws:

ScriptException

isosurface

private void isosurface(int iShape)
                 throws ScriptException

Throws:

ScriptException

lcaoCartoon

private void lcaoCartoon()
                  throws ScriptException

Throws:

ScriptException

contact

private boolean contact()
                 throws ScriptException

Throws:

ScriptException

cgo

private boolean cgo()
             throws ScriptException

Throws:

ScriptException

getAtomicPotentials

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

Parameters:

bsSelected -

bsIgnore -

fileName -

Returns:

calculated atom potentials

getCapSlabObject

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

Throws:

ScriptException

setColorOptions

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

Throws:

ScriptException

createFunction

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

for the ISOSURFACE command

Parameters:

fname -

xyz -

ret -

Returns:

[ ScriptFunction, Params ]

getWithinDistanceVector

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

addShapeProperty

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

floatArraySetXYZ

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

Throws:

ScriptException

floatArraySet

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

Throws:

ScriptException

initIsosurface

private String initIsosurface(int iShape)
                       throws ScriptException

Throws:

ScriptException

listIsosurface

private boolean listIsosurface(int iShape)
                        throws ScriptException

Throws:

ScriptException

getPlaneIntersection

private javajs.util.Lst<Object> getPlaneIntersection(int type,
                                                     javajs.util.P4 plane,
                                                     SymmetryInterface uc,
                                                     float scale,
                                                     int flags)

Parameters:

type - unitcell or boundbox

plane - plane to intersect, or null for just the full box

scale -

uc -

flags - 1 -- edges only 2 -- triangles only 3 -- both

Returns:

Vector