abstract class AtomDataReader extends VolumeDataReader
Modifier and Type | Field and Description |
---|---|
protected int |
atomCount |
protected AtomData |
atomData |
protected AtomDataServer |
atomDataServer |
protected int[] |
atomIndex |
protected int[] |
atomNo |
protected float[] |
atomProp |
protected float[] |
atomRadius |
protected javax.vecmath.Point3f[] |
atomXyz |
protected java.util.BitSet |
bsMyIgnored |
protected java.util.BitSet |
bsMySelected |
protected java.util.BitSet |
bsNearby |
protected boolean |
doAddHydrogens |
protected boolean |
doUseIterator |
protected boolean |
doUsePlane |
protected java.lang.String |
fileDotModel |
protected java.lang.String |
fileName |
protected int |
firstNearbyAtom |
protected float |
maxDistance |
protected int |
modelIndex |
protected int |
myAtomCount |
protected int[] |
myIndex |
protected int |
nearbyAtomCount |
allowMapData, dataType, point, precalculateVoxelData
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 and Description |
---|
AtomDataReader(SurfaceGenerator sg) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
fixTitleLine(int iLine) |
protected void |
getAtoms(float marginAtoms,
boolean doGetAllAtoms,
boolean addNearbyAtoms) |
private float |
getWorkingRadius(int i,
float marginAtoms) |
protected void |
setHeader(java.lang.String calcType,
java.lang.String line2) |
protected void |
setRangesAndAddAtoms(float ptsPerAngstrom,
int maxGrid,
int nWritten) |
protected void |
setup() |
closeReader, generateCube, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVoxelRange
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
protected AtomDataServer atomDataServer
protected float maxDistance
protected java.lang.String fileName
protected java.lang.String fileDotModel
protected int modelIndex
protected AtomData atomData
protected javax.vecmath.Point3f[] atomXyz
protected float[] atomRadius
protected float[] atomProp
protected int[] atomNo
protected int[] atomIndex
protected int[] myIndex
protected int atomCount
protected int myAtomCount
protected int nearbyAtomCount
protected int firstNearbyAtom
protected java.util.BitSet bsMySelected
protected java.util.BitSet bsMyIgnored
protected java.util.BitSet bsNearby
protected boolean doAddHydrogens
protected boolean doUsePlane
protected boolean doUseIterator
AtomDataReader(SurfaceGenerator sg)
protected void setup()
setup
in class VolumeDataReader
protected void getAtoms(float marginAtoms, boolean doGetAllAtoms, boolean addNearbyAtoms)
marginAtoms
- doGetAllAtoms
- UNUSEDaddNearbyAtoms
- private float getWorkingRadius(int i, float marginAtoms)
protected void setHeader(java.lang.String calcType, java.lang.String line2)
protected void setRangesAndAddAtoms(float ptsPerAngstrom, int maxGrid, int nWritten)
protected boolean fixTitleLine(int iLine)