java.lang.Object
- org.jmol.jvxl.readers.SurfaceReader
- - org.jmol.jvxl.readers.VolumeDataReader
  - - org.jmol.jvxl.readers.AtomDataReader
    - - org.jmol.jvxl.readers.IsoMOReader

All Implemented Interfaces:: VertexDataServer

class IsoMOReader
extends AtomDataReader

Field Summary

Fields
Modifier and Type	Field	Description
`private float[]`	`coef`
`private float[][]`	`coefs`
`private int[][]`	`dfCoefMaps`
`private boolean`	`isElectronDensityCalc`
`private boolean`	`isNci`
`private float[]`	`linearCombination`
`private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>`	`mos`
`private javajs.util.P3[]`	`points`
`private QuantumCalculation`	`q`
`private boolean`	`qSetupDone`
`private java.util.Random`	`random`
`private float[]`	`vDist`
`private javajs.util.V3`	`vTemp`

Fields inherited from class org.jmol.jvxl.readers.AtomDataReader
ac, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyzTruncated, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, haveOneProperty, havePlane, margin, maxDistance, maxRS, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptV, ptY0, ptZ0, rs, rs2, sr, theProperty, thisAtomSet, thisPlane, thisX, validSpheres, vl0, vl1, vl2, voxelSource

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

IsoMOReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`createOrbital()`
`private void`	`fixTitleLine(int iLine, java.util.Map<java.lang.String,java.lang.Object> mo)`
`protected void`	`generateCube()`
`float[]`	`getPlane(int x)`
`private float`	`getRnd(float f)`
`protected float`	`getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javajs.util.T3 ptReturn)`
`float`	`getValueAtPoint(javajs.util.T3 pt, boolean getSource)`
`private void`	`getValues()`
`(package private) void`	`init(SurfaceGenerator sg)`	implemented in SurfaceFileReader and
`protected void`	`postProcessVertices()`
`protected void`	`readSurfaceData(boolean isMapData)`
`protected boolean`	`readVolumeParameters(boolean isMapData)`
`protected void`	`setup(boolean isMapData)`
`private boolean`	`setupCalculation()`

Methods inherited from class org.jmol.jvxl.readers.AtomDataReader
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeData, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData, unsetVoxelData2

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, initVDR, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo

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

Field Detail

random
```
private java.util.Random random
```

points
```
private javajs.util.P3[] points
```

vTemp
```
private javajs.util.V3 vTemp
```

q
```
private QuantumCalculation q
```

mos

private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> mos

isNci
```
private boolean isNci
```

coef
```
private float[] coef
```

dfCoefMaps
```
private int[][] dfCoefMaps
```

linearCombination
```
private float[] linearCombination
```

coefs
```
private float[][] coefs
```

isElectronDensityCalc
```
private boolean isElectronDensityCalc
```

vDist
```
private final float[] vDist
```

qSetupDone
```
private boolean qSetupDone
```

Constructor Detail
- IsoMOReader
```
IsoMOReader()
```

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 AtomDataReader

readVolumeParameters
```
protected boolean readVolumeParameters(boolean isMapData)
```
Overrides:

readVolumeParameters in class VolumeDataReader

fixTitleLine

private void fixTitleLine(int iLine,
                          java.util.Map<java.lang.String,java.lang.Object> mo)

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws java.lang.Exception

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

postProcessVertices
```
protected void postProcessVertices()
```
Overrides:

postProcessVertices in class SurfaceReader

getValues
```
private void getValues()
```

getValueAtPoint

public float getValueAtPoint(javajs.util.T3 pt,
                             boolean getSource)

Overrides:: getValueAtPoint in class SurfaceReader; getSource - TODO
Returns:: value

getRnd
```
private float getRnd(float f)
```

generateCube
```
protected void generateCube()
```
Overrides:

generateCube in class VolumeDataReader

createOrbital
```
protected void createOrbital()
```

getPlane
```
public float[] getPlane(int x)
```
Specified by:

getPlane in interface VertexDataServer

Overrides:

getPlane in class SurfaceReader

setupCalculation
```
private boolean setupCalculation()
```

getSurfacePointAndFraction

protected float getSurfacePointAndFraction(float cutoff,
                                           boolean isCutoffAbsolute,
                                           float valueA,
                                           float valueB,
                                           javajs.util.T3 pointA,
                                           javajs.util.V3 edgeVector,
                                           int x,
                                           int y,
                                           int z,
                                           int vA,
                                           int vB,
                                           float[] fReturn,
                                           javajs.util.T3 ptReturn)

Overrides:: getSurfacePointAndFraction in class SurfaceReader

Class IsoMOReader

Field Summary

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

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.AtomDataReader

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

random

points

vTemp

q

mos

isNci

coef

dfCoefMaps

linearCombination

coefs

isElectronDensityCalc

vDist

qSetupDone

Constructor Detail

IsoMOReader

Method Detail

init

setup

readVolumeParameters

fixTitleLine

readSurfaceData

postProcessVertices

getValues

getValueAtPoint

getRnd

generateCube

createOrbital

getPlane

setupCalculation

getSurfacePointAndFraction