Package org.jmol.scriptext
Class IsoExt
- java.lang.Object
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- org.jmol.scriptext.ScriptExt
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- org.jmol.scriptext.IsoExt
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public class IsoExt extends ScriptExt
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Constructor Summary
Constructors Constructor Description IsoExt()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private void
addShapeProperty(javajs.util.Lst<java.lang.Object[]> propertyList, java.lang.String key, java.lang.Object value)
private boolean
cgo()
private boolean
contact()
private java.lang.Object[]
createFunction(java.lang.String fname, java.lang.String xyz, java.lang.String ret)
for the ISOSURFACE commandprivate void
dipole()
java.lang.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, java.lang.String fileName)
private java.lang.Object
getCapSlabObject(int i, boolean isLcaoCartoon)
private javajs.util.Lst<java.lang.Object>
getPlaneIntersection(int type, javajs.util.P4 plane, SymmetryInterface uc, float scale, int flags)
private javajs.util.P3[]
getWithinDistanceVector(javajs.util.Lst<java.lang.Object[]> propertyList, float distance, javajs.util.P3 ptc, javajs.util.BS bs, boolean isShow)
private java.lang.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<java.lang.Object[]> propertyList)
private int
moOffset(int index)
private java.lang.String
setColorOptions(javajs.util.SB sb, int index, int iShape, int nAllowed)
private void
setMoData(javajs.util.Lst<java.lang.Object[]> propertyList, int moNumber, float[] lc, int offset, boolean isNegOffset, int modelIndex, java.lang.String title, java.lang.String nboType, boolean isBeta)
private int
setNBOType(java.util.Map<java.lang.String,java.lang.Object> moData, java.lang.String type)
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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
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Method Detail
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dispatch
public java.lang.String dispatch(int iTok, boolean b, T[] st) throws ScriptException
- Specified by:
dispatch
in classScriptExt
- Throws:
ScriptException
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dipole
private void dipole() throws ScriptException
- Throws:
ScriptException
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draw
private void draw() throws ScriptException
- Throws:
ScriptException
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mo
private void mo(boolean isInitOnly, int iShape) throws ScriptException
- Throws:
ScriptException
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setNBOType
private int setNBOType(java.util.Map<java.lang.String,java.lang.Object> moData, java.lang.String type) throws ScriptException
- Throws:
ScriptException
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moCombo
private float[] moCombo(javajs.util.Lst<java.lang.Object[]> propertyList)
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moOffset
private int moOffset(int index) throws ScriptException
- Throws:
ScriptException
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setMoData
private void setMoData(javajs.util.Lst<java.lang.Object[]> propertyList, int moNumber, float[] lc, int offset, boolean isNegOffset, int modelIndex, java.lang.String title, java.lang.String nboType, boolean isBeta) throws ScriptException
- Throws:
ScriptException
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isosurface
private void isosurface(int iShape) throws ScriptException
- Throws:
ScriptException
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lcaoCartoon
private void lcaoCartoon() throws ScriptException
- Throws:
ScriptException
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contact
private boolean contact() throws ScriptException
- Throws:
ScriptException
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cgo
private boolean cgo() throws ScriptException
- Throws:
ScriptException
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getAtomicPotentials
private float[] getAtomicPotentials(javajs.util.BS bsSelected, javajs.util.BS bsIgnore, java.lang.String fileName)
- Parameters:
bsSelected
-bsIgnore
-fileName
-- Returns:
- calculated atom potentials
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getCapSlabObject
private java.lang.Object getCapSlabObject(int i, boolean isLcaoCartoon) throws ScriptException
- Throws:
ScriptException
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setColorOptions
private java.lang.String setColorOptions(javajs.util.SB sb, int index, int iShape, int nAllowed) throws ScriptException
- Throws:
ScriptException
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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 ]
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getWithinDistanceVector
private javajs.util.P3[] getWithinDistanceVector(javajs.util.Lst<java.lang.Object[]> propertyList, float distance, javajs.util.P3 ptc, javajs.util.BS bs, boolean isShow)
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addShapeProperty
private void addShapeProperty(javajs.util.Lst<java.lang.Object[]> propertyList, java.lang.String key, java.lang.Object value)
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floatArraySetXYZ
private float[][][] floatArraySetXYZ(int i, int nX, int nY, int nZ) throws ScriptException
- Throws:
ScriptException
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floatArraySet
private float[][] floatArraySet(int i, int nX, int nY) throws ScriptException
- Throws:
ScriptException
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initIsosurface
private java.lang.String initIsosurface(int iShape) throws ScriptException
- Throws:
ScriptException
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listIsosurface
private boolean listIsosurface(int iShape) throws ScriptException
- Throws:
ScriptException
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getPlaneIntersection
private javajs.util.Lst<java.lang.Object> getPlaneIntersection(int type, javajs.util.P4 plane, SymmetryInterface uc, float scale, int flags)
- Parameters:
type
- unitcell or boundboxplane
- plane to intersect, or null for just the full boxscale
-uc
-flags
- 1 -- edges only 2 -- triangles only 3 -- both- Returns:
- Vector
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