org.jmol.jvxl.readers
Class AtomDataReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.VolumeDataReader
org.jmol.jvxl.readers.AtomDataReader
- All Implemented Interfaces:
- VertexDataServer
- Direct Known Subclasses:
- AtomPropertyMapper, IsoFxyReader, IsoIntersectReader, IsoMepReader, IsoMOReader, IsoPlaneReader, IsoSolventReader
abstract class AtomDataReader
- extends VolumeDataReader
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 |
Method Summary |
protected boolean |
fixTitleLine(int iLine)
|
protected void |
getAtomMinMax(java.util.BitSet bs,
java.util.BitSet[] bsAtomMinMax)
|
protected void |
getAtoms(java.util.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(javax.vecmath.Point3f p,
float r)
|
protected void |
markSphereVoxels(float r0,
float distance)
|
protected void |
resetPlane(float value)
|
protected void |
resetVoxelData(float value)
|
protected void |
setGridLimitsForAtom(javax.vecmath.Point3f ptA,
float rA,
javax.vecmath.Point3i pt0,
javax.vecmath.Point3i pt1)
|
protected void |
setHeader(java.lang.String calcType,
java.lang.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()
|
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader |
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 |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
maxDistance
protected float maxDistance
contactPair
protected ContactPair contactPair
fileName
protected java.lang.String fileName
fileDotModel
protected java.lang.String fileDotModel
modelIndex
protected int modelIndex
atomData
protected AtomData atomData
atomXyz
protected javax.vecmath.Point3f[] atomXyz
atomRadius
protected float[] atomRadius
atomProp
protected float[] atomProp
atomNo
protected int[] atomNo
atomIndex
protected int[] atomIndex
myIndex
protected int[] myIndex
atomCount
protected int atomCount
myAtomCount
protected int myAtomCount
nearbyAtomCount
protected int nearbyAtomCount
firstNearbyAtom
protected int firstNearbyAtom
bsMySelected
protected java.util.BitSet bsMySelected
bsMyIgnored
protected java.util.BitSet bsMyIgnored
bsNearby
protected java.util.BitSet bsNearby
doAddHydrogens
protected boolean doAddHydrogens
havePlane
protected boolean havePlane
doUseIterator
protected boolean doUseIterator
thisPlane
protected float[] thisPlane
thisAtomSet
protected java.util.BitSet thisAtomSet
thisX
protected int thisX
margin
protected float margin
bsSurfaceVoxels
protected java.util.BitSet bsSurfaceVoxels
validSpheres
protected java.util.BitSet validSpheres
noFaceSpheres
protected java.util.BitSet noFaceSpheres
voxelSource
protected int[] voxelSource
ptY0
protected final javax.vecmath.Point3f ptY0
ptZ0
protected final javax.vecmath.Point3f ptZ0
pt0
protected final javax.vecmath.Point3i pt0
pt1
protected final javax.vecmath.Point3i pt1
ptXyzTemp
protected final javax.vecmath.Point3f ptXyzTemp
AtomDataReader
AtomDataReader(SurfaceGenerator sg)
setup
protected void setup(boolean isMapData)
- Overrides:
setup
in class VolumeDataReader
markPlaneVoxels
protected void markPlaneVoxels(javax.vecmath.Point3f p,
float r)
setVolumeForPlane
protected void setVolumeForPlane()
getAtoms
protected void getAtoms(java.util.BitSet bsSelected,
boolean doAddHydrogens,
boolean getRadii,
boolean getMolecules,
boolean getAllModels,
boolean addNearbyAtoms,
boolean getAtomMinMax,
float marginAtoms)
- Parameters:
bsSelected
- TODOdoAddHydrogens
- TODOgetRadii
- TODOgetMolecules
- TODOgetAllModels
- TODOaddNearbyAtoms
- getAtomMinMax
- TODOmarginAtoms
-
getWorkingRadius
private float getWorkingRadius(int i,
float marginAtoms)
setHeader
protected void setHeader(java.lang.String calcType,
java.lang.String line2)
setRanges
protected void setRanges(float ptsPerAngstrom,
int maxGrid)
setVolumeData
protected void setVolumeData()
- Overrides:
setVolumeData
in class VolumeDataReader
fixTitleLine
protected boolean fixTitleLine(int iLine)
setVertexSource
protected void setVertexSource()
resetPlane
protected void resetPlane(float value)
resetVoxelData
protected void resetVoxelData(float value)
getVoxel
private float getVoxel(int i,
int j,
int k,
int ipt)
unsetVoxelData
protected void unsetVoxelData()
setGridLimitsForAtom
protected void setGridLimitsForAtom(javax.vecmath.Point3f ptA,
float rA,
javax.vecmath.Point3i pt0,
javax.vecmath.Point3i pt1)
getAtomMinMax
protected void getAtomMinMax(java.util.BitSet bs,
java.util.BitSet[] bsAtomMinMax)
markSphereVoxels
protected void markSphereVoxels(float r0,
float distance)
setVoxel
protected void setVoxel(int i,
int j,
int k,
int ipt,
float value)