public class Contact extends Isosurface
Modifier and Type | Field and Description |
---|---|
private int |
ac |
protected Atom[] |
atoms |
private float |
maxData |
private float |
minData |
private javajs.util.P3 |
pt1 |
private javajs.util.P3 |
pt2 |
private static RadiusData |
rdVDW |
private javajs.util.V3 |
vX |
private javajs.util.V3 |
vY |
private javajs.util.V3 |
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, pickedPt, pickedVertex, PREVIOUS_MESH_ID, previousMeshID, title
bsColixSet, bsSizeSet, isBioShape, ms, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, vf, vwr
Constructor and Description |
---|
Contact() |
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(javajs.util.Lst<ContactPair> pairs,
int contactType,
int displayType,
float[] parameters,
java.lang.Object func,
boolean isColorDensity,
boolean colorByType) |
private javajs.util.Lst<ContactPair> |
getPairs(BS bsA,
BS bsB,
RadiusData rd,
int intramolecularMode,
boolean doEditCpList) |
private static void |
getVdwClashRadius(ContactPair cp,
double x0,
double vdwA,
double vdwB,
double d)
well, heh, heh...
|
void |
initShape() |
private boolean |
isWithinFourBonds(Atom atomA,
Atom atomB) |
private void |
mergeMesh(MeshData md) |
private void |
newSurface(int displayType,
ContactPair cp,
BS bs1,
BS bs2,
RadiusData rd,
float[] parameters,
java.lang.Object func,
boolean isColorDensity,
VolumeData volumeData,
float sasurfaceRadius) |
private int |
setColorByScore(float score,
int nV) |
private void |
setContacts(java.lang.Object[] value,
boolean doEditCpList) |
void |
setProperty(java.lang.String propertyName,
java.lang.Object value,
BS bs) |
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, getPropertyData, getPropI, getShapeDetail, getShapeState, getSurfacePointIndexAndFraction, getValue, invalidateTriangles, merge, newSg, notifySurfaceGenerationCompleted, notifySurfaceMappingCompleted, setOutputChannel, setPropI, setScriptInfo, slabPolygons
checkExplicit, clean, deleteMeshI, deleteMeshKey, getIndexFromName, getMesh, getMeshList, getPickedPoint, getPropDataMC, getPropMC, setModelVisibilityFlags, setPropMC, setStatusPicked, setTokenProperty
appendCmd, checkBoundsMinMax, checkObjectDragged, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColixA, getColixB, getColixI, getColorCommand, getColorCommandUnk, getFontCommand, getSize, getSizeG, getTranslucentLabel, initializeShape, initModelSet, setAtomClickability, setModelSet, setPropS, setShapeSizeRD, setShapeVisibility, setSize, setSizeRD, wasClicked
protected Atom[] atoms
private int ac
private float minData
private float maxData
private static final RadiusData rdVDW
private javajs.util.V3 vZ
private javajs.util.V3 vY
private javajs.util.V3 vX
private javajs.util.P3 pt1
private javajs.util.P3 pt2
public void initShape()
initShape
in class Isosurface
public void setProperty(java.lang.String propertyName, java.lang.Object value, BS bs)
setProperty
in class Isosurface
private void setContacts(java.lang.Object[] value, boolean doEditCpList)
private float combineSurfaces(javajs.util.Lst<ContactPair> pairs, int contactType, int displayType, float[] parameters, java.lang.Object func, boolean isColorDensity, boolean colorByType)
pairs
- contactType
- displayType
- parameters
- func
- isColorDensity
- colorByType
- private int setColorByScore(float score, int nV)
private javajs.util.Lst<ContactPair> getPairs(BS bsA, BS bsB, RadiusData rd, int intramolecularMode, boolean doEditCpList)
bsA
- bsB
- rd
- intramolecularMode
- doEditCpList
- private static int checkCp(ContactPair cp1, ContactPair cp2, int i1, int i2)
cp1
- cp2
- i1
- i2
- private void newSurface(int displayType, ContactPair cp, BS bs1, BS bs2, RadiusData rd, float[] parameters, java.lang.Object func, boolean isColorDensity, VolumeData volumeData, float sasurfaceRadius)
private void setVolumeData(int type, VolumeData volumeData, ContactPair cp, float resolution, int nPairs)
private void mergeMesh(MeshData md)
protected void addMeshInfo(IsosurfaceMesh mesh, java.util.Map<java.lang.String,java.lang.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
-