Package org.jmol.jvxl.readers
Class IsoShapeReader
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceReader
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- org.jmol.jvxl.readers.VolumeDataReader
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- org.jmol.jvxl.readers.IsoShapeReader
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- All Implemented Interfaces:
VertexDataServer
final class IsoShapeReader extends VolumeDataReader
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Field Summary
Fields Modifier and Type Field Description private static double
A0
private boolean
allowNegative
private double
angMax2
private double
aoMax
private double
aoMax2
private static float
ATOMIC_ORBITAL_ZERO_CUT_OFF
private static float[]
fact
private int
monteCarloCount
private int
nTries
private double[]
pfactor
private javajs.util.P3
planeCenter
private float
planeRadius
private javajs.util.V3
planeU
private javajs.util.V3
planeV
private int
psi_l
private int
psi_m
private int
psi_n
private double
psi_normalization
private float
psi_Znuc
private javajs.util.P3
ptPsi
private float
radius
private java.util.Random
random
private double[]
rfactor
private double
rnl
private static double
ROOT2
private float
sphere_radiusAngstroms
private boolean
surfaceDone
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Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
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Fields inherited from class org.jmol.jvxl.readers.SurfaceReader
allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isPeriodic, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes
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Constructor Summary
Constructors Constructor Description IsoShapeReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private double
angularPart(double th, double ph, int m)
private void
autoScaleOrbital()
private void
calcFactors(int n, int el, int m)
private void
createGeodesic()
private void
createMonteCarloOrbital()
float
getValue(int x, int y, int z, int ptyz)
for readers onlyfloat
getValueAtPoint(javajs.util.T3 pt, boolean getSource)
private double
hydrogenAtomPsi(javajs.util.P3 pt)
(package private) void
init(SurfaceGenerator sg)
implemented in SurfaceFileReader andprivate double
radialPart(double r)
protected void
readSurfaceData(boolean isMapData)
private void
setHeader(java.lang.String line1)
protected void
setup(boolean isMapData)
protected void
setVolumeData()
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Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, initVDR, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue2, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Field Detail
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psi_n
private int psi_n
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psi_l
private int psi_l
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psi_m
private int psi_m
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psi_Znuc
private float psi_Znuc
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sphere_radiusAngstroms
private float sphere_radiusAngstroms
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monteCarloCount
private int monteCarloCount
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random
private java.util.Random random
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allowNegative
private boolean allowNegative
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rfactor
private double[] rfactor
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pfactor
private double[] pfactor
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A0
private static final double A0
- See Also:
- Constant Field Values
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ROOT2
private static final double ROOT2
- See Also:
- Constant Field Values
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ATOMIC_ORBITAL_ZERO_CUT_OFF
private static final float ATOMIC_ORBITAL_ZERO_CUT_OFF
- See Also:
- Constant Field Values
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radius
private float radius
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ptPsi
private final javajs.util.P3 ptPsi
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fact
private static final float[] fact
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psi_normalization
private double psi_normalization
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aoMax
private double aoMax
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aoMax2
private double aoMax2
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angMax2
private double angMax2
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planeU
private javajs.util.V3 planeU
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planeV
private javajs.util.V3 planeV
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planeCenter
private javajs.util.P3 planeCenter
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planeRadius
private float planeRadius
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rnl
private double rnl
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surfaceDone
private boolean surfaceDone
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nTries
private int nTries
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Method Detail
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init
void init(SurfaceGenerator sg)
Description copied from class:SurfaceReader
implemented in SurfaceFileReader and- Overrides:
init
in classVolumeDataReader
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setup
protected void setup(boolean isMapData)
- Overrides:
setup
in classVolumeDataReader
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setVolumeData
protected void setVolumeData()
- Overrides:
setVolumeData
in classVolumeDataReader
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getValue
public float getValue(int x, int y, int z, int ptyz)
Description copied from interface:VertexDataServer
for readers only- Specified by:
getValue
in interfaceVertexDataServer
- Overrides:
getValue
in classSurfaceReader
- Returns:
- value[x][y][z]
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getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)
- Overrides:
getValueAtPoint
in classSurfaceReader
getSource
- TODO- Returns:
- value
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setHeader
private void setHeader(java.lang.String line1)
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calcFactors
private void calcFactors(int n, int el, int m)
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autoScaleOrbital
private void autoScaleOrbital()
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radialPart
private double radialPart(double r)
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hydrogenAtomPsi
private double hydrogenAtomPsi(javajs.util.P3 pt)
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angularPart
private double angularPart(double th, double ph, int m)
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createMonteCarloOrbital
private void createMonteCarloOrbital()
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readSurfaceData
protected void readSurfaceData(boolean isMapData) throws java.lang.Exception
- Overrides:
readSurfaceData
in classVolumeDataReader
- Throws:
java.lang.Exception
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createGeodesic
private void createGeodesic()
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