Package org.jmol.jvxl.readers
Class AtomDataReader
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceReader
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- org.jmol.jvxl.readers.VolumeDataReader
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- org.jmol.jvxl.readers.AtomDataReader
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- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
AtomPropertyMapper
,IsoFxyReader
,IsoIntersectAtomReader
,IsoIntersectReader
,IsoMepReader
,IsoMOReader
,IsoPlaneReader
,IsoSolventReader
abstract class AtomDataReader extends VolumeDataReader
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Field Summary
Fields Modifier and Type Field Description protected int
ac
protected AtomData
atomData
protected int[]
atomIndex
protected int[]
atomNo
protected float[]
atomProp
protected float[]
atomRadius
protected javajs.util.P3[]
atomXyzTruncated
protected javajs.util.BS
bsMyIgnored
protected javajs.util.BS
bsMySelected
protected javajs.util.BS
bsNearby
protected javajs.util.BS
bsSurfaceVoxels
protected ContactPair
contactPair
protected boolean
doAddHydrogens
protected boolean
doUseIterator
protected String
fileDotModel
protected String
fileName
protected int
firstNearbyAtom
protected boolean
haveOneProperty
protected boolean
havePlane
protected float
margin
protected float
maxDistance
protected float
maxRS
maximun (atom radius + solvent radius)private float
minPtsPerAng
protected int
modelIndex
protected int
myAtomCount
protected int[]
myIndex
protected int
nearbyAtomCount
protected javajs.util.BS
noFaceSpheres
protected javajs.util.P3i
pt0
protected javajs.util.P3i
pt1
protected javajs.util.P3
ptV
protected javajs.util.P3
ptY0
protected javajs.util.P3
ptZ0
protected float[]
rs
atom radius + solvent radiusprotected float[]
rs2
square of (atom radius + solvent radius)protected float
sr
solvent radiusprotected float
theProperty
protected javajs.util.BS
thisAtomSet
protected float[]
thisPlane
protected int
thisX
protected javajs.util.BS
validSpheres
protected float
vl0
protected float
vl1
protected float
vl2
protected int[]
voxelSource
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Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
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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, isPeriodic, 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
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Constructor Summary
Constructors Constructor Description AtomDataReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private void
addAtomProp(int i, float f)
protected void
getAtomMinMax(javajs.util.BS bs, javajs.util.BS[] bsAtomMinMax)
protected void
getAtoms(javajs.util.BS bsSelected, boolean doAddHydrogens, boolean getRadii, boolean getMolecules, boolean getAllModels, boolean addNearbyAtoms, boolean getAtomMinMax, float marginAtoms, javajs.util.M4 modelInvRotation)
private float
getVoxel(int i, int j, int k, int ipt)
private float
getWorkingRadius(int i, float marginAtoms)
protected void
initADR(SurfaceGenerator sg)
protected void
markPlaneVoxels(javajs.util.P3 p, float r)
protected void
markSphereVoxels(float r0, float distance)
protected void
resetPlane(float value)
protected void
resetVoxelData(float value)
protected void
setGridLimitsForAtom(javajs.util.P3 ptA, float rA, javajs.util.P3i pt0, javajs.util.P3i pt1)
protected void
setHeader(String calcType, String line2)
protected void
setRadii()
protected void
setRanges(float ptsPerAngstrom, int maxGrid, float minPtsPerAng)
protected void
setup(boolean isMapData)
protected void
setup2()
protected void
setVertexSource()
protected void
setVolumeData()
protected void
setVolumeDataADR()
protected void
setVolumeForPlane()
protected void
setVoxel(int i, int j, int k, int ipt, float value)
protected void
unsetVoxelData()
protected void
unsetVoxelData2()
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Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, init, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Field Detail
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maxDistance
protected float maxDistance
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contactPair
protected ContactPair contactPair
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fileName
protected String fileName
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fileDotModel
protected String fileDotModel
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modelIndex
protected int modelIndex
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atomData
protected AtomData atomData
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atomXyzTruncated
protected javajs.util.P3[] atomXyzTruncated
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atomRadius
protected float[] atomRadius
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atomProp
protected float[] atomProp
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atomNo
protected int[] atomNo
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atomIndex
protected int[] atomIndex
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myIndex
protected int[] myIndex
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ac
protected int ac
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myAtomCount
protected int myAtomCount
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nearbyAtomCount
protected int nearbyAtomCount
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firstNearbyAtom
protected int firstNearbyAtom
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bsMySelected
protected javajs.util.BS bsMySelected
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bsMyIgnored
