META-INF/MANIFEST.MF
META-INF/SELFSIGN.SF
META-INF/SELFSIGN.RSA
META-INF/
org/
org/jmol/
org/jmol/jvxl/
org/jmol/jvxl/api/
org/jmol/jvxl/calc/
org/jmol/jvxl/data/
org/jmol/jvxl/readers/
org/jmol/shapesurface/
org/jmol/jvxl/api/MeshDataServer.class
<Unknown>
package org.jmol.jvxl.api
public abstract org.jmol.jvxl.api.MeshDataServer extends java.lang.Object implements org.jmol.jvxl.api.VertexDataServer {
public abstract void invalidateTriangles ()
public abstract void fillMeshData (org.jmol.jvxl.data.MeshData, int)
public abstract void notifySurfaceGenerationCompleted ()
public abstract void notifySurfaceMappingCompleted ()
public abstract javax.vecmath.Point3f[] calculateGeodesicSurface (java.util.BitSet, float)
public abstract int getColixArgb (short)
}
org/jmol/jvxl/api/VertexDataServer.class
<Unknown>
package org.jmol.jvxl.api
public abstract org.jmol.jvxl.api.VertexDataServer extends java.lang.Object {
public abstract int getSurfacePointIndexAndFraction (float, boolean, int, int, int, javax.vecmath.Point3i, int, int, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, boolean, float[])
public abstract int addVertexCopy (javax.vecmath.Point3f, float, int)
public abstract void addTriangleCheck (int, int, int, int, boolean, int)
public abstract float getValue (int, int, int)
}
org/jmol/jvxl/calc/MarchingCubes.class
<Unknown>
package org.jmol.jvxl.calc
public org.jmol.jvxl.calc.MarchingCubes extends org.jmol.jvxl.calc.TriangleData {
private org.jmol.jvxl.api.VertexDataServer surfaceReader
private org.jmol.jvxl.data.VolumeData volumeData
private int contourType
private boolean isContoured
private float cutoff
private boolean isCutoffAbsolute
private boolean isSquared
private boolean isXLowToHigh
private int cubeCountX
private int cubeCountY
private int cubeCountZ
private int nY
private int nZ
private int yzCount
private float fractionOutside
private boolean integrateSquared
private java.util.BitSet bsVoxels
private StringBuffer edgeData
private int mode
private static final int MODE_CUBE
private static final int MODE_BITSET
private static final int MODE_GETXYZ
private final float[] vertexValues
int edgeCount
private final javax.vecmath.Vector3f[] voxelVertexVectors
private final javax.vecmath.Vector3f[] edgeVectors
private static int[] yzPlanePts
private final int[] edgePointIndexes
private int[][][] isoPointIndexPlanes
private float[][] yzPlanes
javax.vecmath.Vector3f vTemp
private java.util.BitSet bsValues
private final javax.vecmath.Point3f pt0
private final javax.vecmath.Point3f pointA
private static final int[] edgeVertexPointersLowToHigh
private static final int[] edgeVertexPointersHighToLow
private int[] edgeVertexPointers
private static final int[] edgeVertexPlanesLowToHigh
private static final int[] edgeVertexPlanesHighToLow
private int[] edgeVertexPlanes
private float[] fReturn
private static final javax.vecmath.Vector3f[] cubeVertexVectors
private static final int[] edgeTypeTable
private final int[] linearOffsets
private static final short[] insideMaskTable
public java.util.BitSet getBsVoxels ()
public void <init> ()
public void <init> (org.jmol.jvxl.api.VertexDataServer, org.jmol.jvxl.data.VolumeData, java.util.BitSet, boolean, int, float, boolean, boolean, boolean)
private void calcVoxelVertexVectors ()
private int[][] resetIndexPlane (int[][])
public java.lang.String getEdgeData ()
private void addTriangle (int, int, int, int)
private float getValue (int, int, int, int, int, float[])
public static boolean isInside (float, float, boolean)
private boolean processOneCubical (int, int, int, int, int)
public void calcVertexPoint (int, int, int, int, javax.vecmath.Point3f)
private void setLinearOffsets ()
public int getLinearOffset (int, int, int, int)
static void <clinit> ()
}
org/jmol/jvxl/calc/MarchingSquares$ContourVertex.class
<Unknown>
package org.jmol.jvxl.calc
org.jmol.jvxl.calc.MarchingSquares$ContourVertex extends java.lang.Object {
javax.vecmath.Point3f vertexXYZ
javax.vecmath.Point3i voxelLocation
int[] pixelLocation
float value
int vertexIndex
void <init> (int, int, int, javax.vecmath.Point3f, int)
void setValue (float, org.jmol.jvxl.data.VolumeData)
void setPixelLocation (javax.vecmath.Point3i)
}
org/jmol/jvxl/calc/MarchingSquares$PlanarSquare.class
<Unknown>
package org.jmol.jvxl.calc
org.jmol.jvxl.calc.MarchingSquares$PlanarSquare extends java.lang.Object {
int[] edgeMask12
int edgeMask12All
int nInside
int nOutside
int nThrough
int contourBits
final int[] vertexes
float[][] fractions
int[][] intersectionPoints
void <init> (int)
void setIntersectionPoints (int, int[], float[])
void setVertex (int, int)
void addEdgeMask (int, int, int)
}
org/jmol/jvxl/calc/MarchingSquares.class
<Unknown>
package org.jmol.jvxl.calc
public org.jmol.jvxl.calc.MarchingSquares extends java.lang.Object {
public static final int CONTOUR_POINT
public static final int VERTEX_POINT
public static final int EDGE_POINT
private boolean logMessages
private org.jmol.jvxl.api.VertexDataServer surfaceReader
private org.jmol.jvxl.data.VolumeData volumeData
private static final int nContourMax
public static final int defaultContourCount
private int nContourSegments
private int nContoursSpecified
private int contourType
private javax.vecmath.Point4f thePlane
private boolean is3DContour
private int thisContour
private float valueMin
private float valueMax
private int nVertices
private final javax.vecmath.Vector3f pointVector
private final javax.vecmath.Point3f pointA
private final javax.vecmath.Point3f pointB
private final javax.vecmath.Vector3f edgeVector
private final javax.vecmath.Point3f planarOrigin
private final javax.vecmath.Vector3f[] planarVectors
private final javax.vecmath.Vector3f[] unitPlanarVectors
private final float[] planarVectorLengths
private final javax.vecmath.Matrix3f matXyzToPlane
private boolean contourFromZero
private static final javax.vecmath.Point3i[] squareVertexOffsets
private static final javax.vecmath.Vector3f[] squareVertexVectors
private static final byte[] edgeVertexes2d
private static final byte[] insideMaskTable2d
private int contourVertexCount
private org.jmol.jvxl.calc.MarchingSquares$ContourVertex[] contourVertexes
private final int[] pixelCounts
private final javax.vecmath.Matrix3f planarMatrix
private float[][] pixelData
private final float[] vertexValues2d
private final javax.vecmath.Point3f[] contourPoints
private int squareCountX
private int squareCountY
private org.jmol.jvxl.calc.MarchingSquares$PlanarSquare[] planarSquares
private int nSquares
private float contourPlaneMinimumValue
private float contourPlaneMaximumValue
private int contourIndex
private float[] squareFractions
