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

Fields

Modifier and Type	Field and Description
private int	calcType
private boolean	doSmoothProperty
private AtomIndexIterator	iter
private MepCalculationInterface	m
private java.lang.String	mepType
private float	smoothingPower

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

atomCount, atomData, atomDataServer, atomIndex, atomNo, atomProp, atomRadius, atomXyz, bsMyIgnored, bsMySelected, bsNearby, doAddHydrogens, doUseIterator, doUsePlane, fileDotModel, fileName, firstNearbyAtom, maxDistance, modelIndex, myAtomCount, myIndex, nearbyAtomCount

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

allowMapData, dataType, point, precalculateVoxelData

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, isAnisotropic, isEccentric, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, mappingPlane, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin

Constructor Summary

Constructors

Constructor and Description
AtomPropertyMapper(SurfaceGenerator sg, java.lang.String mepType)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	finalizeMapping()
protected void	generateCube()
float	getValueAtPoint(javax.vecmath.Point3f pt)
protected void	initializeMapping()
protected void	setup()

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

fixTitleLine, getAtoms, setHeader, setRangesAndAddAtoms

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

closeReader, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVoxelRange

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, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, 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

m

private MepCalculationInterface m

mepType

private java.lang.String mepType

calcType

private int calcType

doSmoothProperty

private boolean doSmoothProperty

iter

private AtomIndexIterator iter

smoothingPower

private float smoothingPower

Constructor Detail

AtomPropertyMapper

AtomPropertyMapper(SurfaceGenerator sg,
                  java.lang.String mepType)

Method Detail

setup

protected void setup()

Overrides:

setup 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

getValueAtPoint

public float getValueAtPoint(javax.vecmath.Point3f pt)

Overrides:

getValueAtPoint in class SurfaceReader

Returns:

value