Package org.jmol.jvxl.readers
Class IsoMOReader
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
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate float[]
private float[][]
private int[][]
private boolean
private boolean
private float[]
private javajs.util.P3[]
private QuantumCalculation
private boolean
private Random
private final float[]
private javajs.util.V3
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, 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
private void
fixTitleLine
(int iLine, Map<String, Object> mo) protected void
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
(package private) void
init
(SurfaceGenerator sg) implemented in SurfaceFileReader andprotected void
protected void
readSurfaceData
(boolean isMapData) protected boolean
readVolumeParameters
(boolean isMapData) protected void
setup
(boolean isMapData) private boolean
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 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 Details
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random
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points
private javajs.util.P3[] points -
vTemp
private javajs.util.V3 vTemp -
q
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mos
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isNci
private boolean isNci -
coef
private float[] coef -
dfCoefMaps
private int[][] dfCoefMaps -
linearCombination
private float[] linearCombination -
coefs
private float[][] coefs -
isElectronDensityCalc
private boolean isElectronDensityCalc -
mo
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vDist
private final float[] vDist -
qSetupDone
private boolean qSetupDone
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Constructor Details
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IsoMOReader
IsoMOReader()
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Method Details
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init
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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fixTitleLine
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readSurfaceData
- 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() -
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) -
generateCube
protected void generateCube()- Overrides:
generateCube
in classVolumeDataReader
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createOrbital
protected void createOrbital() -
getPlane
public float[] getPlane(int x) - Specified by:
getPlane
in interfaceVertexDataServer
- Overrides:
getPlane
in classSurfaceReader
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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 classSurfaceReader
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