private final javax.vecmath.Point3f pixelOrigin
private javax.vecmath.Vector3f[] pixelVertexVectors
private final int[] triangleVertexList
private final javax.vecmath.Point3i ptiTemp
public void <init> (org.jmol.jvxl.api.VertexDataServer, org.jmol.jvxl.data.VolumeData, javax.vecmath.Point4f, int, int, boolean)
public int getContourType ()
public void setMinMax (float, float)
private void setContourType ()
private static int getContourType (javax.vecmath.Point4f, javax.vecmath.Vector3f[])
public int generateContourData (boolean)
private void getPlanarVectors ()
private void setPlanarTransform ()
private void getPlanarOrigin ()
public int addContourVertex (int, int, int, javax.vecmath.Point3i, javax.vecmath.Point3f, float)
public int getContourVertexCount ()
public void setContourData (int, float)
private void loadPixelData (boolean)
public float getInterpolatedPixelValue (javax.vecmath.Point3f)
private void getPixelCounts ()
private void createPlanarSquares ()
public boolean createContours (float, float)
private int generateContourData (float)
private boolean isInside2d (float, float)
private int[] propagateNeighborPointIndexes2d (int, int, int[][], float[][])
private void processOneQuadrilateral (int, float, int[], int, int)
private void calcVertexPoints2d (int, int, int, int)
private void calcVertexPoints3d (int, int, int, int)
private void contourLocateXYZ (int, int, javax.vecmath.Point3f)
private int findContourVertex (int, int)
private float calcContourPoint (float, float, float, javax.vecmath.Point3f)
private void calcPixelVertexVectors ()
private void triangulateContours (boolean)
private void fillSquare (org.jmol.jvxl.calc.MarchingSquares$PlanarSquare, int, int, boolean, int)
private void createTriangleSet (int, int, int)
private static void setupMatrix (javax.vecmath.Matrix3f, javax.vecmath.Vector3f[])
private void xyzToPixelVector (javax.vecmath.Vector3f)
private javax.vecmath.Point3f pixelPtToXYZ (int, int)
private javax.vecmath.Point3i locatePixel (javax.vecmath.Point3f)
static void <clinit> ()
}
org/jmol/jvxl/calc/TriangleData.class
<Unknown>
package org.jmol.jvxl.calc
public org.jmol.jvxl.calc.TriangleData extends java.lang.Object implements org.jmol.api.TriangleServer {
protected static final int[] Pwr2
protected static final javax.vecmath.Point3i[] cubeVertexOffsets
protected static final byte[] edgeVertexes
protected static final byte[][] triangleTable2
public void <init> ()
public javax.vecmath.Point3i[] getCubeVertexOffsets ()
public java.util.Vector intersectPlane (javax.vecmath.Point4f, javax.vecmath.Point3f[], int)
static void <clinit> ()
}
org/jmol/jvxl/data/JvxlData.class
<Unknown>
package org.jmol.jvxl.data
public org.jmol.jvxl.data.JvxlData extends java.lang.Object {
public boolean wasJvxl
public boolean wasCubic
public String jvxlFileTitle
public String jvxlFileMessage
public String jvxlFileHeader
public String jvxlExtraLine
public String jvxlDefinitionLine
public String jvxlSurfaceData
public String jvxlEdgeData
public String jvxlColorData
public String jvxlInfoLine
public javax.vecmath.Point4f jvxlPlane
public int jvxlCompressionRatio
public boolean isJvxlPrecisionColor
public boolean jvxlDataIsColorMapped
public boolean jvxlDataIs2dContour
public boolean isColorReversed
public int edgeFractionBase
public int edgeFractionRange
public int colorFractionBase
public int colorFractionRange
public boolean insideOut
public boolean isXLowToHigh
public boolean isContoured
public boolean isBicolorMap
public boolean isTruncated
public boolean vertexDataOnly
public float mappedDataMin
public float mappedDataMax
public float valueMappedToRed
public float valueMappedToBlue
public float cutoff
public float pointsPerAngstrom
public int nPointsX
public int nPointsY
public int nPointsZ
public int nBytes
public int nContours
public int nEdges
public int nSurfaceInts
public int vertexCount
public java.util.Vector[] vContours
public int[] contourColors
public short minColorIndex
public short maxColorIndex
public String[] title
public String version
public void <init> ()
}
org/jmol/jvxl/data/MeshData.class
<Unknown>
package org.jmol.jvxl.data
public org.jmol.jvxl.data.MeshData extends java.lang.Object {
private static final int SEED_COUNT
public static final int MODE_GET_VERTICES
public static final int MODE_GET_COLOR_INDEXES
public static final int MODE_PUT_SETS
public static final int MODE_PUT_VERTICES
public int polygonCount
public javax.vecmath.Point3f[] vertices
public short[] vertexColixes
public int vertexCount
public float[] vertexValues
public int[][] polygonIndexes
public short[] polygonColixes
public java.util.BitSet[] surfaceSet
public int[] vertexSets
public int nSets
public javax.vecmath.Point3f[] dots
private boolean setsSuccessful
public int vertexIncrement
private int lastColor
private short lastColix
public void <init> ()
public int addVertexCopy (javax.vecmath.Point3f, float, int)
private int addVertexCopy (javax.vecmath.Point3f)
public void addTriangleCheck (int, int, int, int, int)
public java.util.BitSet[] getSurfaceSet ()
public java.util.BitSet[] getSurfaceSet (int)
private int findSet (int)
private void createSet (int, int, int)
private void mergeSets (int, int)
public void invalidateSurfaceSet (int)
public static boolean checkCutoff (int, int, int, float[])
private boolean setABC (int)
public void invalidateTriangles ()
}
org/jmol/jvxl/data/VolumeData.class
<Unknown>
package org.jmol.jvxl.data
public org.jmol.jvxl.data.VolumeData extends java.lang.Object implements org.jmol.api.VolumeDataInterface {
public final javax.vecmath.Point3f volumetricOrigin
public final float[] origin
public final javax.vecmath.Vector3f[] volumetricVectors
public final int[] voxelCounts
public int nPoints
public float[][][] voxelData
public final float[] volumetricVectorLengths
public final javax.vecmath.Vector3f[] unitVolumetricVectors
private final javax.vecmath.Matrix3f volumetricMatrix
private javax.vecmath.Point4f thePlane
private float thePlaneNormalMag
private final javax.vecmath.Point3f ptXyzTemp
private final javax.vecmath.Vector3f pointVector
public void <init> ()
public void setVolumetricOrigin (float, float, float)
public float[] getOriginFloat ()
public float[] getVolumetricVectorLengths ()
public void setVolumetricVector (int, float, float, float)
public int[] getVoxelCounts ()
public int setVoxelCounts (int, int, int)
public float[][][] getVoxelData ()
public void setVoxelData (float[][][])
public void setMatrix ()
public void transform (javax.vecmath.Vector3f, javax.vecmath.Vector3f)
public void setPlaneParameters (javax.vecmath.Point4f)
public float calcVoxelPlaneDistance (int, int, int)
