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 javajs.util.P3[]

getBoxPoints(int type, SymmetryInterface uc, javajs.util.BS bsAtoms, float scale)

private Object

getCapSlabObject(int i, boolean isLcaoCartoon)

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, bsToArray, 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 Details
- IsoExt
  
  public IsoExt()
Method Details
- 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
- getBoxPoints
  
  private javajs.util.P3[] getBoxPoints(int type, SymmetryInterface uc, javajs.util.BS bsAtoms, float scale)

Class IsoExt

Field Summary

Fields inherited from class org.jmol.scriptext.ScriptExt

Constructor Summary

Method Summary

Methods inherited from class org.jmol.scriptext.ScriptExt

Methods inherited from class java.lang.Object

Constructor Details

IsoExt

Method Details

dispatch

dipole

draw

mo

setNBOType

moCombo

moOffset

setMoData

isosurface

lcaoCartoon

contact

cgo

getAtomicPotentials

getCapSlabObject

setColorOptions

createFunction

getWithinDistanceVector

addShapeProperty

floatArraySetXYZ

floatArraySet

initIsosurface

listIsosurface

getBoxPoints