Package 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
,IsoIntersectAtomReader
,IsoIntersectReader
,IsoMepReader
,IsoMOReader
,IsoPlaneReader
,IsoSolventReader
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected int
protected AtomData
protected int[]
protected int[]
protected float[]
protected float[]
protected javajs.util.P3[]
protected javajs.util.BS
protected javajs.util.BS
protected javajs.util.BS
protected javajs.util.BS
protected ContactPair
protected boolean
protected boolean
protected String
protected String
protected int
protected boolean
protected boolean
protected float
protected float
protected float
maximun (atom radius + solvent radius)private float
protected int
protected int
protected int[]
protected int
protected javajs.util.BS
protected final javajs.util.P3i
protected final javajs.util.P3i
protected final javajs.util.P3
protected final javajs.util.P3
protected final javajs.util.P3
protected float[]
atom radius + solvent radiusprotected float[]
square of (atom radius + solvent radius)protected float
solvent radiusprotected float
protected javajs.util.BS
protected float[]
protected int
protected javajs.util.BS
protected float
protected float
protected float
protected int[]
Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
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, jvxlCutoffRange, 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 -
Method Summary
Modifier and TypeMethodDescriptionprivate 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
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
protected void
setRadii()
protected void
setRanges
(float ptsPerAngstrom, int maxGrid, float minPtsPerAng) protected void
setup
(boolean isMapData) protected void
setup2()
protected void
protected void
protected void
protected void
protected void
setVoxel
(int i, int j, int k, int ipt, float value) protected void
protected void
Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, init, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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 Details
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maxDistance
protected float maxDistance -
contactPair
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fileName
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fileDotModel
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modelIndex
protected int modelIndex -
atomData
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atomXyzTruncated
protected javajs.util.P3[] atomXyzTruncated -
atomRadius
protected float[] atomRadius -
atomProp
protected float[] atomProp -
atomNo
protected int[] atomNo -
atomIndex
protected int[] atomIndex -
myIndex
protected int[] myIndex -
ac
protected int ac -
myAtomCount
protected int myAtomCount -
nearbyAtomCount
protected int nearbyAtomCount -
firstNearbyAtom
protected int firstNearbyAtom -
bsMySelected
protected javajs.util.BS bsMySelected -
bsMyIgnored
protected javajs.util.BS bsMyIgnored -
bsNearby
protected javajs.util.BS bsNearby -
doAddHydrogens
protected boolean doAddHydrogens -
havePlane
protected boolean havePlane -
doUseIterator
protected boolean doUseIterator -
theProperty
protected float theProperty -
haveOneProperty
protected boolean haveOneProperty -
minPtsPerAng
private float minPtsPerAng -
sr
protected float srsolvent radius -
rs
protected float[] rsatom radius + solvent radius -
rs2
protected float[] rs2square of (atom radius + solvent radius) -
maxRS
protected float maxRSmaximun (atom radius + solvent radius) -
thisPlane
protected float[] thisPlane -
thisAtomSet
protected javajs.util.BS thisAtomSet -
thisX
protected int thisX -
margin
protected float margin -
vl0
protected float vl0 -
vl1
protected float vl1 -
vl2
protected float vl2 -
bsSurfaceVoxels
protected javajs.util.BS bsSurfaceVoxels -
validSpheres
protected javajs.util.BS validSpheres -
noFaceSpheres
protected javajs.util.BS noFaceSpheres -
voxelSource
protected int[] voxelSource -
ptY0
protected final javajs.util.P3 ptY0 -
ptZ0
protected final javajs.util.P3 ptZ0 -
pt0
protected final javajs.util.P3i pt0 -
pt1
protected final javajs.util.P3i pt1 -
ptV
protected final javajs.util.P3 ptV
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Constructor Details
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AtomDataReader
AtomDataReader()
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Method Details
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initADR
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setup
protected void setup(boolean isMapData) - Overrides:
setup
in classVolumeDataReader
- Parameters:
isMapData
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setup2
protected void setup2() -
markPlaneVoxels
protected void markPlaneVoxels(javajs.util.P3 p, float r) -
setVolumeForPlane
protected void setVolumeForPlane() -
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() -
addAtomProp
private void addAtomProp(int i, float f) -
getWorkingRadius
private float getWorkingRadius(int i, float marginAtoms) -
setHeader
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setRanges
protected void setRanges(float ptsPerAngstrom, int maxGrid, float minPtsPerAng) -
setVolumeData
protected void setVolumeData()- Overrides:
setVolumeData
in classVolumeDataReader
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setVolumeDataADR
protected void setVolumeDataADR() -
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() -
unsetVoxelData2
protected void unsetVoxelData2() -
setGridLimitsForAtom
protected void setGridLimitsForAtom(javajs.util.P3 ptA, float rA, javajs.util.P3i pt0, javajs.util.P3i pt1) -
getAtomMinMax
protected void getAtomMinMax(javajs.util.BS bs, javajs.util.BS[] bsAtomMinMax) -
markSphereVoxels
protected void markSphereVoxels(float r0, float distance) -
setVoxel
protected void setVoxel(int i, int j, int k, int ipt, float value)
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