org.jmol.jvxl.readers.IsoShapeReader

All Implemented Interfaces:: VertexDataServer

final class IsoShapeReader extends VolumeDataReader

Field Summary

Fields

Modifier and Type

Field

Description

private static final double

A0

private boolean

allowNegative

private double

angMax2

private double

aoMax

private double

aoMax2

private static final float

ATOMIC_ORBITAL_ZERO_CUT_OFF

private static final 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 final javajs.util.P3

ptPsi

private float

radius

private Random

random

private double[]

rfactor

private double

rnl

private static final double

ROOT2

private float

sphere_radiusAngstroms

private boolean

surfaceDone

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

Constructor

Description

IsoShapeReader()
Method Summary

Modifier and Type

Method

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(String line1)

protected void

setup(boolean isMapData)

protected void

setVolumeData()

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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
  
  private 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 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
  
  void init(SurfaceGenerator sg)
  
  Description copied from class: SurfaceReader
  
  implemented in SurfaceFileReader and
  
  Overrides:
  
  init in class VolumeDataReader
- 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(javajs.util.T3 pt, boolean getSource)
  
  Overrides:
  
  getValueAtPoint in class SurfaceReader
  
  getSource - TODO
  
  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(javajs.util.P3 pt)
- angularPart
  
  private double angularPart(double th, double ph, int m)
- createMonteCarloOrbital
  
  private void createMonteCarloOrbital()
- readSurfaceData
  
  protected void readSurfaceData(boolean isMapData) throws Exception
  
  Overrides:
  
  readSurfaceData in class VolumeDataReader
  
  Throws:
  
  Exception
- createGeodesic
  
  private void createGeodesic()

Class IsoShapeReader

Field Summary

Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

Methods inherited from class java.lang.Object

Field Details

psi_n

psi_l

psi_m

psi_Znuc

sphere_radiusAngstroms

monteCarloCount

random

allowNegative

rfactor

pfactor

A0

ROOT2

ATOMIC_ORBITAL_ZERO_CUT_OFF

radius

ptPsi

fact

psi_normalization

aoMax

aoMax2

angMax2

planeU

planeV

planeCenter

planeRadius

rnl

surfaceDone

nTries

Constructor Details

IsoShapeReader

Method Details

init

setup

setVolumeData

getValue

getValueAtPoint

setHeader

calcFactors

autoScaleOrbital

radialPart

hydrogenAtomPsi

angularPart

createMonteCarloOrbital

readSurfaceData

createGeodesic