Package org.jmol.scriptext
Class IsoExt
java.lang.Object
org.jmol.scriptext.ScriptExt
org.jmol.scriptext.IsoExt
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate 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 commandprivate void
dipole()
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
private boolean
listIsosurface
(int iShape) private void
mo
(boolean isInitOnly, int iShape) private float[]
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
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Constructor Details
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IsoExt
public IsoExt()
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Method Details
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dispatch
- Specified by:
dispatch
in classScriptExt
- Throws:
ScriptException
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dipole
- Throws:
ScriptException
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draw
- Throws:
ScriptException
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mo
- Throws:
ScriptException
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setNBOType
- Throws:
ScriptException
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moCombo
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moOffset
- Throws:
ScriptException
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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
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isosurface
- Throws:
ScriptException
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lcaoCartoon
- Throws:
ScriptException
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contact
- Throws:
ScriptException
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cgo
- Throws:
ScriptException
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getAtomicPotentials
private float[] getAtomicPotentials(javajs.util.BS bsSelected, javajs.util.BS bsIgnore, String fileName) - Parameters:
bsSelected
-bsIgnore
-fileName
-- Returns:
- calculated atom potentials
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getCapSlabObject
- Throws:
ScriptException
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setColorOptions
private String setColorOptions(javajs.util.SB sb, int index, int iShape, int nAllowed) throws ScriptException - Throws:
ScriptException
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createFunction
for the ISOSURFACE command- Parameters:
fname
-xyz
-ret
-- Returns:
- [ ScriptFunction, Params ]
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getWithinDistanceVector
private javajs.util.P3[] getWithinDistanceVector(javajs.util.Lst<Object[]> propertyList, float distance, javajs.util.P3 ptc, javajs.util.BS bs, boolean isShow) -
addShapeProperty
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floatArraySetXYZ
- Throws:
ScriptException
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floatArraySet
- Throws:
ScriptException
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initIsosurface
- Throws:
ScriptException
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listIsosurface
- Throws:
ScriptException
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getBoxPoints
private javajs.util.P3[] getBoxPoints(int type, SymmetryInterface uc, javajs.util.BS bsAtoms, float scale)
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