org.jmol.jvxl.readers
Class IsoShapeReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.VolumeDataReader
          extended by org.jmol.jvxl.readers.IsoShapeReader
All Implemented Interfaces:
VertexDataServer

 class IsoShapeReader
extends VolumeDataReader


Field Summary
private static double A0
           
private  boolean allowNegative
           
private static float[] fact
           
private  int maxGrid
           
private  double[] pfactor
           
private  float ppa
           
private  int psi_l
           
private  int psi_m
           
private  int psi_n
           
private  float psi_Znuc
           
private  Point3f ptPsi
           
private  float radius
           
private  double[] rfactor
           
private static double ROOT2
           
private  float sphere_radiusAngstroms
           
 
Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, point, precalculateVoxelData
 
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, isAnisotropic, isEccentric, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, mappingPlane, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin
 
Constructor Summary
IsoShapeReader(SurfaceGenerator sg, float radius)
           
IsoShapeReader(SurfaceGenerator sg, int n, int l, int m, float z_eff)
           
 
Method Summary
private  void autoScaleOrbital()
           
private  void calcFactors(int n, int el, int m)
           
 float getValue(int x, int y, int z, int ptyz)
          for readers only
 float getValueAtPoint(Point3f pt)
           
private  double hydrogenAtomPsi(Point3f pt)
           
private  double radialPart(double r)
           
protected  void readSurfaceData(boolean isMapData)
           
private  void setHeader(String line1)
           
protected  void setup()
           
 
Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVoxelRange
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, 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
 

Field Detail

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

ptPsi

private final Point3f ptPsi

fact

private static final float[] fact
Constructor Detail

IsoShapeReader

IsoShapeReader(SurfaceGenerator sg,
               float radius)

IsoShapeReader

IsoShapeReader(SurfaceGenerator sg,
               int n,
               int l,
               int m,
               float z_eff)
Method Detail

setup

protected void setup()
Overrides:
setup 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(Point3f pt)
Overrides:
getValueAtPoint in class SurfaceReader
Returns:
value

setHeader

private void setHeader(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(Point3f pt)

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws Exception
Overrides:
readSurfaceData in class VolumeDataReader
Throws:
Exception