abstract class AtomDataReader extends VolumeDataReader
Modifier and Type | Field and Description |
---|---|
protected int |
ac |
protected AtomData |
atomData |
protected int[] |
atomIndex |
protected int[] |
atomNo |
protected float[] |
atomProp |
protected float[] |
atomRadius |
protected javajs.util.P3[] |
atomXyz |
protected BS |
bsMyIgnored |
protected BS |
bsMySelected |
protected BS |
bsNearby |
protected BS |
bsSurfaceVoxels |
protected ContactPair |
contactPair |
protected boolean |
doAddHydrogens |
protected boolean |
doUseIterator |
protected java.lang.String |
fileDotModel |
protected java.lang.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 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 radius
|
protected float[] |
rs2
square of (atom radius + solvent radius)
|
protected float |
sr
solvent radius
|
protected float |
theProperty |
protected BS |
thisAtomSet |
protected float[] |
thisPlane |
protected int |
thisX |
protected BS |
validSpheres |
protected float |
vl0 |
protected float |
vl1 |
protected float |
vl2 |
protected int[] |
voxelSource |
allowMapData, 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, 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
Constructor and Description |
---|
AtomDataReader() |
Modifier and Type | Method and Description |
---|---|
private void |
addAtomProp(int i,
float f) |
protected void |
getAtomMinMax(BS bs,
BS[] bsAtomMinMax) |
protected void |
getAtoms(BS 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 |
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(java.lang.String calcType,
java.lang.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() |
closeReader, generateCube, init, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlane2, 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
protected float maxDistance
protected ContactPair contactPair
protected java.lang.String fileName
protected java.lang.String fileDotModel
protected int modelIndex
protected AtomData atomData
protected javajs.util.P3[] atomXyz
protected float[] atomRadius
protected float[] atomProp
protected int[] atomNo
protected int[] atomIndex
protected int[] myIndex
protected int ac
protected int myAtomCount
protected int nearbyAtomCount
protected int firstNearbyAtom
protected BS bsMySelected
protected BS bsMyIgnored
protected BS bsNearby
protected boolean doAddHydrogens
protected boolean havePlane
protected boolean doUseIterator
protected float theProperty
protected boolean haveOneProperty
private float minPtsPerAng
protected float sr
protected float[] rs
protected float[] rs2
protected float maxRS
protected float[] thisPlane
protected BS thisAtomSet
protected int thisX
protected float margin
protected float vl0
protected float vl1
protected float vl2
protected BS bsSurfaceVoxels
protected BS validSpheres
protected BS noFaceSpheres
protected int[] voxelSource
protected final javajs.util.P3 ptY0
protected final javajs.util.P3 ptZ0
protected final javajs.util.P3i pt0
protected final javajs.util.P3i pt1
protected final javajs.util.P3 ptV
protected void initADR(SurfaceGenerator sg)
protected void setup(boolean isMapData)
setup
in class VolumeDataReader
isMapData
- protected void setup2()
protected void markPlaneVoxels(javajs.util.P3 p, float r)
protected void setVolumeForPlane()
protected void getAtoms(BS bsSelected, boolean doAddHydrogens, boolean getRadii, boolean getMolecules, boolean getAllModels, boolean addNearbyAtoms, boolean getAtomMinMax, float marginAtoms)
bsSelected
- doAddHydrogens
- getRadii
- getMolecules
- getAllModels
- addNearbyAtoms
- getAtomMinMax
- marginAtoms
- protected void setRadii()
private void addAtomProp(int i, float f)
private float getWorkingRadius(int i, float marginAtoms)
protected void setHeader(java.lang.String calcType, java.lang.String line2)
protected void setRanges(float ptsPerAngstrom, int maxGrid, float minPtsPerAng)
protected void setVolumeData()
setVolumeData
in class VolumeDataReader
protected void setVolumeDataADR()
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 unsetVoxelData2()
protected void setGridLimitsForAtom(javajs.util.P3 ptA, float rA, javajs.util.P3i pt0, javajs.util.P3i pt1)
protected void markSphereVoxels(float r0, float distance)
protected void setVoxel(int i, int j, int k, int ipt, float value)