org.jmol.shapesurface

Class Contact

java.lang.Object

org.jmol.shape.Shape

org.jmol.shape.MeshCollection

org.jmol.shapesurface.Isosurface

org.jmol.shapesurface.Contact

All Implemented Interfaces:

MeshDataServer, VertexDataServer

public class Contact
extends Isosurface

Field Summary

Fields

Modifier and Type	Field and Description
private int	atomCount
protected Atom[]	atoms
private float	maxData
private float	minData
private javax.vecmath.Point3f	pt1
private javax.vecmath.Point3f	pt2
private static RadiusData	rdVDW
private javax.vecmath.Vector3f	vX
private javax.vecmath.Vector3f	vY
private javax.vecmath.Vector3f	vZ

Fields inherited from class org.jmol.shapesurface.Isosurface

allowMesh, iHaveBitSets, jvxlData, keyXy, sg, thisMesh

Fields inherited from class org.jmol.shape.MeshCollection

bsDisplay, colix, color, connections, currentMesh, displayWithinDistance2, displayWithinPoints, explicitID, htObjects, isDisplayWithinNot, isFixed, linkedMesh, meshCount, meshes, modelIndex, myType, nUnnamed, pickedMesh, pickedModel, pickedVertex, PREVIOUS_MESH_ID, previousMeshID, title

Fields inherited from class org.jmol.shape.Shape

g3d, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer, xmlProperties

Constructor Summary

Constructors

Constructor and Description
Contact()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addMeshInfo(IsosurfaceMesh mesh, java.util.Map<java.lang.String,java.lang.Object> info)
private static int	checkCp(ContactPair cp1, ContactPair cp2, int i1, int i2)
private float	combineSurfaces(java.util.List<ContactPair> pairs, int contactType, int displayType, float[] parameters, java.lang.Object func, boolean isColorDensity, boolean colorByType)
private java.util.List<ContactPair>	getPairs(java.util.BitSet bsA, java.util.BitSet bsB, RadiusData rd, int intramolecularMode)
private static void	getVdwClashRadius(ContactPair cp, double x0, double vdwA, double vdwB, double d) well, heh, heh...
void	initShape()
private void	mergeMesh(MeshData md)
private void	newSurface(int displayType, ContactPair cp, java.util.BitSet bs1, java.util.BitSet bs2, RadiusData rd, float[] parameters, java.lang.Object func, boolean isColorDensity, VolumeData volumeData)
private int	setColorByScore(float score, int nV)
private void	setContacts(java.lang.Object[] value)
void	setProperty(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs) may come from any source -- executed AFTER a shape's own setProperty method
private void	setVolumeData(int type, VolumeData volumeData, ContactPair cp, float resolution, int nPairs)

Methods inherited from class org.jmol.shapesurface.Isosurface

addRequiredFile, addTriangleCheck, addVertexCopy, allocMesh, calculateGeodesicSurface, checkObjectClicked, checkObjectHovered, clearSg, discardTempData, fillMeshData, getCapSlabInfo, getCmd, getPlane, getPolygonColorData, getProperty, getProperty, getShapeDetail, getShapeState, getSurfacePointIndexAndFraction, getValue, invalidateTriangles, merge, newSg, notifySurfaceGenerationCompleted, notifySurfaceMappingCompleted, setOutputStream, setScriptInfo, slabPolygons

Methods inherited from class org.jmol.shape.MeshCollection

checkExplicit, clean, deleteMesh, deleteMesh, getIndexFromName, getMesh, getPickedPoint, setStatusPicked, setVisibilityFlags

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectDragged, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColorCommand, getColorCommand, getFontCommand, getShapeCommands, getShapeCommands, getSize, getSize, getTranslucentLabel, getViewer, initializeShape, initModelSet, setColix, setColix, setColix, setModelClickability, setModelSet, setShapeProperty, setShapeSize, setSize, setSize, setStateInfo, setStateInfo, wasClicked

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

atoms

protected Atom[] atoms

atomCount

private int atomCount

minData

private float minData

maxData

private float maxData

rdVDW

private static final RadiusData rdVDW

vZ

private javax.vecmath.Vector3f vZ

vY

private javax.vecmath.Vector3f vY

vX

private javax.vecmath.Vector3f vX

pt1

private javax.vecmath.Point3f pt1

pt2

private javax.vecmath.Point3f pt2

Constructor Detail

Contact

public Contact()

Method Detail

initShape

public void initShape()

Overrides:

initShape in class Isosurface

setProperty

public void setProperty(java.lang.String propertyName,
               java.lang.Object value,
               java.util.BitSet bs)

Description copied from class: Shape

may come from any source -- executed AFTER a shape's own setProperty method

Overrides:

setProperty in class Isosurface

setContacts

private void setContacts(java.lang.Object[] value)

combineSurfaces

private float combineSurfaces(java.util.List<ContactPair> pairs,
                    int contactType,
                    int displayType,
                    float[] parameters,
                    java.lang.Object func,
                    boolean isColorDensity,
                    boolean colorByType)

Parameters:

pairs -

contactType -

displayType -

parameters -

func -

isColorDensity -

colorByType -

Returns:

volume

setColorByScore

private int setColorByScore(float score,
                  int nV)

getPairs

private java.util.List<ContactPair> getPairs(java.util.BitSet bsA,
                                   java.util.BitSet bsB,
                                   RadiusData rd,
                                   int intramolecularMode)

Parameters:

bsA -

bsB -

rd -

intramolecularMode -

Returns:

a list of pairs of atoms to process

checkCp

private static int checkCp(ContactPair cp1,
          ContactPair cp2,
          int i1,
          int i2)

Parameters:

cp1 -

cp2 -

i1 -

i2 -

Returns:

0 (no clash); 1 (remove #1); 2 (remove #2)

newSurface

private void newSurface(int displayType,
              ContactPair cp,
              java.util.BitSet bs1,
              java.util.BitSet bs2,
              RadiusData rd,
              float[] parameters,
              java.lang.Object func,
              boolean isColorDensity,
              VolumeData volumeData)

setVolumeData

private void setVolumeData(int type,
                 VolumeData volumeData,
                 ContactPair cp,
                 float resolution,
                 int nPairs)

mergeMesh

private void mergeMesh(MeshData md)

addMeshInfo

protected void addMeshInfo(IsosurfaceMesh mesh,
               java.util.Map<java.lang.String,java.lang.Object> info)

Overrides:

addMeshInfo in class Isosurface

getVdwClashRadius

private static void getVdwClashRadius(ContactPair cp,
                     double x0,
                     double vdwA,
                     double vdwB,
                     double d)

well, heh, heh... This calculates the VDW extension x at a given distance for a clashing pair that will produce a volume that is equivalent to the volume for the vdw contact at the point of touching (d0 = vdwA + vdwB) and the transition to clash. This will provide the surface that will surround the clash until the clash size is larger than it.

Parameters:

cp -

x0 -

vdwA -

vdwB -

d -