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.VolumeDataReader |
allowMapData, anisotropy, center, dataType, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, isAnisotropic, isEccentric, point, precalculateVoxelData |
Fields inherited from class org.jmol.jvxl.readers.SurfaceReader |
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vContours, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData |
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader |
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, getArgbFromPalette, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, gotoAndReadVoxelData, gotoData, initializeVolumetricData, jvxlUpdateInfo, readColorData, resetIsosurface, selectPocket, setVolumeData, 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
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
radius
private float radius
ppa
private float ppa
maxGrid
private int maxGrid
fact
private static final float[] fact
ptPsi
private final javax.vecmath.Point3f ptPsi
IsoShapeReader
IsoShapeReader(SurfaceGenerator sg,
float radius)
IsoShapeReader
IsoShapeReader(SurfaceGenerator sg,
int n,
int l,
int m,
float z_eff)
setup
protected void setup()
- Overrides:
setup
in class VolumeDataReader
getValue
public float getValue(int x,
int y,
int z)
- Description copied from interface:
VertexDataServer
- for readers only
- Specified by:
getValue
in interface VertexDataServer
- Overrides:
getValue
in class SurfaceReader
- Returns:
- value[x][y][z]
setHeader
private void setHeader(java.lang.String line1)
autoScaleOrbital
private float autoScaleOrbital()
calcFactors
private void calcFactors(int n,
int el,
int m)
hydrogenAtomPsiAt
private double hydrogenAtomPsiAt(javax.vecmath.Point3f pt,
int n,
int el,
int m)
readSurfaceData
protected void readSurfaceData(boolean isMapData)
throws java.lang.Exception
- Overrides:
readSurfaceData
in class VolumeDataReader
- Throws:
java.lang.Exception