java.lang.Object
- org.jmol.jvxl.readers.SurfaceReader
- - org.jmol.jvxl.readers.VolumeDataReader
  - - org.jmol.jvxl.readers.AtomDataReader
    - - org.jmol.jvxl.readers.IsoSolventReader

All Implemented Interfaces:: VertexDataServer

class IsoSolventReader
extends AtomDataReader

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class IsoSolventReader.Edge

private class IsoSolventReader.Face

Field Summary

Fields
Modifier and Type	Field	Description
`private BS[]`	`bsAtomMinMax`
`private BS[]`	`bsLocale`
`private BS`	`bsSurfaceDone`
`private BS`	`bsSurfacePoints`
`private float`	`cavityRadius`
`private float`	`dAB`
`private float`	`dAB2`
`private boolean`	`doCalculateTroughs`
`private javajs.util.P3[]`	`dots`
`private float`	`ecosASB2`
`private float`	`envelopeRadius`
`private java.util.Map<java.lang.String,IsoSolventReader.Edge>`	`htEdges`
`private int`	`iAtomSurface`
`private boolean`	`isCavity`
`private boolean`	`isPocket`
`private boolean`	`isSurfacePoint`
`private AtomIndexIterator`	`iter`
`(package private) int`	`nTest`
`protected javajs.util.P3`	`p`
`protected javajs.util.P4`	`plane`
`private javajs.util.P3`	`ptS1`
`private javajs.util.P3`	`ptS2`
`protected javajs.util.P3`	`ptTemp2`
`private float`	`rAS`
`private float`	`rAS2`
`private float`	`rBS`
`private float`	`rBS2`
`private static boolean`	`testLinear`
`protected javajs.util.Lst<IsoSolventReader.Edge>`	`vEdges`
`private javajs.util.Lst<IsoSolventReader.Face>`	`vFaces`
`protected javajs.util.V3`	`vTemp`
`protected javajs.util.V3`	`vTemp2`

Fields inherited from class org.jmol.jvxl.readers.AtomDataReader
ac, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyzTruncated, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, haveOneProperty, havePlane, margin, maxDistance, maxRS, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptV, ptY0, ptZ0, rs, rs2, sr, theProperty, thisAtomSet, thisPlane, thisX, validSpheres, vl0, vl1, vl2, 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

IsoSolventReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`addVertexCopy(javajs.util.T3 vertexXYZ, float value, int assocVertex, boolean asCopy)`	addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
`private float`	`checkSpecialVoxel(javajs.util.P3 ptA, javajs.util.P3 ptB, javajs.util.P3 ptV)`
`(package private) void`	`discardTempData(boolean discardAll)`
`(package private) void`	`dumpLine(javajs.util.P3 pt1, javajs.util.T3 pt2, java.lang.String label, java.lang.String color)`
`(package private) void`	`dumpLine2(javajs.util.P3 pt1, javajs.util.P3 pt2, java.lang.String label, float d, java.lang.String color1, java.lang.String color2)`
`(package private) void`	`dumpPoint(javajs.util.P3 pt, java.lang.String label, java.lang.String color)`
`protected IsoSolventReader.Edge`	`findEdge(int i, int j)`
`protected void`	`generateCube()`
`private void`	`generateSolventCavity()`
`private void`	`generateSolventCube()`
`private void`	`getEdges()`
`private void`	`getFaces()`
`float[]`	`getPlane(int x)`
`private boolean`	`getSolventPoints(IsoSolventReader.Edge edge, int ia, int ib, int ic)`
`protected float`	`getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, int x, int y, int z, int vA0, int vB0, float[] fReturn, javajs.util.T3 ptReturn)`	TEST: alternative EXACT position of fraction for spherical MarchingCubes FOR: ttest.xyz: 2 isosurface molecular test showing discontinuities C -2.70 0 0 C 2.75 0 0 RESULT: LINEAR (points slightly within R): $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.06620391572324] isosurfaceVolume = [41.639681683494324] NONLINEAR: $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.11873783245028] isosurfaceVolume = [41.727027252180655] revision 3/16/2014: isosurfaceArea = [75.13146821881998] isosurfaceVolume = [41.74598178064965] MSMS: msms -if ttest.xyzrn -of ttest -density 5 MSMS 2.6.1 started on Local PC Copyright M.F.
`float`	`getValueAtPoint(javajs.util.T3 pt, boolean getSource)`
`(package private) void`	`init(SurfaceGenerator sg)`	implemented in SurfaceFileReader and
`private void`	`markFaceVoxels(boolean firstPass)`
`private void`	`markToroidVoxels()`
`protected void`	`postProcessVertices()`
`protected boolean`	`readVolumeParameters(boolean isMapData)`
`void`	`selectPocket(boolean doExclude)`
`protected void`	`setup(boolean isMapData)`
`private float`	`solventDistance(float rAS, float rAS2, float rBS2, float dAV, float dAV2, float dBV2)`
`protected void`	`unsetVoxelData()`
`private IsoSolventReader.Face`	`validateFace(int ia, int ib, int ic, IsoSolventReader.Edge edge, javajs.util.P3 ptS)`