public float distancePointToPlane (javax.vecmath.Point3f)
public void voxelPtToXYZ (int, int, int, javax.vecmath.Point3f)
public void setUnitVectors ()
private float scaleByVoxelVector (javax.vecmath.Vector3f, int)
public void xyzToVoxelPt (float, float, float, javax.vecmath.Point3i)
private void setVoxelPoint ()
public float lookupInterpolatedVoxelValue (javax.vecmath.Point3f)
private float getInterpolatedVoxelValue (javax.vecmath.Point3f)
public static float getFractional2DValue (float, float, float, float, float, float)
private static int indexDown (float, int)
void offsetCenter (javax.vecmath.Point3f)
public void setDataDistanceToPlane (javax.vecmath.Point4f)
public void filterData (boolean, float)
public void capData (javax.vecmath.Point4f, float)
}
org/jmol/jvxl/readers/ApbsReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.ApbsReader extends org.jmol.jvxl.readers.VolumeFileReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected void readTitleLines () throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected void readVoxelVector (int) throws java.lang.Exception
}
org/jmol/jvxl/readers/AtomDataReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.AtomDataReader extends org.jmol.jvxl.readers.VolumeDataReader {
protected org.jmol.atomdata.AtomDataServer atomDataServer
protected String fileName
protected String fileDotModel
protected int modelIndex
protected org.jmol.atomdata.AtomData atomData
protected javax.vecmath.Point3f[] atomXyz
protected float[] atomRadius
protected float[] atomProp
protected int[] atomNo
protected int[] atomIndex
protected int[] myIndex
protected int atomCount
protected int myAtomCount
protected int nearbyAtomCount
protected int firstNearbyAtom
protected java.util.BitSet bsMySelected
protected java.util.BitSet bsMyIgnored
private javax.vecmath.Point3f xyzMin
private javax.vecmath.Point3f xyzMax
protected boolean doAddHydrogens
protected boolean doUsePlane
protected boolean doUseIterator
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
protected void getAtoms (float, boolean, boolean)
private float getWorkingRadius (int, float)
protected void setHeader (java.lang.String, java.lang.String)
protected void setRangesAndAddAtoms (float, int, int)
protected boolean fixTitleLine (int)
}
org/jmol/jvxl/readers/CubeReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.CubeReader extends org.jmol.jvxl.readers.VolumeFileReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected void readTitleLines () throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
}
org/jmol/jvxl/readers/EfvetReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.EfvetReader extends org.jmol.jvxl.readers.PolygonFileReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
void getSurfaceData () throws java.lang.Exception
private void getHeader () throws java.lang.Exception
private void getVertices () throws java.lang.Exception
private void getTriangles () throws java.lang.Exception
}
org/jmol/jvxl/readers/IsoFxyReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoFxyReader extends org.jmol.jvxl.readers.VolumeDataReader {
private String functionName
private float[][] data
private boolean isPlanarMapping
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
public float getValue (int, int, int)
}
org/jmol/jvxl/readers/IsoFxyzReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoFxyzReader extends org.jmol.jvxl.readers.VolumeDataReader {
private String functionName
private float[][][] data
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
public float getValue (int, int, int)
}
org/jmol/jvxl/readers/IsoMOReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoMOReader extends org.jmol.jvxl.readers.AtomDataReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
private void fixTitleLine (int, java.util.Hashtable)
protected void generateCube ()
private void getData (org.jmol.api.MOCalculationInterface, java.util.Hashtable, float[], float[])
}
org/jmol/jvxl/readers/IsoMepReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoMepReader extends org.jmol.jvxl.readers.AtomDataReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
protected void generateCube ()
}
org/jmol/jvxl/readers/IsoPlaneReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoPlaneReader extends org.jmol.jvxl.readers.AtomDataReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
public float getValue (int, int, int)
}
org/jmol/jvxl/readers/IsoShapeReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoShapeReader extends org.jmol.jvxl.readers.VolumeDataReader {
private int psi_n
private int psi_l
private int psi_m
private float psi_Znuc
private float sphere_radiusAngstroms
private boolean allowNegative
private double[] rfactor
private double[] pfactor
private static final double A0
private static final double ROOT2
private float radius
private float ppa
private int maxGrid
private static final float[] fact
private final javax.vecmath.Point3f ptPsi
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, float)
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, int, int, int, float)
protected void setup ()
public float getValue (int, int, int)
private void setHeader (java.lang.String)
private float autoScaleOrbital ()
private void calcFactors (int, int, int)
private double hydrogenAtomPsiAt (javax.vecmath.Point3f, int, int, int)
protected void readSurfaceData (boolean) throws java.lang.Exception
static void <clinit> ()
}
org/jmol/jvxl/readers/IsoSolventReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.IsoSolventReader extends org.jmol.jvxl.readers.AtomDataReader {
private float cavityRadius
private float envelopeRadius
private boolean doCalculateTroughs
private boolean isCavity
private boolean isPocket
private float solventRadius
private boolean isProperty
private boolean doSmoothProperty
final javax.vecmath.Point3f ptXyzTemp
final javax.vecmath.Point3f ptS
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
protected void setup ()
public void selectPocket (boolean)
protected void generateCube ()
private void generateSolventCavity ()
void generateSolventCube (boolean)
void setGridLimitsForAtom (javax.vecmath.Point3f, float, javax.vecmath.Point3i, javax.vecmath.Point3i)
float checkSpecialVoxel (javax.vecmath.Point3f, float, javax.vecmath.Point3f, float, float, javax.vecmath.Point3f)
boolean voxelIsInTrough (float, float, float, float, float, float)
float solventDistance (javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f, float, float, float, float, float)
}
org/jmol/jvxl/readers/JaguarReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.JaguarReader extends org.jmol.jvxl.readers.VolumeFileReader {
private float[] extents
