final class IsoShapeReader extends VolumeDataReader
| Modifier and Type | Field and 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 |
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPointsallowSigma, 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| Constructor and Description |
|---|
IsoShapeReader() |
| Modifier and Type | Method and 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 only
|
float |
getValueAtPoint(javajs.util.T3 pt,
boolean getSource) |
private double |
hydrogenAtomPsi(javajs.util.P3 pt) |
(package private) void |
init(SurfaceGenerator sg)
implemented in SurfaceFileReader and
|
private double |
radialPart(double r) |
protected void |
readSurfaceData(boolean isMapData) |
private void |
setHeader(java.lang.String line1) |
protected void |
setup(boolean isMapData) |
protected void |
setVolumeData() |
closeReader, generateCube, initVDR, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfoaddTriangleCheck, 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, updateTrianglesprivate int psi_n
private int psi_l
private int psi_m
private float psi_Znuc
private float sphere_radiusAngstroms
private int monteCarloCount
private java.util.Random random
private boolean allowNegative
private double[] rfactor
private double[] pfactor
private static final double A0
private static final double ROOT2
private static final float ATOMIC_ORBITAL_ZERO_CUT_OFF
private float radius
private final javajs.util.P3 ptPsi
private static final float[] fact
private double psi_normalization
private double aoMax
private double aoMax2
private double angMax2
private javajs.util.V3 planeU
private javajs.util.V3 planeV
private javajs.util.P3 planeCenter
private float planeRadius
private double rnl
private boolean surfaceDone
private int nTries
void init(SurfaceGenerator sg)
SurfaceReaderinit in class VolumeDataReaderprotected void setup(boolean isMapData)
setup in class VolumeDataReaderprotected void setVolumeData()
setVolumeData in class VolumeDataReaderpublic float getValue(int x,
int y,
int z,
int ptyz)
VertexDataServergetValue in interface VertexDataServergetValue in class SurfaceReaderpublic float getValueAtPoint(javajs.util.T3 pt,
boolean getSource)
getValueAtPoint in class SurfaceReadergetSource - TODOprivate void setHeader(java.lang.String line1)
private void calcFactors(int n,
int el,
int m)
private void autoScaleOrbital()
private double radialPart(double r)
private double hydrogenAtomPsi(javajs.util.P3 pt)
private double angularPart(double th,
double ph,
int m)
private void createMonteCarloOrbital()
protected void readSurfaceData(boolean isMapData)
throws java.lang.Exception
readSurfaceData in class VolumeDataReaderjava.lang.Exceptionprivate void createGeodesic()