class AtomPropertyMapper extends AtomDataReader
Modifier and Type | Field and Description |
---|---|
private int |
calcType |
private boolean |
doSmoothProperty |
private int |
iAtomSurface |
private AtomIndexIterator |
iter |
private MepCalculationInterface |
mepCalc |
private java.lang.String |
mepType |
private float |
smoothingPower |
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
allowMapData, atomDataServer, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
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 and Description |
---|
AtomPropertyMapper(SurfaceGenerator sg,
java.lang.String mepType) |
Modifier and Type | Method and Description |
---|---|
protected void |
finalizeMapping() |
protected void |
generateCube() |
int |
getSurfaceAtomIndex() |
float |
getValueAtPoint(javax.vecmath.Point3f pt) |
protected void |
initializeMapping() |
protected void |
setup(boolean isMapData) |
protected void |
setVolumeData() |
fixTitleLine, getAtomMinMax, getAtoms, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRanges, setVertexSource, setVolumeForPlane, setVoxel, unsetVoxelData
closeReader, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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
private MepCalculationInterface mepCalc
private java.lang.String mepType
private int calcType
private boolean doSmoothProperty
private AtomIndexIterator iter
private float smoothingPower
private int iAtomSurface
AtomPropertyMapper(SurfaceGenerator sg, java.lang.String mepType)
protected void setup(boolean isMapData)
setup
in class AtomDataReader
protected void setVolumeData()
setVolumeData
in class AtomDataReader
protected void initializeMapping()
initializeMapping
in class SurfaceReader
protected void finalizeMapping()
finalizeMapping
in class SurfaceReader
protected void generateCube()
generateCube
in class VolumeDataReader
public int getSurfaceAtomIndex()
getSurfaceAtomIndex
in class SurfaceReader
public float getValueAtPoint(javax.vecmath.Point3f pt)
getValueAtPoint
in class SurfaceReader