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected void readTitleLines () throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected void readVoxelVector (int) throws java.lang.Exception
protected float nextVoxel () throws java.lang.Exception
}
org/jmol/jvxl/readers/JvxlReader.class
<Unknown>
package org.jmol.jvxl.readers
public org.jmol.jvxl.readers.JvxlReader extends org.jmol.jvxl.readers.VolumeFileReader {
private static final String JVXL_VERSION
public static final int defaultEdgeFractionBase
public static final int defaultEdgeFractionRange
public static final int defaultColorFractionBase
public static final int defaultColorFractionRange
private int surfaceDataCount
private int edgeDataCount
private int colorDataCount
private boolean haveContourData
private int nThisValue
private boolean thisInside
private int fractionPtr
private String strFractionTemp
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected static void jvxlUpdateInfo (org.jmol.jvxl.data.JvxlData, java.lang.String[], int)
public static void jvxlUpdateInfoLines (org.jmol.jvxl.data.JvxlData)
protected boolean readVolumeData (boolean)
protected boolean gotoAndReadVoxelData (boolean)
protected void initializeVoxelData ()
protected void readSurfaceData (boolean) throws java.lang.Exception
protected void readTitleLines () throws java.lang.Exception
protected static boolean jvxlCheckAtomLine (boolean, boolean, java.lang.String, java.lang.String, java.lang.StringBuffer)
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected static void jvxlReadAtoms (java.io.BufferedReader, java.lang.StringBuffer, int, org.jmol.jvxl.data.VolumeData) throws java.lang.Exception
protected int readExtraLine () throws java.lang.Exception
private void jvxlReadDefinitionLine (boolean) throws java.lang.Exception
private java.lang.String jvxlReadData (java.lang.String, int)
public static java.lang.String jvxlCompressString (java.lang.String)
private static java.lang.String jvxlUncompressString (java.lang.String)
protected java.util.BitSet getVoxelBitSet (int) throws java.lang.Exception
protected float getNextVoxelValue (java.lang.StringBuffer) throws java.lang.Exception
public static void setSurfaceInfoFromBitSet (org.jmol.jvxl.data.JvxlData, java.util.BitSet, javax.vecmath.Point4f)
private static int jvxlEncodeBitSet (java.util.BitSet, int, java.lang.StringBuffer)
private static java.util.BitSet jvxlDecodeBitSet (java.lang.String)
protected static void setSurfaceInfo (org.jmol.jvxl.data.JvxlData, javax.vecmath.Point4f, int, java.lang.StringBuffer)
protected float getSurfacePointAndFraction (float, boolean, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, float[], javax.vecmath.Point3f)
private float jvxlGetNextFraction (int, int, float)
protected java.lang.String readColorData ()
protected void gotoData (int, int) throws java.lang.Exception
private void jvxlSkipData (int, boolean) throws java.lang.Exception
private void jvxlSkipDataBlock (int, boolean) throws java.lang.Exception
private int countData (java.lang.String)
protected static void jvxlCreateHeaderWithoutTitleOrAtoms (org.jmol.jvxl.data.VolumeData, java.lang.StringBuffer)
protected static void jvxlCreateHeader (org.jmol.jvxl.data.VolumeData, int, javax.vecmath.Point3f[], int[], java.lang.StringBuffer)
private static void jvxlAddDummyAtomList (org.jmol.jvxl.data.VolumeData, java.lang.StringBuffer)
public static java.lang.String jvxlGetDefinitionLine (org.jmol.jvxl.data.JvxlData, boolean)
protected static java.lang.String jvxlExtraLine (org.jmol.jvxl.data.JvxlData, int)
public static java.lang.String jvxlGetFile (org.jmol.jvxl.api.MeshDataServer, org.jmol.jvxl.data.JvxlData, org.jmol.jvxl.data.MeshData, java.lang.String[], java.lang.String, boolean, int, java.lang.String, java.lang.String)
private static void jvxlEncodeContourData (java.util.Vector[], java.lang.StringBuffer)
protected static float jvxlFractionFromCharacter (int, int, int, float)
protected static float jvxlValueFromCharacter2 (int, int, float, float, int, int)
protected static float jvxlFractionFromCharacter2 (int, int, int, int)
protected static char jvxlValueAsCharacter (float, float, float, int, int)
public static char jvxlFractionAsCharacter (float)
protected static char jvxlFractionAsCharacter (float, int, int)
private static void jvxlAppendCharacter2 (float, float, float, int, int, java.lang.StringBuffer, java.lang.StringBuffer)
public static void jvxlUpdateSurfaceData (org.jmol.jvxl.data.JvxlData, float[], int, int, char)
public static void jvxlCreateColorData (org.jmol.jvxl.data.JvxlData, float[])
public static java.lang.String jvxlEncodeTriangleData (int[][], int, int[])
public static java.lang.String jvxlEncodeVertexData (org.jmol.jvxl.api.MeshDataServer, org.jmol.jvxl.data.JvxlData, int[], javax.vecmath.Point3f[], float[], int, short[], int, boolean)
private void getEncodedVertexData () throws java.lang.Exception
private void jvxlDecodeContourData (java.lang.String) throws java.lang.Exception
public static void set3dContourVector (java.util.Vector, int[][], javax.vecmath.Point3f[])
private java.lang.String getXmlData (java.lang.String, java.lang.String, boolean) throws java.lang.Exception
public javax.vecmath.Point3f[] jvxlDecodeVertexData (java.lang.String, boolean)
int[][] jvxlDecodeTriangleData (java.lang.String, java.lang.String, boolean)
private static java.lang.String getXmlAttrib (java.lang.String, java.lang.String)
private static int setNext (java.lang.String, java.lang.String, int[], int)
}
org/jmol/jvxl/readers/LimitedLineReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.LimitedLineReader extends java.lang.Object {
private char[] buf
private int cchBuf
private int ichCurrent
private int iLine
void <init> (java.io.BufferedReader, int)
java.lang.String info ()
int iLine ()
java.lang.String readNonCommentLine ()
}
org/jmol/jvxl/readers/MapFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.MapFileReader extends org.jmol.jvxl.readers.VolumeFileReader {
protected int mapc
protected int mapr
protected int maps
protected int nx
protected int ny
protected int nz
protected int mode
protected int[] nxyzStart
protected int na
protected int nb
protected int nc
protected float a
protected float b
protected float c
protected float alpha
protected float beta
protected float gamma
protected javax.vecmath.Point3f origin
protected javax.vecmath.Point3f adjustment
protected javax.vecmath.Point3f[] vectors
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected abstract void readParameters () throws java.lang.Exception
protected int readVolumetricHeader ()
protected void getVectorsAndOrigin ()
}
