org.jmol.shapespecial
public class Polyhedra extends AtomShape
Modifier and Type | Class and Description |
---|---|
(package private) class |
Polyhedra.Polyhedron |
Modifier and Type | Field and Description |
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private Vector3f |
align1 |
private Vector3f |
align2 |
private boolean |
bondedOnly |
private BitSet |
bsVertexCount |
private BitSet |
bsVertices |
private BitSet |
centers |
private static float |
DEFAULT_DISTANCE_FACTOR |
private static float |
DEFAULT_FACECENTEROFFSET |
(package private) float |
distanceFactor |
(package private) int |
drawEdges |
(package private) static int |
EDGES_ALL |
(package private) static int |
EDGES_FRONT |
private static int |
EDGES_NONE |
private static int |
FACE_COUNT_MAX |
(package private) float |
faceCenterOffset |
private boolean |
haveBitSetVertices |
private boolean |
iHaveCenterBitSet |
(package private) boolean |
isCollapsed |
private static int |
MAX_VERTICES |
private static float |
minDistanceForPlanarity |
private short[] |
normixesT |
private int |
nVertices |
private Point3f[] |
otherAtoms |
private byte[] |
planesT |
(package private) int |
polyhedronCount |
(package private) Polyhedra.Polyhedron[] |
polyhedrons |
private float |
radius |
private static Point3f |
randomPoint |
private Vector3f |
vAB |
private Vector3f |
vAC |
atomCount, atoms, bsColixSet, bsSizeSet, colixes, isActive, mads, paletteIDs
g3d, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer, xmlProperties
Constructor and Description |
---|
Polyhedra() |
Modifier and Type | Method and Description |
---|---|
private BitSet |
andBitSet(BitSet bs) |
private void |
buildPolyhedra() |
private Polyhedra.Polyhedron |
constructBitSetPolyhedron(int atomIndex) |
private Polyhedra.Polyhedron |
constructBondsPolyhedron(int atomIndex) |
private Polyhedra.Polyhedron |
constructRadiusPolyhedron(int atomIndex,
AtomIndexIterator iter) |
private void |
deletePolyhedra() |
private String |
faceId(int i,
int j,
int k) |
String |
getShapeState() |
private boolean |
isAligned(Point3f pt1,
Point3f pt2,
Point3f pt3) |
private boolean |
isPlanar(Point3f pt1,
Point3f pt2,
Point3f pt3,
Point3f ptX) |
void |
setProperty(String propertyName,
Object value,
BitSet bs)
may come from any source -- executed AFTER a shape's own setProperty method
|
void |
setVisibilityFlags(BitSet bs) |
private void |
setVisible(boolean visible) |
private Polyhedra.Polyhedron |
validatePolyhedronNew(Atom centralAtom,
int vertexCount,
Point3f[] otherAtoms) |
getSize, initModelSet, setColixAndPalette, setModelClickability, setSize, setSize
appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColorCommand, getColorCommand, getFontCommand, getIndexFromName, getProperty, getProperty, getShapeCommands, getShapeCommands, getShapeDetail, getSize, getTranslucentLabel, getViewer, initializeShape, initShape, merge, setColix, setColix, setColix, setModelSet, setShapeProperty, setShapeSize, setStateInfo, setStateInfo, wasClicked
private static final float DEFAULT_DISTANCE_FACTOR
private static final float DEFAULT_FACECENTEROFFSET
private static final int EDGES_NONE
static final int EDGES_ALL
static final int EDGES_FRONT
private static final int MAX_VERTICES
private static final int FACE_COUNT_MAX
private Point3f[] otherAtoms
int polyhedronCount
Polyhedra.Polyhedron[] polyhedrons
int drawEdges
private float radius
private int nVertices
float faceCenterOffset
float distanceFactor
boolean isCollapsed
private boolean iHaveCenterBitSet
private boolean bondedOnly
private boolean haveBitSetVertices
private BitSet centers
private BitSet bsVertices
private BitSet bsVertexCount
private short[] normixesT
private byte[] planesT
private static final Point3f randomPoint
private Vector3f align1
private Vector3f align2
private final Vector3f vAB
private final Vector3f vAC
private static float minDistanceForPlanarity
public void setProperty(String propertyName, Object value, BitSet bs)
Shape
setProperty
in class AtomShape
private void deletePolyhedra()
private void setVisible(boolean visible)
private void buildPolyhedra()
private Polyhedra.Polyhedron constructBondsPolyhedron(int atomIndex)
private Polyhedra.Polyhedron constructBitSetPolyhedron(int atomIndex)
private Polyhedra.Polyhedron constructRadiusPolyhedron(int atomIndex, AtomIndexIterator iter)
private Polyhedra.Polyhedron validatePolyhedronNew(Atom centralAtom, int vertexCount, Point3f[] otherAtoms)
private String faceId(int i, int j, int k)
public void setVisibilityFlags(BitSet bs)
setVisibilityFlags
in class Shape
public String getShapeState()
getShapeState
in class AtomShape