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
```

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 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`

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, 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 Summary

Constructors
Constructor Description

AtomDataReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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, 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(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()`

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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
```

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 BS bsMySelected
```

bsMyIgnored
```
protected BS bsMyIgnored
```

bsNearby
```
protected 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 sr
```
solvent radius

rs
```
protected float[] rs
```
atom radius + solvent radius

rs2
```
protected float[] rs2
```
square of (atom radius + solvent radius)

maxRS
```
protected float maxRS
```
maximun (atom radius + solvent radius)

thisPlane
```
protected float[] thisPlane
```

thisAtomSet
```
protected BS thisAtomSet
```

thisX
```
protected int thisX
```

margin
```
protected float margin
```

vl0
```
protected float vl0
```

vl1
```
protected float vl1
```

vl2
```
protected float vl2
```

bsSurfaceVoxels
```
protected BS bsSurfaceVoxels
```

validSpheres
```
protected BS validSpheres
```

noFaceSpheres
```
protected 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
```

Constructor Detail
- AtomDataReader
```
AtomDataReader()
```

Method Detail

initADR

protected void initADR(SurfaceGenerator sg)

setup
```
protected void setup(boolean isMapData)
```
Overrides:

setup in class VolumeDataReader

Parameters:

isMapData -

setup2
```
protected void setup2()
```

markPlaneVoxels

protected void markPlaneVoxels(javajs.util.P3 p,
                               float r)

setVolumeForPlane
```
protected void setVolumeForPlane()
```

getAtoms

protected void getAtoms(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 -

setRadii
```
protected void setRadii()
```

addAtomProp

private void addAtomProp(int i,
                         float f)

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,
                         float minPtsPerAng)

setVolumeData
```
protected void setVolumeData()
```
Overrides:

setVolumeData in class VolumeDataReader

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(BS bs,
                             BS[] bsAtomMinMax)

markSphereVoxels

protected void markSphereVoxels(float r0,
                                float distance)

setVoxel

protected void setVoxel(int i,
                        int j,
                        int k,
                        int ipt,
                        float value)

Class AtomDataReader

Field Summary

Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

Methods inherited from class java.lang.Object

Field Detail

maxDistance

contactPair

fileName

fileDotModel

modelIndex

atomData

atomXyzTruncated

atomRadius

atomProp

atomNo

atomIndex

myIndex

ac

myAtomCount

nearbyAtomCount

firstNearbyAtom

bsMySelected

bsMyIgnored

bsNearby

doAddHydrogens

havePlane

doUseIterator

theProperty

haveOneProperty

minPtsPerAng

sr

rs

rs2

maxRS

thisPlane

thisAtomSet

thisX

margin

vl0

vl1

vl2

bsSurfaceVoxels

validSpheres

noFaceSpheres

voxelSource

ptY0

ptZ0

pt0

pt1

ptV

Constructor Detail

AtomDataReader

Method Detail

initADR

setup

setup2

markPlaneVoxels

setVolumeForPlane

getAtoms

setRadii

addAtomProp

getWorkingRadius

setHeader

setRanges

setVolumeData

setVolumeDataADR

setVertexSource

resetPlane

resetVoxelData

getVoxel

unsetVoxelData

unsetVoxelData2

setGridLimitsForAtom

getAtomMinMax

markSphereVoxels