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:
- IsoMepReader, IsoMOReader, IsoPlaneReader, IsoSolventReader
abstract class AtomDataReader
- extends VolumeDataReader
Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader |
allowMapData, anisotropy, center, dataType, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, isAnisotropic, isEccentric, point, precalculateVoxelData |
Fields inherited from class org.jmol.jvxl.readers.SurfaceReader |
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vContours, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData |
Method Summary |
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()
|
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader |
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, getArgbFromPalette, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, gotoData, initializeVolumetricData, jvxlUpdateInfo, readColorData, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
atomDataServer
protected AtomDataServer atomDataServer
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
xyzMin
private javax.vecmath.Point3f xyzMin
xyzMax
private javax.vecmath.Point3f xyzMax
doAddHydrogens
protected boolean doAddHydrogens
doUsePlane
protected boolean doUsePlane
doUseIterator
protected boolean doUseIterator
AtomDataReader
AtomDataReader(SurfaceGenerator sg)
setup
protected void setup()
- Overrides:
setup
in class VolumeDataReader
getAtoms
protected void getAtoms(float marginAtoms,
boolean doGetAllAtoms,
boolean addNearbyAtoms)
getWorkingRadius
private float getWorkingRadius(int i,
float marginAtoms)
setHeader
protected void setHeader(java.lang.String calcType,
java.lang.String line2)
setRangesAndAddAtoms
protected void setRangesAndAddAtoms(float ptsPerAngstrom,
int maxGrid,
int nWritten)
fixTitleLine
protected boolean fixTitleLine(int iLine)