Package org.jmol.jvxl.readers
Class AtomPropertyMapper
- 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.AtomPropertyMapper
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- All Implemented Interfaces:
VertexDataServer
class AtomPropertyMapper extends AtomDataReader
maps property data
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Field Summary
Fields Modifier and Type Field Description private intcalcTypeprivate booleandoSmoothPropertyprivate intiAtomSurfaceprivate AtomIndexIteratoriterprivate MepCalculationmepCalcprivate java.lang.StringmepTypeprivate floatsmoothingPower-
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 AtomPropertyMapper()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected voidfinalizeMapping()protected voidgenerateCube()intgetSurfaceAtomIndex()floatgetValueAtPoint(javajs.util.T3 pt, boolean getSource)(package private) voidinit(SurfaceGenerator sg)implemented in SurfaceFileReader andprotected voidinitializeMapping()protected voidsetup(boolean isMapData)protected voidsetVolumeData()-
Methods inherited from class org.jmol.jvxl.readers.AtomDataReader
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData, unsetVoxelData2
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Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVolumeParameters, 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, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlaneSR, getSPF, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, gotoAndReadVoxelData, gotoData, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Field Detail
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mepCalc
private MepCalculation mepCalc
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mepType
private java.lang.String mepType
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calcType
private int calcType
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doSmoothProperty
private boolean doSmoothProperty
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iter
private AtomIndexIterator iter
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smoothingPower
private float smoothingPower
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iAtomSurface
private int iAtomSurface
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Method Detail
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init
void init(SurfaceGenerator sg)
Description copied from class:SurfaceReaderimplemented in SurfaceFileReader and- Overrides:
initin classVolumeDataReader
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setup
protected void setup(boolean isMapData)
- Overrides:
setupin classAtomDataReader
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setVolumeData
protected void setVolumeData()
- Overrides:
setVolumeDatain classAtomDataReader
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initializeMapping
protected void initializeMapping()
- Overrides:
initializeMappingin classSurfaceReader
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finalizeMapping
protected void finalizeMapping()
- Overrides:
finalizeMappingin classSurfaceReader
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generateCube
protected void generateCube()
- Overrides:
generateCubein classVolumeDataReader
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getSurfaceAtomIndex
public int getSurfaceAtomIndex()
- Overrides:
getSurfaceAtomIndexin classSurfaceReader
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getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)- Overrides:
getValueAtPointin classSurfaceReadergetSource- TODO- Returns:
- value
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