Methods inherited from class org.jmol.jvxl.readers.AtomDataReader
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeData, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData2

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo

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

Field Detail

cavityRadius
```
private float cavityRadius
```

envelopeRadius
```
private float envelopeRadius
```

dots
```
private javajs.util.P3[] dots
```

doCalculateTroughs
```
private boolean doCalculateTroughs
```

isCavity
```
private boolean isCavity
```

isPocket
```
private boolean isPocket
```

iter
```
private AtomIndexIterator iter
```

bsSurfacePoints
```
private BS bsSurfacePoints
```

bsSurfaceDone
```
private BS bsSurfaceDone
```

bsLocale
```
private BS[] bsLocale
```

htEdges

private java.util.Map<java.lang.String,IsoSolventReader.Edge> htEdges

vEdges

protected javajs.util.Lst<IsoSolventReader.Edge> vEdges

vFaces

private javajs.util.Lst<IsoSolventReader.Face> vFaces

ptS1
```
private final javajs.util.P3 ptS1
```

ptS2
```
private final javajs.util.P3 ptS2
```

vTemp
```
protected final javajs.util.V3 vTemp
```

plane
```
protected final javajs.util.P4 plane
```

ptTemp2
```
protected final javajs.util.P3 ptTemp2
```

vTemp2
```
protected final javajs.util.V3 vTemp2
```

p
```
protected final javajs.util.P3 p
```

testLinear
```
private static boolean testLinear
```

bsAtomMinMax
```
private BS[] bsAtomMinMax
```

isSurfacePoint
```
private boolean isSurfacePoint
```

iAtomSurface
```
private int iAtomSurface
```

nTest
```
int nTest
```

rAS
```
private float rAS
```

rBS
```
private float rBS
```

rAS2
```
private float rAS2
```

rBS2
```
private float rBS2
```

dAB
```
private float dAB
```

dAB2
```
private float dAB2
```

ecosASB2
```
private float ecosASB2
```

Constructor Detail
- IsoSolventReader
```
IsoSolventReader()
```

Method Detail
- init
```
void init(SurfaceGenerator sg)
```
  Description copied from class: SurfaceReader
  
  implemented in SurfaceFileReader and
  
  Overrides:
  
  init in class VolumeDataReader
- readVolumeParameters
```
protected boolean readVolumeParameters(boolean isMapData)
```
  Overrides:
  
  readVolumeParameters in class VolumeDataReader
- setup
```
protected void setup(boolean isMapData)
```
  Overrides:
  
  setup in class AtomDataReader
- generateCube
```
protected void generateCube()
```
  Overrides:
  
  generateCube in class VolumeDataReader
- getSurfacePointAndFraction
```
protected float getSurfacePointAndFraction(float cutoff,
                                           boolean isCutoffAbsolute,
                                           float valueA,
                                           float valueB,
                                           javajs.util.T3 pointA,
                                           javajs.util.V3 edgeVector,
                                           int x,
                                           int y,
                                           int z,
                                           int vA0,
                                           int vB0,
                                           float[] fReturn,
                                           javajs.util.T3 ptReturn)
```
  TEST: alternative EXACT position of fraction for spherical MarchingCubes FOR: ttest.xyz: 2 isosurface molecular test showing discontinuities C -2.70 0 0 C 2.75 0 0 RESULT: LINEAR (points slightly within R): $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.06620391572324] isosurfaceVolume = [41.639681683494324] NONLINEAR: $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.11873783245028] isosurfaceVolume = [41.727027252180655] revision 3/16/2014: isosurfaceArea = [75.13146821881998] isosurfaceVolume = [41.74598178064965] MSMS: msms -if ttest.xyzrn -of ttest -density 5 MSMS 2.6.1 started on Local PC Copyright M.F. Sanner (1994) Compilation flags INPUT ttest.xyzrn 2 spheres 0 collision only, radii 1.700 to 1.700 PARAM Probe_radius 1.500 density 5.000 hdensity 3.000 Couldn't find first face trying -all option ANALYTICAL SURFACE AREA : Comp. probe_radius, reent, toric, contact SES SAS 0 1.500 0.000 8.144 67.243 75.387 238.258 NUMERICAL VOLUMES AND AREA Comp. probe_radius SES_volume SES_area) 0 1.50 40.497 74.132 Total ses_volume: 40.497 MSMS terminated normally CONCLUSION: -- surfaces are essentially identical -- nonlinear is slightly closer to analytical area (75.387), as expected -- both are better than MSMS triangulation for same "resolution": prog parameters %Error MSMS -density 5 1.66% (1412 faces) MSMS -density 20 0.36% (2968 faces) JMOL LINEAR resol 5 0.42% (2720 faces) JMOL NONLINEAR resol 5 0.32% (2720 faces) -- Marching Cubes is slightly improved using nonlinear calc.
  
