Package org.jmol.jvxl.readers
Class IsoShapeReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.VolumeDataReader
org.jmol.jvxl.readers.IsoShapeReader
- All Implemented Interfaces:
VertexDataServer
-
Field Summary
FieldsModifier and TypeFieldDescriptionprivate static final double
private boolean
private double
private double
private double
private static final float
private static final float[]
private int
private int
private double[]
private javajs.util.P3
private float
private javajs.util.V3
private javajs.util.V3
private int
private int
private int
private double
private float
private final javajs.util.P3
private float
private Random
private double[]
private double
private static final double
private float
private boolean
Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
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, jvxlCutoffRange, 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
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate double
angularPart
(double th, double ph, int m) private void
private void
calcFactors
(int n, int el, int m) private void
private void
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
protected void
setup
(boolean isMapData) protected void
Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, initVDR, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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
-
Field Details
-
psi_n
private int psi_n -
psi_l
private int psi_l -
psi_m
private int psi_m -
psi_Znuc
private float psi_Znuc -
sphere_radiusAngstroms
private float sphere_radiusAngstroms -
monteCarloCount
private int monteCarloCount -
random
-
allowNegative
private boolean allowNegative -
rfactor
private double[] rfactor -
pfactor
private double[] pfactor -
A0
private static final double A0- See Also:
-
ROOT2
private static final double ROOT2- See Also:
-
ATOMIC_ORBITAL_ZERO_CUT_OFF
private static final float ATOMIC_ORBITAL_ZERO_CUT_OFF- See Also:
-
radius
private float radius -
ptPsi
private final javajs.util.P3 ptPsi -
fact
private static final float[] fact -
psi_normalization
private double psi_normalization -
aoMax
private double aoMax -
aoMax2
private double aoMax2 -
angMax2
private double angMax2 -
planeU
private javajs.util.V3 planeU -
planeV
private javajs.util.V3 planeV -
planeCenter
private javajs.util.P3 planeCenter -
planeRadius
private float planeRadius -
rnl
private double rnl -
surfaceDone
private boolean surfaceDone -
nTries
private int nTries
-
-
Constructor Details
-
IsoShapeReader
IsoShapeReader()
-
-
Method Details
-
init
Description copied from class:SurfaceReader
implemented in SurfaceFileReader and- Overrides:
init
in classVolumeDataReader
-
setup
protected void setup(boolean isMapData) - Overrides:
setup
in classVolumeDataReader
-
setVolumeData
protected void setVolumeData()- Overrides:
setVolumeData
in classVolumeDataReader
-
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]
-
getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource) - Overrides:
getValueAtPoint
in classSurfaceReader
getSource
- TODO- Returns:
- value
-
setHeader
-
calcFactors
private void calcFactors(int n, int el, int m) -
autoScaleOrbital
private void autoScaleOrbital() -
radialPart
private double radialPart(double r) -
hydrogenAtomPsi
private double hydrogenAtomPsi(javajs.util.P3 pt) -
angularPart
private double angularPart(double th, double ph, int m) -
createMonteCarloOrbital
private void createMonteCarloOrbital() -
readSurfaceData
- Overrides:
readSurfaceData
in classVolumeDataReader
- Throws:
Exception
-
createGeodesic
private void createGeodesic()
-