org/jmol/jvxl/readers/MrcBinaryReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.MrcBinaryReader extends org.jmol.jvxl.readers.MapFileReader {
protected String[] labels
private static byte[] b8
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.lang.String, boolean)
protected void readParameters () throws java.lang.Exception
protected float nextVoxel () throws java.lang.Exception
protected void skipData (int) throws java.lang.Exception
static void <clinit> ()
}
org/jmol/jvxl/readers/ObjReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.ObjReader extends org.jmol.jvxl.readers.PolygonFileReader {
private int nPolygons
String pmeshError
javax.vecmath.Point3f pt
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.lang.String, java.io.BufferedReader)
void getSurfaceData () throws java.lang.Exception
private boolean readPmesh ()
private boolean readVertices () throws java.lang.Exception
private boolean readPolygons ()
}
org/jmol/jvxl/readers/Parameters.class
<Unknown>
package org.jmol.jvxl.readers
public org.jmol.jvxl.readers.Parameters extends java.lang.Object {
public static final int STATE_UNINITIALIZED
public static final int STATE_INITIALIZED
public static final int STATE_DATA_READ
public static final int STATE_DATA_COLORED
int state
boolean logMessages
boolean logCompression
boolean logCube
boolean isSilent
float assocCutoff
static final int NO_ANISOTROPY
static final int IS_SILENT
public static final int IS_SOLVENTTYPE
static final int HAS_MAXGRID
static final int CAN_CONTOUR
public int dataType
int surfaceType
static final int SURFACE_NONE
static final int SURFACE_SPHERE
static final int SURFACE_ELLIPSOID2
static final int SURFACE_ELLIPSOID3
static final int SURFACE_LOBE
static final int SURFACE_LCAOCARTOON
public static final int SURFACE_LONEPAIR
public static final int SURFACE_RADICAL
static final int SURFACE_FUNCTIONXY
static final int SURFACE_FUNCTIONXYZ
static final int SURFACE_SOLVENT
static final int SURFACE_SASURFACE
static final int SURFACE_MOLECULARORBITAL
static final int SURFACE_ATOMICORBITAL
static final int SURFACE_MEP
static final int SURFACE_FILE
static final int SURFACE_INFO
static final int SURFACE_MOLECULAR
static final int SURFACE_NOMAP
static final int SURFACE_PROPERTY
String calculationType
boolean addHydrogens
float solventRadius
float solventExtendedAtomRadius
float solventAtomRadiusFactor
float solventAtomRadiusAbsolute
float solventAtomRadiusOffset
boolean propertySmoothing
boolean useIonic
float envelopeRadius
float cavityRadius
boolean isCavity
Boolean pocket
int minSet
javax.vecmath.Point4f cappingPlane
boolean doCapIsosurface
float[] theProperty
float solvent_ptsPerAngstrom
int solvent_gridMax
static final float ANGSTROMS_PER_BOHR
static final int defaultEdgeFractionBase
static final int defaultEdgeFractionRange
static final int defaultColorFractionBase
static final int defaultColorFractionRange
static final float defaultMappedDataMin
static final float defaultMappedDataMax
static final float defaultCutoff
static final float defaultOrbitalCutoff
public static final float defaultQMOrbitalCutoff
static final float defaultQMElectronDensityCutoff
static final int defaultContourCount
static final int nContourMax
static final int defaultColorNegative
static final int defaultColorPositive
static final int defaultColorNegativeLCAO
static final int defaultColorPositiveLCAO
static final float defaultSolventRadius
static final float defaultMepCutoff
static final float defaultMepMin
static final float defaultMepMax
boolean colorBySign
boolean colorByPhase
boolean colorBySets
int colorNeg
int colorPos
int colorPosLCAO
int colorNegLCAO
int colorPhase
boolean iAddGridPoints
boolean remappable
int atomIndex
boolean isAngstroms
float scale
float[] anisotropy
boolean isAnisotropic
javax.vecmath.Matrix3f eccentricityMatrix
javax.vecmath.Matrix3f eccentricityMatrixInverse
boolean isEccentric
float eccentricityScale
float eccentricityRatio
float[] aniosU
float[] anisoB
String lcaoType
public java.util.Vector functionXYinfo
int psi_n
int psi_l
int psi_m
float psi_Znuc
float psi_ptsPerAngstrom
public static final int MEP_MAX_GRID
int mep_gridMax
float mep_ptsPerAngstrom
float mep_marginAngstroms
int qmOrbitalType
int qmOrbitalCount
static final int QM_TYPE_UNKNOWN
static final int QM_TYPE_GAUSSIAN
static final int QM_TYPE_SLATER
java.util.Hashtable moData
java.util.Hashtable mo
float[] moCoefficients
public static final int MO_MAX_GRID
int qm_gridMax
float qm_ptsPerAngstrom
float qm_marginAngstroms
int qm_nAtoms
int qm_moNumber
javax.vecmath.Point3f center
javax.vecmath.Point3f point
float distance
String script
java.util.BitSet bsSelected
java.util.BitSet bsIgnore
java.util.BitSet bsSolvent
boolean iUseBitSets
String[] title
boolean blockCubeData
boolean readAllData
int fileIndex
String fileName
int modelIndex
boolean isXLowToHigh
boolean insideOut
float cutoff
boolean isCutoffAbsolute
boolean isPositiveOnly
boolean rangeAll
public boolean rangeDefined
float valueMappedToRed
float valueMappedToBlue
float mappedDataMin
float mappedDataMax
boolean isColorReversed
boolean isBicolorMap
boolean isSquared
javax.vecmath.Point4f thePlane
boolean isContoured
int nContours
int thisContour
boolean contourFromZero
float resolution
int downsampleFactor
int maxSet
public void <init> ()
void initialize ()
void setAnisotropy (javax.vecmath.Point3f)
void setEccentricity (javax.vecmath.Point4f)
void setPlane (javax.vecmath.Point4f)
void setSphere (float)
void setEllipsoid (javax.vecmath.Point4f)
public void setEllipsoid (float[])
void setLobe (javax.vecmath.Point4f)
void setLp (javax.vecmath.Point4f)
void setRadical (javax.vecmath.Point4f)
void setLcao (java.lang.String, int)
void setRadius (boolean, float)
void setSolvent (java.lang.String, float)
void setFunctionXY (java.util.Vector)
void setFunctionXYZ (java.util.Vector)
boolean setAtomicOrbital (float[])
void setMep (float[], boolean)
void setMO (int, boolean)
void setMapRanges (org.jmol.jvxl.readers.SurfaceReader)
}
org/jmol/jvxl/readers/PltFormattedReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.PltFormattedReader extends org.jmol.jvxl.readers.VolumeFileReader {
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected int readVolumetricHeader ()
protected void readTitleLines () throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected void readVoxelVectors () throws java.lang.Exception
private java.lang.String getLine () throws java.io.IOException
}
org/jmol/jvxl/readers/PmeshReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.PmeshReader extends org.jmol.jvxl.readers.PolygonFileReader {
private int nPolygons
private boolean isBinary
static final String PMESH_BINARY_MAGIC_NUMBER
