java.lang.Object
- org.jmol.jvxl.readers.SurfaceReader
- - org.jmol.jvxl.readers.VolumeDataReader
  - - org.jmol.jvxl.readers.IsoShapeReader

All Implemented Interfaces:: VertexDataServer

final class IsoShapeReader
extends VolumeDataReader

Field Summary

Fields
Modifier and Type	Field	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`

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, 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

All Methods Instance Methods Concrete Methods
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(java.lang.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 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
```

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 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 Detail
- IsoShapeReader
```
IsoShapeReader()
```

Method Detail

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(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(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 java.lang.Exception

Overrides:: readSurfaceData in class VolumeDataReader
Throws:: java.lang.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 Detail

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 Detail

IsoShapeReader

Method Detail

init

setup

setVolumeData

getValue

getValueAtPoint

setHeader

calcFactors

autoScaleOrbital

radialPart

hydrogenAtomPsi

angularPart

createMonteCarloOrbital

readSurfaceData

createGeodesic