  Overrides:
  
  getSurfacePointAndFraction in class SurfaceReader
  
  Parameters:
  
  cutoff -
  
  isCutoffAbsolute -
  
  valueA -
  
  valueB -
  
  pointA -
  
  edgeVector -
  
  fReturn -
  
  ptReturn -
  
  Returns:
  
  fractional distance from A to B
- addVertexCopy
```
public int addVertexCopy(javajs.util.T3 vertexXYZ,
                         float value,
                         int assocVertex,
                         boolean asCopy)
```
  Description copied from interface: VertexDataServer
  
  addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane. The implementing method should COPY the Point3f using Point3f.set(). The data consumer can use the association key to group this vertex with others near the same gridpoint.
  
  Specified by:
  
  addVertexCopy in interface VertexDataServer
  
  Overrides:
  
  addVertexCopy in class SurfaceReader
  
  assocVertex - unique association vertex or -1
  
  Returns:
  
  new vertex index
- selectPocket
```
public void selectPocket(boolean doExclude)
```
  Overrides:
  
  selectPocket in class SurfaceReader
- postProcessVertices
```
protected void postProcessVertices()
```
  Overrides:
  
  postProcessVertices in class SurfaceReader
- generateSolventCavity
```
private void generateSolventCavity()
```
- generateSolventCube
```
private void generateSolventCube()
```
- getEdges
```
private void getEdges()
```
- findEdge
```
protected IsoSolventReader.Edge findEdge(int i,
                                         int j)
```
- getFaces
```
private void getFaces()
```
- validateFace
```
private IsoSolventReader.Face validateFace(int ia,
                                           int ib,
                                           int ic,
                                           IsoSolventReader.Edge edge,
                                           javajs.util.P3 ptS)
```
- markFaceVoxels
```
private void markFaceVoxels(boolean firstPass)
```
- markToroidVoxels
```
private void markToroidVoxels()
```
- unsetVoxelData
```
protected void unsetVoxelData()
```
  Overrides:
  
  unsetVoxelData in class AtomDataReader
- getSolventPoints
```
private boolean getSolventPoints(IsoSolventReader.Edge edge,
                                 int ia,
                                 int ib,
                                 int ic)
```
- checkSpecialVoxel
```
private float checkSpecialVoxel(javajs.util.P3 ptA,
                                javajs.util.P3 ptB,
                                javajs.util.P3 ptV)
```
- solventDistance
```
private float solventDistance(float rAS,
                              float rAS2,
                              float rBS2,
                              float dAV,
                              float dAV2,
                              float dBV2)
```
- dumpLine
```
void dumpLine(javajs.util.P3 pt1,
              javajs.util.T3 pt2,
              java.lang.String label,
              java.lang.String color)
```
- dumpLine2
```
void dumpLine2(javajs.util.P3 pt1,
               javajs.util.P3 pt2,
               java.lang.String label,
               float d,
               java.lang.String color1,
               java.lang.String color2)
```
- dumpPoint
```
void dumpPoint(javajs.util.P3 pt,
               java.lang.String label,
               java.lang.String color)
```
- getValueAtPoint
```
public float getValueAtPoint(javajs.util.T3 pt,
                             boolean getSource)
```
  Overrides:
  
  getValueAtPoint in class SurfaceReader
  
  getSource - TODO
  
  Returns:
  
  value
- discardTempData
```
void discardTempData(boolean discardAll)
```
  Overrides:
  
  discardTempData in class SurfaceReader
- getPlane
```
public float[] getPlane(int x)
```
  Specified by:
  
  getPlane in interface VertexDataServer
  
  Overrides:
  
  getPlane in class SurfaceReader

Modifier and Type	Class	Description
`private class`	`IsoSolventReader.Edge`
`private class`	`IsoSolventReader.Face`

Class IsoSolventReader

Nested Class Summary

Field Summary

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

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.AtomDataReader

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

cavityRadius

envelopeRadius

dots

doCalculateTroughs

isCavity

isPocket

iter

bsSurfacePoints

bsSurfaceDone

bsLocale

htEdges

vEdges

vFaces

ptS1

ptS2

vTemp

plane

ptTemp2

vTemp2

p

testLinear

bsAtomMinMax

isSurfacePoint

iAtomSurface

nTest

rAS

rBS

rAS2

rBS2

dAB

dAB2

ecosASB2

Constructor Detail

IsoSolventReader

Method Detail

init

readVolumeParameters

setup

generateCube

getSurfacePointAndFraction

addVertexCopy

selectPocket

postProcessVertices

generateSolventCavity

generateSolventCube

getEdges

findEdge

getFaces

validateFace

markFaceVoxels

markToroidVoxels

unsetVoxelData

getSolventPoints

checkSpecialVoxel

solventDistance

dumpLine

dumpLine2

dumpPoint

getValueAtPoint

discardTempData

getPlane