String pmeshError
private String[] tokens
private int iToken
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.lang.String, java.io.BufferedReader)
private boolean checkBinary (java.lang.String)
void getSurfaceData () throws java.lang.Exception
private boolean readPmesh ()
boolean readBinaryHeader ()
private boolean readVertices () throws java.lang.Exception
private boolean readPolygons () throws java.lang.Exception
private java.lang.String nextToken () throws java.lang.Exception
private int getInt () throws java.lang.Exception
private float getFloat () throws java.lang.Exception
}
org/jmol/jvxl/readers/PolygonFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.PolygonFileReader extends org.jmol.jvxl.readers.SurfaceFileReader {
protected int nVertices
protected int nTriangles
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
void discardTempData (boolean)
boolean readVolumeParameters ()
boolean readVolumeData (boolean)
protected void readSurfaceData (boolean) throws java.lang.Exception
abstract void getSurfaceData () throws java.lang.Exception
}
org/jmol/jvxl/readers/SurfaceFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.SurfaceFileReader extends org.jmol.jvxl.readers.SurfaceReader {
protected java.io.BufferedReader br
protected org.jmol.util.BinaryDocument binarydoc
String line
int[] next
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
static java.lang.String determineFileType (java.io.BufferedReader)
void discardTempData (boolean)
java.lang.String[] getTokens ()
float parseFloat ()
float parseFloat (java.lang.String)
int parseInt ()
int parseInt (java.lang.String)
int parseIntNext (java.lang.String)
protected void skipTo (java.lang.String, java.lang.String) throws java.lang.Exception
}
org/jmol/jvxl/readers/SurfaceGenerator.class
<Unknown>
package org.jmol.jvxl.readers
public org.jmol.jvxl.readers.SurfaceGenerator extends java.lang.Object {
private org.jmol.util.ColorEncoder colorEncoder
private org.jmol.jvxl.data.JvxlData jvxlData
private org.jmol.jvxl.data.MeshData meshData
private org.jmol.jvxl.readers.Parameters params
private org.jmol.jvxl.data.VolumeData volumeData
private org.jmol.jvxl.api.MeshDataServer meshDataServer
private org.jmol.atomdata.AtomDataServer atomDataServer
private org.jmol.jvxl.calc.MarchingSquares marchingSquares
private String version
private String fileType
org.jmol.jvxl.readers.SurfaceReader surfaceReader
int colorPtr
private boolean rangeDefined
final javax.vecmath.Vector3f vAC
final javax.vecmath.Vector3f vAB
final javax.vecmath.Vector3f vNorm
final javax.vecmath.Point3f ptRef
public void setVersion (java.lang.String)
public void <init> ()
public void <init> (org.jmol.atomdata.AtomDataServer, org.jmol.jvxl.api.MeshDataServer, org.jmol.util.ColorEncoder, org.jmol.jvxl.data.MeshData, org.jmol.jvxl.data.JvxlData)
private void setup (org.jmol.atomdata.AtomDataServer, org.jmol.jvxl.api.MeshDataServer, org.jmol.util.ColorEncoder, org.jmol.jvxl.data.MeshData, org.jmol.jvxl.data.JvxlData)
public boolean isStateDataRead ()
public int getDataType ()
org.jmol.jvxl.api.MeshDataServer getMeshDataServer ()
org.jmol.atomdata.AtomDataServer getAtomDataServer ()
org.jmol.util.ColorEncoder getColorEncoder ()
public void setJvxlData (org.jmol.jvxl.data.JvxlData)
public org.jmol.jvxl.data.JvxlData getJvxlData ()
org.jmol.jvxl.data.MeshData getMeshData ()
void setMarchingSquares (org.jmol.jvxl.calc.MarchingSquares)
org.jmol.jvxl.calc.MarchingSquares getMarchingSquares ()
public org.jmol.jvxl.readers.Parameters getParams ()
public java.lang.String getScript ()
public java.lang.String[] getTitle ()
public java.util.BitSet getBsSelected ()
public java.util.BitSet getBsIgnore ()
public java.util.Vector getFunctionXYinfo ()
org.jmol.jvxl.data.VolumeData getVolumeData ()
public javax.vecmath.Point4f getPlane ()
public int getColor (int)
public void setModelIndex (int)
public boolean getIUseBitSets ()
public boolean getIAddGridPoints ()
public boolean getIsPositiveOnly ()
public boolean isInsideOut ()
public float getCutoff ()
public java.util.Hashtable getMoData ()
public boolean isCubeData ()
public boolean setParameter (java.lang.String, java.lang.Object)
public boolean setParameter (java.lang.String, java.lang.Object, java.util.BitSet)
private void getSurfaceSets ()
private void processState ()
private boolean setReader ()
private void generateSurface ()
private void mapSurface (java.lang.Object)
void colorIsosurface ()
public java.lang.Object getProperty (java.lang.String, int)
private org.jmol.jvxl.readers.SurfaceReader setFileData (java.lang.Object)
void initializeIsosurface ()
public void initState ()
public java.lang.String setLcao ()
private void getFunctionZfromXY ()
private float distanceVerticalToPlane (float, float, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Point3f)
private static float findNearestThreePoints (float, float, float[][], int[])
}
org/jmol/jvxl/readers/SurfaceReader.class
<Unknown>
package org.jmol.jvxl.readers
public abstract org.jmol.jvxl.readers.SurfaceReader extends java.lang.Object implements org.jmol.jvxl.api.VertexDataServer {
protected org.jmol.jvxl.readers.SurfaceGenerator sg
protected org.jmol.jvxl.api.MeshDataServer meshDataServer
protected org.jmol.util.ColorEncoder colorEncoder
protected org.jmol.jvxl.readers.Parameters params
protected org.jmol.jvxl.data.MeshData meshData
protected org.jmol.jvxl.data.JvxlData jvxlData
protected org.jmol.jvxl.data.VolumeData volumeData
private String edgeData
protected boolean isProgressive
protected boolean isXLowToHigh
private float assocCutoff
boolean vertexDataOnly
boolean hasColorData
static final float ANGSTROMS_PER_BOHR
static final float defaultMappedDataMin
static final float defaultMappedDataMax
static final float defaultCutoff
private int edgeCount
protected javax.vecmath.Point3f volumetricOrigin
protected javax.vecmath.Vector3f[] volumetricVectors
protected int[] voxelCounts
protected float[][][] voxelData
protected long nBytes
protected int nDataPoints
protected int nPointsX
protected int nPointsY
protected int nPointsZ
protected boolean isJvxl
protected boolean isApbsDx
protected int edgeFractionBase
protected int edgeFractionRange
protected int colorFractionBase
protected int colorFractionRange
protected StringBuffer jvxlFileHeaderBuffer
protected StringBuffer fractionData
protected String jvxlEdgeDataRead
protected String jvxlColorDataRead
protected java.util.BitSet jvxlVoxelBitSet
protected java.util.Vector[] vContours
protected boolean jvxlDataIsColorMapped
protected boolean jvxlDataIsPrecisionColor
protected boolean jvxlDataIs2dContour
protected float jvxlCutoff
protected int jvxlNSurfaceInts
