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
class IsoShapeReader
- extends VolumeDataReader
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, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, 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 |
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader |
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
private java.util.Random random
allowNegative
private boolean allowNegative
rfactor
private double[] rfactor
pfactor
private double[] pfactor
A0
private static final double A0
- See Also:
- Constant Field Values
ROOT2
private static final double ROOT2
- See Also:
- Constant Field Values
ATOMIC_ORBITAL_ZERO_CUT_OFF
private static final float ATOMIC_ORBITAL_ZERO_CUT_OFF
- See Also:
- Constant Field Values
radius
private float radius
ptPsi
private final javax.vecmath.Point3f 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 javax.vecmath.Vector3f planeU
planeV
private javax.vecmath.Vector3f planeV
planeCenter
private javax.vecmath.Point3f planeCenter
planeRadius
private float planeRadius
rnl
private double rnl
monteCarloDone
private boolean monteCarloDone
nTries
private int nTries
IsoShapeReader
IsoShapeReader(SurfaceGenerator sg,
float radius)
IsoShapeReader
IsoShapeReader(SurfaceGenerator sg,
int n,
int l,
int m,
float z_eff,
int monteCarloCount)
setup
protected void setup(boolean isMapData)
- Overrides:
setup
in class VolumeDataReader
setVolumeData
protected void setVolumeData()
- Overrides:
setVolumeData
in class VolumeDataReader
getValue
public float getValue(int x,
int y,
int z,
int ptyz)
- Description copied from interface:
VertexDataServer
- for readers only
- Specified by:
getValue
in interface VertexDataServer
- Overrides:
getValue
in class SurfaceReader
- Returns:
- value[x][y][z]
getValueAtPoint
public float getValueAtPoint(javax.vecmath.Point3f pt)
- Overrides:
getValueAtPoint
in class SurfaceReader
- Returns:
- value
setHeader
private void setHeader(java.lang.String line1)
calcFactors
private void calcFactors(int n,
int el,
int m)
autoScaleOrbital
private void autoScaleOrbital()
radialPart
private double radialPart(double r)
hydrogenAtomPsi
private double hydrogenAtomPsi(javax.vecmath.Point3f pt)
angularPart
private double angularPart(double th,
double ph,
int m)
createMonteCarloOrbital
private void createMonteCarloOrbital()
readSurfaceData
protected void readSurfaceData(boolean isMapData)
throws java.lang.Exception
- Overrides:
readSurfaceData
in class VolumeDataReader
- Throws:
java.lang.Exception