org.jmol.jvxl.readers
Class AtomPropertyMapper

java.lang.Object
  org.jmol.jvxl.readers.SurfaceReader
      org.jmol.jvxl.readers.VolumeDataReader
          org.jmol.jvxl.readers.AtomDataReader
              org.jmol.jvxl.readers.AtomPropertyMapper

All Implemented Interfaces:

VertexDataServer

 class AtomPropertyMapper
extends AtomDataReader

Field Summary

private int	calcType
private boolean	doSmoothProperty
private int	iAtomSurface
private AtomIndexIterator	iter
private MepCalculationInterface	mepCalc
private String	mepType
private float	smoothingPower

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

atomCount, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyz, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, havePlane, margin, maxDistance, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptXyzTemp, ptY0, ptZ0, thisAtomSet, thisPlane, thisX, validSpheres, voxelSource

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

allowMapData, atomDataServer, 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, 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

AtomPropertyMapper(SurfaceGenerator sg, String mepType)

Method Summary

protected void	finalizeMapping()
protected void	generateCube()
int	getSurfaceAtomIndex()
float	getValueAtPoint(Point3f pt)
protected void	initializeMapping()
protected void	setup(boolean isMapData)
protected void	setVolumeData()

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

fixTitleLine, getAtomMinMax, getAtoms, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRanges, setVertexSource, setVolumeForPlane, setVoxel, unsetVoxelData

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader

closeReader, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, gotoData, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mepCalc

private MepCalculationInterface mepCalc

mepType

private String mepType

calcType

private int calcType

doSmoothProperty

private boolean doSmoothProperty

iter

private AtomIndexIterator iter

smoothingPower

private float smoothingPower

iAtomSurface

private int iAtomSurface

Constructor Detail

AtomPropertyMapper

AtomPropertyMapper(SurfaceGenerator sg,
                   String mepType)

Method Detail

setup

protected void setup(boolean isMapData)

Overrides:

setup in class AtomDataReader

setVolumeData

protected void setVolumeData()

Overrides:

setVolumeData in class AtomDataReader

initializeMapping

protected void initializeMapping()

Overrides:

initializeMapping in class SurfaceReader

finalizeMapping

protected void finalizeMapping()

Overrides:

finalizeMapping in class SurfaceReader

generateCube

protected void generateCube()

Overrides:

generateCube in class VolumeDataReader

getSurfaceAtomIndex

public int getSurfaceAtomIndex()

Overrides:

getSurfaceAtomIndex in class SurfaceReader

getValueAtPoint

public float getValueAtPoint(Point3f pt)

Overrides:

getValueAtPoint in class SurfaceReader

Returns:

value