protected javajs.util.BS bsMyIgnored
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bsNearby
protected javajs.util.BS bsNearby
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doAddHydrogens
protected boolean doAddHydrogens
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havePlane
protected boolean havePlane
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doUseIterator
protected boolean doUseIterator
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theProperty
protected float theProperty
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haveOneProperty
protected boolean haveOneProperty
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minPtsPerAng
private float minPtsPerAng
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sr
protected float sr
solvent radius
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rs
protected float[] rs
atom radius + solvent radius
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rs2
protected float[] rs2
square of (atom radius + solvent radius)
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maxRS
protected float maxRS
maximun (atom radius + solvent radius)
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thisPlane
protected float[] thisPlane
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thisAtomSet
protected javajs.util.BS thisAtomSet
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thisX
protected int thisX
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margin
protected float margin
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vl0
protected float vl0
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vl1
protected float vl1
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vl2
protected float vl2
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bsSurfaceVoxels
protected javajs.util.BS bsSurfaceVoxels
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validSpheres
protected javajs.util.BS validSpheres
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noFaceSpheres
protected javajs.util.BS noFaceSpheres
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voxelSource
protected int[] voxelSource
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ptY0
protected final javajs.util.P3 ptY0
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ptZ0
protected final javajs.util.P3 ptZ0
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pt0
protected final javajs.util.P3i pt0
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pt1
protected final javajs.util.P3i pt1
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ptV
protected final javajs.util.P3 ptV
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Method Detail
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initADR
protected void initADR(SurfaceGenerator sg)
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setup
protected void setup(boolean isMapData)
- Overrides:
setup
in classVolumeDataReader
- Parameters:
isMapData
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setup2
protected void setup2()
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markPlaneVoxels
protected void markPlaneVoxels(javajs.util.P3 p, float r)
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setVolumeForPlane
protected void setVolumeForPlane()
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getAtoms
protected void getAtoms(javajs.util.BS bsSelected, boolean doAddHydrogens, boolean getRadii, boolean getMolecules, boolean getAllModels, boolean addNearbyAtoms, boolean getAtomMinMax, float marginAtoms, javajs.util.M4 modelInvRotation)
- Parameters:
bsSelected
-doAddHydrogens
-getRadii
-getMolecules
-getAllModels
-addNearbyAtoms
-getAtomMinMax
-marginAtoms
-modelInvRotation
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setRadii
protected void setRadii()
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addAtomProp
private void addAtomProp(int i, float f)
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getWorkingRadius
private float getWorkingRadius(int i, float marginAtoms)
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setRanges
protected void setRanges(float ptsPerAngstrom, int maxGrid, float minPtsPerAng)
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setVolumeData
protected void setVolumeData()
- Overrides:
setVolumeData
in classVolumeDataReader
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setVolumeDataADR
protected void setVolumeDataADR()
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setVertexSource
protected void setVertexSource()
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resetPlane
protected void resetPlane(float value)
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resetVoxelData
protected void resetVoxelData(float value)
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getVoxel
private float getVoxel(int i, int j, int k, int ipt)
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unsetVoxelData
protected void unsetVoxelData()
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unsetVoxelData2
protected void unsetVoxelData2()
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setGridLimitsForAtom
protected void setGridLimitsForAtom(javajs.util.P3 ptA, float rA, javajs.util.P3i pt0, javajs.util.P3i pt1)
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getAtomMinMax
protected void getAtomMinMax(javajs.util.BS bs, javajs.util.BS[] bsAtomMinMax)
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markSphereVoxels
protected void markSphereVoxels(float r0, float distance)
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setVoxel
protected void setVoxel(int i, int j, int k, int ipt, float value)
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