org.jmol.shapespecial

Class Polyhedra

public class Polyhedra extends AtomShape

Nested Class Summary
classPolyhedra.Polyhedron
Field Summary
Vector3falign1
Vector3falign2
booleanbondedOnly
BitSetbsVertexCount
BitSetbsVertices
BitSetcenters
floatdistanceFactor
intdrawEdges
static floatDEFAULT_DISTANCE_FACTOR
static floatDEFAULT_FACECENTEROFFSET
static intEDGES_ALL
static intEDGES_FRONT
static intEDGES_NONE
floatfaceCenterOffset
static intFACE_COUNT_MAX
booleanhaveBitSetVertices
booleaniHaveCenterBitSet
booleanisCollapsed
static floatminDistanceForPlanarity
static intMAX_VERTICES
short[]normixesT
intnVertices
Atom[]otherAtoms
byte[]planesT
intpolyhedronCount
Polyhedra.Polyhedron[]polyhedrons
floatradius
static Point3frandomPoint
Vector3fvAB
Vector3fvAC
Method Summary
voidbuildPolyhedra()
Polyhedra.PolyhedronconstructBitSetPolyhedron(int atomIndex)
Polyhedra.PolyhedronconstructBondsPolyhedron(int atomIndex)
Polyhedra.PolyhedronconstructRadiusPolyhedron(int atomIndex)
voiddeletePolyhedra()
StringfaceId(int i, int j, int k)
StringgetShapeState()
booleanisAligned(Point3f pt1, Point3f pt2, Point3f pt3)
booleanisPlanar(Point3f pt1, Point3f pt2, Point3f pt3, Point3f ptX)
voidsetProperty(String propertyName, Object value, BitSet bs)
voidsetVisibilityFlags(BitSet bs)
voidsetVisible(boolean visible)
Polyhedra.PolyhedronvalidatePolyhedronNew(Atom centralAtom, int vertexCount, Atom[] otherAtoms)

Field Detail

align1

private Vector3f align1

align2

private Vector3f align2

bondedOnly

private boolean bondedOnly

bsVertexCount

private BitSet bsVertexCount

bsVertices

private BitSet bsVertices

centers

private BitSet centers

distanceFactor

float distanceFactor

drawEdges

int drawEdges

DEFAULT_DISTANCE_FACTOR

private static final float DEFAULT_DISTANCE_FACTOR

DEFAULT_FACECENTEROFFSET

private static final float DEFAULT_FACECENTEROFFSET

EDGES_ALL

static final int EDGES_ALL

EDGES_FRONT

static final int EDGES_FRONT

EDGES_NONE

private static final int EDGES_NONE

faceCenterOffset

float faceCenterOffset

FACE_COUNT_MAX

private static final int FACE_COUNT_MAX

haveBitSetVertices

private boolean haveBitSetVertices

iHaveCenterBitSet

private boolean iHaveCenterBitSet

isCollapsed

boolean isCollapsed

minDistanceForPlanarity

private static float minDistanceForPlanarity

MAX_VERTICES

private static final int MAX_VERTICES

normixesT

private short[] normixesT

nVertices

private int nVertices

otherAtoms

private Atom[] otherAtoms

planesT

private byte[] planesT

polyhedronCount

int polyhedronCount

polyhedrons

Polyhedra.Polyhedron[] polyhedrons

radius

private float radius

randomPoint

private static final Point3f randomPoint

vAB

private final Vector3f vAB

vAC

private final Vector3f vAC

Method Detail

buildPolyhedra

private void buildPolyhedra()

constructBitSetPolyhedron

private Polyhedra.Polyhedron constructBitSetPolyhedron(int atomIndex)

constructBondsPolyhedron

private Polyhedra.Polyhedron constructBondsPolyhedron(int atomIndex)

constructRadiusPolyhedron

private Polyhedra.Polyhedron constructRadiusPolyhedron(int atomIndex)

deletePolyhedra

private void deletePolyhedra()

faceId

private String faceId(int i, int j, int k)

getShapeState

public String getShapeState()

isAligned

private boolean isAligned(Point3f pt1, Point3f pt2, Point3f pt3)

isPlanar

private boolean isPlanar(Point3f pt1, Point3f pt2, Point3f pt3, Point3f ptX)

setProperty

public void setProperty(String propertyName, Object value, BitSet bs)

setVisibilityFlags

public void setVisibilityFlags(BitSet bs)

setVisible

private void setVisible(boolean visible)

validatePolyhedronNew

private Polyhedra.Polyhedron validatePolyhedronNew(Atom centralAtom, int vertexCount, Atom[] otherAtoms)