Package org.jmol.jvxl.readers
Class IsoMOReader
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceReader
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- org.jmol.jvxl.readers.VolumeDataReader
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- org.jmol.jvxl.readers.AtomDataReader
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- org.jmol.jvxl.readers.IsoMOReader
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- All Implemented Interfaces:
VertexDataServer
class IsoMOReader extends AtomDataReader
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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 Map<String,Object>
mo
private javajs.util.Lst<Map<String,Object>>
mos
private javajs.util.P3[]
points
private QuantumCalculation
q
private boolean
qSetupDone
private Random
random
private float[]
vDist
private javajs.util.V3
vTemp
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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
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Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
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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
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Constructor Summary
Constructors Constructor Description IsoMOReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
createOrbital()
private void
fixTitleLine(int iLine, Map<String,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 andprotected void
postProcessVertices()
protected void
readSurfaceData(boolean isMapData)
protected boolean
readVolumeParameters(boolean isMapData)
protected void
setup(boolean isMapData)
private boolean
setupCalculation()
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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
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Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, initVDR, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue, getValue2, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Field Detail
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random
private Random random
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points
private javajs.util.P3[] points
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vTemp
private javajs.util.V3 vTemp
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q
private QuantumCalculation q
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isNci
private boolean isNci
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coef
private float[] coef
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dfCoefMaps
private int[][] dfCoefMaps
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linearCombination
private float[] linearCombination
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coefs
private float[][] coefs
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isElectronDensityCalc
private boolean isElectronDensityCalc
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vDist
private final float[] vDist
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qSetupDone
private boolean qSetupDone
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Method Detail
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init
void init(SurfaceGenerator sg)
Description copied from class:SurfaceReader
implemented in SurfaceFileReader and- Overrides:
init
in classVolumeDataReader
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setup
protected void setup(boolean isMapData)
- Overrides:
setup
in classAtomDataReader
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData)
- Overrides:
readVolumeParameters
in classVolumeDataReader
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readSurfaceData
protected void readSurfaceData(boolean isMapData) throws Exception
- Overrides:
readSurfaceData
in classVolumeDataReader
- Throws:
Exception
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postProcessVertices
protected void postProcessVertices()
- Overrides:
postProcessVertices
in classSurfaceReader
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getValues
private void getValues()
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getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)
- Overrides:
getValueAtPoint
in classSurfaceReader
getSource
- TODO- Returns:
- value
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getRnd
private float getRnd(float f)
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generateCube
protected void generateCube()
- Overrides:
generateCube
in classVolumeDataReader
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createOrbital
protected void createOrbital()
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getPlane
public float[] getPlane(int x)
- Specified by:
getPlane
in interfaceVertexDataServer
- Overrides:
getPlane
in classSurfaceReader
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setupCalculation
private boolean setupCalculation()
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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 classSurfaceReader
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