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 |
ac, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyz, 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
allowMapData, 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, 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
Constructor and Description |
---|
AtomPropertyMapper() |
Modifier and Type | Method and Description |
---|---|
protected void |
finalizeMapping() |
protected void |
generateCube() |
int |
getSurfaceAtomIndex() |
float |
getValueAtPoint(javajs.util.T3 pt,
boolean getSource) |
(package private) void |
init(SurfaceGenerator sg)
implemented in SurfaceFileReader and
|
protected void |
initializeMapping() |
protected void |
setup(boolean isMapData) |
protected void |
setVolumeData() |
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData, unsetVoxelData2
closeReader, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlane2, 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
private MepCalculationInterface mepCalc
private java.lang.String mepType
private int calcType
private boolean doSmoothProperty
private AtomIndexIterator iter
private float smoothingPower
private int iAtomSurface
void init(SurfaceGenerator sg)
SurfaceReader
init
in class VolumeDataReader
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(javajs.util.T3 pt, boolean getSource)
getValueAtPoint
in class SurfaceReader
getSource
- TODO