org.jmol.jvxl.readers
abstract class AtomDataReader extends VolumeDataReader
Modifier and Type | Field and Description |
---|---|
protected int |
atomCount |
protected AtomData |
atomData |
protected int[] |
atomIndex |
protected int[] |
atomNo |
protected float[] |
atomProp |
protected float[] |
atomRadius |
protected Point3f[] |
atomXyz |
protected BitSet |
bsMyIgnored |
protected BitSet |
bsMySelected |
protected BitSet |
bsNearby |
protected BitSet |
bsSurfaceVoxels |
protected ContactPair |
contactPair |
protected boolean |
doAddHydrogens |
protected boolean |
doUseIterator |
protected String |
fileDotModel |
protected String |
fileName |
protected int |
firstNearbyAtom |
protected boolean |
havePlane |
protected float |
margin |
protected float |
maxDistance |
protected int |
modelIndex |
protected int |
myAtomCount |
protected int[] |
myIndex |
protected int |
nearbyAtomCount |
protected BitSet |
noFaceSpheres |
protected Point3i |
pt0 |
protected Point3i |
pt1 |
protected Point3f |
ptXyzTemp |
protected Point3f |
ptY0 |
protected Point3f |
ptZ0 |
protected BitSet |
thisAtomSet |
protected float[] |
thisPlane |
protected int |
thisX |
protected BitSet |
validSpheres |
protected int[] |
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 |
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AtomDataReader(SurfaceGenerator sg) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
fixTitleLine(int iLine) |
protected void |
getAtomMinMax(BitSet bs,
BitSet[] bsAtomMinMax) |
protected void |
getAtoms(BitSet bsSelected,
boolean doAddHydrogens,
boolean getRadii,
boolean getMolecules,
boolean getAllModels,
boolean addNearbyAtoms,
boolean getAtomMinMax,
float marginAtoms) |
private float |
getVoxel(int i,
int j,
int k,
int ipt) |
private float |
getWorkingRadius(int i,
float marginAtoms) |
protected void |
markPlaneVoxels(Point3f p,
float r) |
protected void |
markSphereVoxels(float r0,
float distance) |
protected void |
resetPlane(float value) |
protected void |
resetVoxelData(float value) |
protected void |
setGridLimitsForAtom(Point3f ptA,
float rA,
Point3i pt0,
Point3i pt1) |
protected void |
setHeader(String calcType,
String line2) |
protected void |
setRanges(float ptsPerAngstrom,
int maxGrid) |
protected void |
setup(boolean isMapData) |
protected void |
setVertexSource() |
protected void |
setVolumeData() |
protected void |
setVolumeForPlane() |
protected void |
setVoxel(int i,
int j,
int k,
int ipt,
float value) |
protected void |
unsetVoxelData() |
closeReader, generateCube, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
protected float maxDistance
protected ContactPair contactPair
protected String fileName
protected String fileDotModel
protected int modelIndex
protected AtomData atomData
protected 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 BitSet bsMySelected
protected BitSet bsMyIgnored
protected BitSet bsNearby
protected boolean doAddHydrogens
protected boolean havePlane
protected boolean doUseIterator
protected float[] thisPlane
protected BitSet thisAtomSet
protected int thisX
protected float margin
protected BitSet bsSurfaceVoxels
protected BitSet validSpheres
protected BitSet noFaceSpheres
protected int[] voxelSource
protected final Point3f ptY0
protected final Point3f ptZ0
protected final Point3i pt0
protected final Point3i pt1
protected final Point3f ptXyzTemp
AtomDataReader(SurfaceGenerator sg)
protected void setup(boolean isMapData)
setup
in class VolumeDataReader
protected void markPlaneVoxels(Point3f p, float r)
protected void setVolumeForPlane()
protected void getAtoms(BitSet bsSelected, boolean doAddHydrogens, boolean getRadii, boolean getMolecules, boolean getAllModels, boolean addNearbyAtoms, boolean getAtomMinMax, float marginAtoms)
bsSelected
- TODOdoAddHydrogens
- TODOgetRadii
- TODOgetMolecules
- TODOgetAllModels
- TODOaddNearbyAtoms
- getAtomMinMax
- TODOmarginAtoms
- private float getWorkingRadius(int i, float marginAtoms)
protected void setRanges(float ptsPerAngstrom, int maxGrid)
protected void setVolumeData()
setVolumeData
in class VolumeDataReader
protected boolean fixTitleLine(int iLine)
protected void setVertexSource()
protected void resetPlane(float value)
protected void resetVoxelData(float value)
private float getVoxel(int i, int j, int k, int ipt)
protected void unsetVoxelData()
protected void setGridLimitsForAtom(Point3f ptA, float rA, Point3i pt0, Point3i pt1)
protected void markSphereVoxels(float r0, float distance)
protected void setVoxel(int i, int j, int k, int ipt, float value)