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
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.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, 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 |
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.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 |
mepCalc
private MepCalculationInterface mepCalc
mepType
private java.lang.String mepType
calcType
private int calcType
doSmoothProperty
private boolean doSmoothProperty
iter
private AtomIndexIterator iter
smoothingPower
private float smoothingPower
iAtomSurface
private int iAtomSurface
AtomPropertyMapper
AtomPropertyMapper(SurfaceGenerator sg,
java.lang.String mepType)
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(javax.vecmath.Point3f pt)
- Overrides:
getValueAtPoint
in class SurfaceReader
- Returns:
- value