org.jmol.jvxl.readers

Class IsoSolventReader

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 and Description
private class	IsoSolventReader.Edge
private class	IsoSolventReader.Face

Field Summary

Fields

Modifier and Type	Field and Description
private BS[]	bsAtomMinMax
private BS[]	bsLocale
private BS	bsSurfaceDone
private BS	bsSurfacePoints
private float	cavityRadius
private boolean	doCalculateTroughs
private P3[]	dots
private float	dPX
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
private float	maxRadius
protected P3	p
protected P4	plane
private P3	ptS1
private P3	ptS2
protected P3	ptTemp2
protected float	solventRadius
private static boolean	testLinear
private JmolList<IsoSolventReader.Edge>	vEdges
private JmolList<IsoSolventReader.Face>	vFaces
protected V3	vTemp
protected V3	vTemp2
private V3	vTemp3

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

atomCount, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyz, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, haveOneProperty, havePlane, margin, maxDistance, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptXyzTemp, ptY0, ptZ0, theProperty, thisAtomSet, thisPlane, thisX, validSpheres, voxelSource

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

allowMapData, atomDataServer, 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, 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 and Description
IsoSolventReader()

Method Summary

Methods

Modifier and Type	Method and Description
int	addVertexCopy(P3 vertexXYZ, float value, int assocVertex) 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(P3 ptA, float rAS, P3 ptB, float rBS, float dAB, P3 ptV)
protected IsoSolventReader.Edge	findEdge(int i, int j)
protected void	generateCube()
private void	generateSolventCavity()
private void	generateSolventCube()
private void	getEdges()
private void	getFaces()
(package private) void	getMaxRadius()
float[]	getPlane(int x)
protected double	getPointP(int ia, int ib)
private boolean	getSolventPoints(int ia, int ib, int ic)
protected float	getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, P3 pointA, V3 edgeVector, int x, int y, int z, int vA0, int vB0, float[] fReturn, P3 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] MSMS: msms -if ttest.xyzrn -of ttest -density 5 MSMS 2.6.1 started on Local PC Copyright M.F.
float	getValueAtPoint(P3 pt, boolean getSource)
(package private) void	init(SurfaceGenerator sg) implemented in SurfaceFileReader and
private void	markFaceVoxels(boolean firstPass)
private void	markToroidVoxels()
private static void	mergeLimits(P3i ptA, P3i ptB, P3i pt0, P3i pt1)
protected void	postProcessVertices()
protected boolean	readVolumeParameters(boolean isMapData)
void	selectPocket(boolean doExclude)
protected void	setup(boolean isMapData)
private float	solventDistance(float rAS, float rBS, float dAB, float dAV, float dBV)
protected void	unsetVoxelData()
private boolean	validateFace(IsoSolventReader.Face f)
private static boolean	voxelIsInTrough(float dXC, float rAC2, float rBC, float dAB, float dAX)

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

fixTitleLine, getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, 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 org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVC, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane2, getSpanningVectors, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue, getValue2, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, readColorData, resetIsosurface, setBBox, setOutputStream, 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

cavityRadius

private float cavityRadius

envelopeRadius

private float envelopeRadius

dots

private P3[] dots

doCalculateTroughs

private boolean doCalculateTroughs

isCavity

private boolean isCavity

isPocket

private boolean isPocket

solventRadius

protected float solventRadius

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

private JmolList<IsoSolventReader.Edge> vEdges

vFaces

private JmolList<IsoSolventReader.Face> vFaces

vTemp

protected V3 vTemp

plane

protected P4 plane

ptTemp2

protected P3 ptTemp2

ptS1

private P3 ptS1

ptS2

private P3 ptS2

vTemp2

protected V3 vTemp2

vTemp3

private V3 vTemp3

dPX

private float dPX

p

protected final P3 p

maxRadius

private float maxRadius

bsAtomMinMax

private BS[] bsAtomMinMax

isSurfacePoint

private boolean isSurfacePoint

iAtomSurface

private int iAtomSurface

testLinear

private static boolean testLinear

Constructor Detail

IsoSolventReader

IsoSolventReader()

Method Detail

init

void init(SurfaceGenerator sg)

Description copied from class: SurfaceReader

implemented in SurfaceFileReader and

Specified by:

init in class SurfaceReader

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,
                               P3 pointA,
                               V3 edgeVector,
                               int x,
                               int y,
                               int z,
                               int vA0,
                               int vB0,
                               float[] fReturn,
                               P3 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] 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(P3 vertexXYZ,
                float value,
                int assocVertex)

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()

getSolventPoints

private boolean getSolventPoints(int ia,
                       int ib,
                       int ic)

validateFace

private boolean validateFace(IsoSolventReader.Face f)

markFaceVoxels

private void markFaceVoxels(boolean firstPass)

markToroidVoxels

private void markToroidVoxels()

unsetVoxelData

protected void unsetVoxelData()

Overrides:

unsetVoxelData in class AtomDataReader

getMaxRadius

void getMaxRadius()

mergeLimits

private static void mergeLimits(P3i ptA,
               P3i ptB,
               P3i pt0,
               P3i pt1)

checkSpecialVoxel

private float checkSpecialVoxel(P3 ptA,
                      float rAS,
                      P3 ptB,
                      float rBS,
                      float dAB,
                      P3 ptV)

voxelIsInTrough

private static boolean voxelIsInTrough(float dXC,
                      float rAC2,
                      float rBC,
                      float dAB,
                      float dAX)

solventDistance

private float solventDistance(float rAS,
                    float rBS,
                    float dAB,
                    float dAV,
                    float dBV)

getPointP

protected double getPointP(int ia,
               int ib)

getValueAtPoint

public float getValueAtPoint(P3 pt,
                    boolean getSource)

Overrides:

getValueAtPoint in class SurfaceReader

getSource - TODO

Returns:

value

getPlane

public float[] getPlane(int x)

Specified by:

getPlane in interface VertexDataServer

Overrides:

getPlane in class SurfaceReader