protected char cJvxlEdgeNaN
protected int contourVertexCount
protected org.jmol.jvxl.calc.MarchingSquares marchingSquares
private org.jmol.jvxl.calc.MarchingCubes marchingCubes
protected final javax.vecmath.Point3f ptTemp
private static final String[] colorPhases
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
void setVolumeData (org.jmol.jvxl.data.VolumeData)
abstract boolean readVolumeParameters ()
abstract boolean readVolumeData (boolean)
void jvxlUpdateInfo ()
boolean createIsosurface (boolean)
void resetIsosurface ()
void discardTempData (boolean)
protected void initializeVolumetricData ()
protected abstract void readSurfaceData (boolean) throws java.lang.Exception
protected boolean gotoAndReadVoxelData (boolean)
protected void gotoData (int, int) throws java.lang.Exception
protected java.lang.String readColorData ()
public float getValue (int, int, int)
private void generateSurfaceData ()
public int getSurfacePointIndexAndFraction (float, boolean, int, int, int, javax.vecmath.Point3i, int, int, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, boolean, float[])
protected float getSurfacePointAndFraction (float, boolean, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, float[], javax.vecmath.Point3f)
public int addVertexCopy (javax.vecmath.Point3f, float, int)
public void addTriangleCheck (int, int, int, int, boolean, int)
void colorIsosurface ()
void applyColorScale ()
private void colorData ()
static int getColorPhaseIndex (java.lang.String)
private float getPhase (javax.vecmath.Point3f)
float getMinMappedValue ()
float getMaxMappedValue ()
protected short getColorIndexFromPalette (float)
protected int getArgbFromPalette (float)
void updateTriangles ()
void updateSurfaceData ()
public void selectPocket (boolean)
void excludeMinimumSet ()
void excludeMaximumSet ()
static void <clinit> ()
}
org/jmol/jvxl/readers/VolumeDataReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.VolumeDataReader extends org.jmol.jvxl.readers.SurfaceReader {
protected int dataType
protected boolean precalculateVoxelData
protected boolean allowMapData
protected javax.vecmath.Point3f center
protected javax.vecmath.Point3f point
protected float[] anisotropy
protected boolean isAnisotropic
protected javax.vecmath.Matrix3f eccentricityMatrix
protected javax.vecmath.Matrix3f eccentricityMatrixInverse
protected boolean isEccentric
protected float eccentricityScale
protected float eccentricityRatio
void <init> (org.jmol.jvxl.readers.SurfaceGenerator)
void setup ()
boolean readVolumeParameters ()
boolean readVolumeData (boolean)
protected void readVoxelDataIndividually (boolean) throws java.lang.Exception
protected int setVoxelRange (int, float, float, float, int)
protected void readSurfaceData (boolean) throws java.lang.Exception
protected void generateCube ()
}
org/jmol/jvxl/readers/VolumeFileReader.class
<Unknown>
package org.jmol.jvxl.readers
abstract org.jmol.jvxl.readers.VolumeFileReader extends org.jmol.jvxl.readers.SurfaceFileReader {
protected boolean endOfData
protected boolean negativeAtomCount
protected int atomCount
private int nSurfaces
protected boolean isAngstroms
protected boolean canDownsample
protected int[] downsampleRemainders
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
boolean readVolumeParameters ()
boolean readVolumeData (boolean)
protected int readVolumetricHeader ()
protected void readTitleLines () throws java.lang.Exception
protected java.lang.String skipComments (boolean) throws java.lang.Exception
protected void readAtomCountAndOrigin () throws java.lang.Exception
protected void readVoxelVector (int) throws java.lang.Exception
protected int readExtraLine () throws java.lang.Exception
protected void readSurfaceData (boolean) throws java.lang.Exception
private void skipVoxels (int) throws java.lang.Exception
protected java.util.BitSet getVoxelBitSet (int) throws java.lang.Exception
protected float getNextVoxelValue () throws java.lang.Exception
protected float nextVoxel () throws java.lang.Exception
protected void gotoData (int, int) throws java.lang.Exception
protected void skipData (int) throws java.lang.Exception
private int countData (java.lang.String)
}
org/jmol/jvxl/readers/XplorReader.class
<Unknown>
package org.jmol.jvxl.readers
org.jmol.jvxl.readers.XplorReader extends org.jmol.jvxl.readers.MapFileReader {
private int nBlock
private int linePt
private int nRead
void <init> (org.jmol.jvxl.readers.SurfaceGenerator, java.io.BufferedReader)
protected void readParameters () throws java.lang.Exception
private java.lang.String getLine () throws java.io.IOException
protected float nextVoxel () throws java.lang.Exception
}
org/jmol/shapesurface/Isosurface.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.Isosurface extends org.jmol.shape.MeshCollection implements org.jmol.jvxl.api.MeshDataServer {
private org.jmol.shapesurface.IsosurfaceMesh[] isomeshes
private org.jmol.shapesurface.IsosurfaceMesh thisMesh
private int lighting
private boolean iHaveBitSets
private boolean explicitContours
private int atomIndex
private int moNumber
private short defaultColix
private javax.vecmath.Point3f center
private boolean isPhaseColored
private boolean isColorExplicit
protected org.jmol.jvxl.readers.SurfaceGenerator sg
private org.jmol.jvxl.data.JvxlData jvxlData
private org.jmol.util.ColorEncoder colorEncoder
private int indexColorPositive
private int indexColorNegative
private int nLCAO
private javax.vecmath.Point4f lcaoDir
private boolean associateNormals
private static final int MAX_OBJECT_CLICK_DISTANCE_SQUARED
private final javax.vecmath.Point3i ptXY
public void <init> ()
public void allocMesh (java.lang.String)
public void initShape ()
private void newSg ()
protected void clearSg ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void setPropertySuper (java.lang.String, java.lang.Object, java.util.BitSet)
public java.lang.Object getProperty (java.lang.String, int)
protected void getColorState (java.lang.StringBuffer, org.jmol.shape.Mesh)
private boolean getScriptBitSets (java.lang.String, java.util.BitSet[])
private void initializeIsosurface ()
private void initState ()
private void discardTempData (boolean)
private short getDefaultColix ()
private void drawLcaoCartoon (javax.vecmath.Vector3f, javax.vecmath.Vector3f, javax.vecmath.Vector3f, int)
private void createLcaoLobe (javax.vecmath.Vector3f, float, int)
public void invalidateTriangles ()
public void fillMeshData (org.jmol.jvxl.data.MeshData, int)
public void notifySurfaceGenerationCompleted ()
public void notifySurfaceMappingCompleted ()
public javax.vecmath.Point3f[] calculateGeodesicSurface (java.util.BitSet, float)
