org.jmol.shapesurface
public class Contact extends Isosurface
Modifier and Type | Field and Description |
---|---|
private int |
atomCount |
protected Atom[] |
atoms |
private float |
maxData |
private float |
minData |
private Point3f |
pt1 |
private Point3f |
pt2 |
private static RadiusData |
rdVDW |
private Vector3f |
vX |
private Vector3f |
vY |
private Vector3f |
vZ |
allowMesh, iHaveBitSets, jvxlData, keyXy, sg, thisMesh
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
g3d, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer, xmlProperties
Constructor and Description |
---|
Contact() |
Modifier and Type | Method and Description |
---|---|
protected void |
addMeshInfo(IsosurfaceMesh mesh,
Map<String,Object> info) |
private static int |
checkCp(ContactPair cp1,
ContactPair cp2,
int i1,
int i2) |
private float |
combineSurfaces(List<ContactPair> pairs,
int contactType,
int displayType,
float[] parameters,
Object func,
boolean isColorDensity,
boolean colorByType) |
private List<ContactPair> |
getPairs(BitSet bsA,
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,
BitSet bs1,
BitSet bs2,
RadiusData rd,
float[] parameters,
Object func,
boolean isColorDensity,
VolumeData volumeData) |
private int |
setColorByScore(float score,
int nV) |
private void |
setContacts(Object[] value) |
void |
setProperty(String propertyName,
Object value,
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) |
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
checkExplicit, clean, deleteMesh, deleteMesh, getIndexFromName, getMesh, getPickedPoint, setStatusPicked, setVisibilityFlags
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
protected Atom[] atoms
private int atomCount
private float minData
private float maxData
private static final RadiusData rdVDW
private Vector3f vZ
private Vector3f vY
private Vector3f vX
private Point3f pt1
private Point3f pt2
public void initShape()
initShape
in class Isosurface
public void setProperty(String propertyName, Object value, BitSet bs)
Shape
setProperty
in class Isosurface
private void setContacts(Object[] value)
private float combineSurfaces(List<ContactPair> pairs, int contactType, int displayType, float[] parameters, Object func, boolean isColorDensity, boolean colorByType)
pairs
- contactType
- displayType
- parameters
- func
- isColorDensity
- colorByType
- private int setColorByScore(float score, int nV)
private List<ContactPair> getPairs(BitSet bsA, BitSet bsB, RadiusData rd, int intramolecularMode)
bsA
- bsB
- rd
- intramolecularMode
- private static int checkCp(ContactPair cp1, ContactPair cp2, int i1, int i2)
cp1
- cp2
- i1
- i2
- private void newSurface(int displayType, ContactPair cp, BitSet bs1, BitSet bs2, RadiusData rd, float[] parameters, Object func, boolean isColorDensity, VolumeData volumeData)
private void setVolumeData(int type, VolumeData volumeData, ContactPair cp, float resolution, int nPairs)
private void mergeMesh(MeshData md)
protected void addMeshInfo(IsosurfaceMesh mesh, Map<String,Object> info)
addMeshInfo
in class Isosurface
private static void getVdwClashRadius(ContactPair cp, double x0, double vdwA, double vdwB, double d)
cp
- x0
- vdwA
- vdwB
- d
-