public int getSurfacePointIndexAndFraction (float, boolean, int, int, int, javax.vecmath.Point3i, int, int, float, float, javax.vecmath.Point3f, javax.vecmath.Vector3f, boolean, float[])
public int addVertexCopy (javax.vecmath.Point3f, float, int)
public void addTriangleCheck (int, int, int, int, boolean, int)
private void setModelIndex ()
protected void setScriptInfo ()
private void setJvxlInfo ()
public java.util.Vector getShapeDetail ()
protected void remapColors ()
private java.lang.String getUserColorScheme (java.lang.String)
public float getValue (int, int, int)
public boolean checkObjectHovered (int, int, java.util.BitSet)
public org.jmol.util.Point3fi checkObjectClicked (int, int, int, java.util.BitSet)
private void navigate (int)
private void setHeading (javax.vecmath.Point3f, javax.vecmath.Vector3f, int)
private boolean getClosestNormal (org.jmol.shapesurface.IsosurfaceMesh, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f)
private void getClosestPoint (org.jmol.shapesurface.IsosurfaceMesh, int, javax.vecmath.Point3f, javax.vecmath.Point3f, javax.vecmath.Vector3f)
private java.lang.String findValue (int, int, boolean, java.util.BitSet)
public int getColixArgb (short)
}
org/jmol/shapesurface/IsosurfaceMesh.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.IsosurfaceMesh extends org.jmol.shape.Mesh {
org.jmol.jvxl.data.JvxlData jvxlData
int vertexIncrement
int firstRealVertex
int dataType
boolean hasGridPoints
Object calculatedArea
Object calculatedVolume
public boolean isSolvent
public float[] vertexValues
public short[] vertexColixes
java.util.Hashtable assocGridPointMap
java.util.Hashtable assocGridPointNormals
public short[] polygonColixes
private int lastColor
private short lastColix
private int iA
private int iB
private int iC
java.util.BitSet[] surfaceSet
int[] vertexSets
int nSets
int thisSet
javax.vecmath.Point3f[] centers
public static final int CONTOUR_NPOLYGONS
public static final int CONTOUR_BITSET
public static final int CONTOUR_VALUE
public static final int CONTOUR_COLOR
public static final int CONTOUR_FDATA
public static final int CONTOUR_POINTS
void <init> (java.lang.String, org.jmol.g3d.Graphics3D, short, int)
void clear (java.lang.String, boolean)
void allocVertexColixes ()
int addVertexCopy (javax.vecmath.Point3f, float, int, boolean)
int addVertexCopy (javax.vecmath.Point3f, float)
public void setTranslucent (boolean, float)
void addTriangleCheck (int, int, int, int, int)
void invalidateTriangles ()
private boolean setABC (int)
java.lang.Object calculateArea ()
java.lang.Object calculateVolume ()
public void sumVertexNormals (javax.vecmath.Vector3f[])
javax.vecmath.Point3f[] getCenters ()
javax.vecmath.Point4f getFacePlane (int, javax.vecmath.Vector3f)
java.util.Vector[] getContours ()
public static void setContourVector (java.util.Vector, int, java.util.BitSet, float, int, java.lang.StringBuffer)
private void get3dContour (java.util.Vector, float, int)
private float checkPt (int, int, float)
public static javax.vecmath.Point3f getContourPoint (javax.vecmath.Point3f[], int, int, float)
private void dumpData ()
}
org/jmol/shapesurface/IsosurfaceRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.IsosurfaceRenderer extends org.jmol.shape.MeshRenderer {
private boolean iShowNormals
protected boolean iHideBackground
protected boolean isBicolorMap
protected short backgroundColix
protected int nError
protected float[] vertexValues
protected org.jmol.shapesurface.IsosurfaceMesh imesh
private final javax.vecmath.Point3f ptTemp
private final javax.vecmath.Point3i ptTempi
public void <init> ()
protected void render ()
protected void transform ()
protected void render2 (boolean)
private void renderLonePair (boolean)
private void renderContourLines ()
protected void renderPoints ()
protected void renderTriangles (boolean, boolean, boolean)
private void renderNormals ()
}
org/jmol/shapesurface/LcaoCartoon.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.LcaoCartoon extends org.jmol.shapesurface.Isosurface {
private String thisType
private int myColorPt
private String lcaoID
private java.util.BitSet thisSet
private boolean isMolecular
private javax.vecmath.Vector3f rotationAxis
private Float lcaoScale
private boolean isTranslucent
private float translucentLevel
private Integer lcaoColorPos
private Integer lcaoColorNeg
boolean isLonePair
boolean isRadical
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private void setLcaoOn (boolean)
private void setLcaoOn (int, boolean)
private void deleteLcaoCartoon ()
private void deleteLcaoCartoon (int)
private void createLcaoCartoon ()
private void createLcaoCartoon (int)
private java.lang.String getID (java.lang.String, int)
public java.lang.String getShapeState ()
}
org/jmol/shapesurface/LcaoCartoonRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.LcaoCartoonRenderer extends org.jmol.shapesurface.IsosurfaceRenderer {
public void <init> ()
}
org/jmol/shapesurface/MolecularOrbital.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.MolecularOrbital extends org.jmol.shapesurface.Isosurface {
private String moTranslucency
private Float moTranslucentLevel
private javax.vecmath.Point4f moPlane
private Float moCutoff
private Float moResolution
private Float moScale
private Integer moColorPos
private Integer moColorNeg
private boolean moIsPositiveOnly
private int moFill
private int moMesh
private int moDots
private int moFrontOnly
private String moTitleFormat
private boolean moDebug
private int myColorPt
private String strID
private int moNumber
private java.util.Hashtable htModels
private java.util.Hashtable thisModel
public void <init> ()
public void initShape ()
public void setProperty (java.lang.String, java.lang.Object, java.util.BitSet)
private java.lang.String getId (int)
public java.lang.Object getProperty (java.lang.String, int)
protected void clearSg ()
private boolean getSettings (java.lang.String)
private void setOrbital (int)
public java.lang.String getShapeState ()
private java.lang.String getMoState (int)
}
org/jmol/shapesurface/MolecularOrbitalRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.MolecularOrbitalRenderer extends org.jmol.shapesurface.IsosurfaceRenderer {
private java.text.NumberFormat nf
public void <init> ()
protected void render ()
private void renderInfo ()
}
org/jmol/shapesurface/Pmesh.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.Pmesh extends org.jmol.shapesurface.Isosurface {
public void <init> ()
public void initShape ()
}
org/jmol/shapesurface/PmeshRenderer.class
<Unknown>
package org.jmol.shapesurface
public org.jmol.shapesurface.PmeshRenderer extends org.jmol.shapesurface.IsosurfaceRenderer {
public void <init> ()
}