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Classes | Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | Protected Member Functions | Protected Attributes | Static Package Functions | Package Attributes | Static Package Attributes | Private Member Functions | Private Attributes | Static Private Attributes

org::jmol::shapespecial::Polyhedra Class Reference

Inheritance diagram for org::jmol::shapespecial::Polyhedra:
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List of all members.


class  Polyhedron

Public Member Functions

void checkBoundsMinMax (Point3f pointMin, Point3f pointMax)
Point3fi checkObjectClicked (int x, int y, int modifiers, BitSet bsVisible)
boolean checkObjectDragged (int prevX, int prevY, int x, int y, int modifiers, BitSet bsVisible)
boolean checkObjectHovered (int x, int y, BitSet bsVisible)
void findNearestAtomIndex (int xMouse, int yMouse, Atom[] closest, BitSet bsNot)
String getColorCommand (String type, short colix)
String getColorCommand (String type, byte pid, short colix)
int getIndexFromName (String thisID)
boolean getProperty (String property, Object[] data)
Object getProperty (String property, int index)
List getShapeDetail ()
String getShapeState ()
int getSize (int atomIndex)
int getSize (Group group)
Viewer getViewer ()
final void initializeShape (Viewer viewer, Graphics3D g3d, ModelSet modelSet, int shapeID)
void initShape ()
void merge (Shape shape)
short setColix (short colix, byte paletteID, int atomIndex)
void setModelClickability ()
void setModelSet (ModelSet modelSet)
void setProperty (String propertyName, Object value, BitSet bs)
void setShapeProperty (String propertyName, Object value, BitSet bsSelected)
void setShapeSize (int size, RadiusData rd, BitSet bsSelected)
void setVisibilityFlags (BitSet bs)
boolean wasClicked (int x, int y)

Static Public Member Functions

static void appendCmd (StringBuffer s, String cmd)
static short getColix (short[] colixes, int i, Atom atom)
static String getFontCommand (String type, Font3D font)
static String getShapeCommands (Hashtable htDefine, Hashtable htMore, String selectCmd)
static String getShapeCommands (Hashtable htDefine, Hashtable htMore)
static void setStateInfo (Hashtable ht, int i, String key)
static void setStateInfo (Hashtable ht, int i1, int i2, String key)

Public Attributes

int atomCount
Atom[] atoms
short[] colixes
Graphics3D g3d
boolean isActive
boolean isBioShape
short[] mads
ModelSet modelSet
int myVisibilityFlag
byte[] paletteIDs
int shapeID
Viewer viewer

Static Public Attributes

static final float RADIUS_MAX = 4

Protected Member Functions

int coordinateInRange (int x, int y, Point3f vertex, int dmin2, Point3i ptXY)
void initModelSet ()
short setColix (short colix, byte paletteID, Bond bond)
short setColix (short colix, byte paletteID, Atom atom)
void setColixAndPalette (short colix, byte paletteID, int atomIndex)
void setSize (RadiusData rd, BitSet bsSelected)
void setSize (int size, BitSet bsSelected)

Protected Attributes

BitSet bsColixSet
BitSet bsSizeSet
boolean translucentAllowed = true
float translucentLevel
List xmlProperties

Static Package Functions

static String encodeColor (short colix)

Package Attributes

float distanceFactor
int drawEdges
float faceCenterOffset
boolean isCollapsed
int polyhedronCount
Polyhedron[] polyhedrons = new Polyhedron[32]

Static Package Attributes

static final int EDGES_ALL = 1
static final int EDGES_FRONT = 2

Private Member Functions

void andBitSet (BitSet bs)
void buildPolyhedra ()
Polyhedron constructBitSetPolyhedron (int atomIndex)
Polyhedron constructBondsPolyhedron (int atomIndex)
Polyhedron constructRadiusPolyhedron (int atomIndex, AtomIndexIterator iter)
void deletePolyhedra ()
String faceId (int i, int j, int k)
boolean isAligned (Point3f pt1, Point3f pt2, Point3f pt3)
boolean isPlanar (Point3f pt1, Point3f pt2, Point3f pt3, Point3f ptX)
void setVisible (boolean visible)
Polyhedron validatePolyhedronNew (Atom centralAtom, int vertexCount, Point3f[] otherAtoms)

Private Attributes

Vector3f align1 = new Vector3f()
Vector3f align2 = new Vector3f()
boolean bondedOnly
BitSet bsVertexCount
BitSet bsVertices
BitSet centers
boolean haveBitSetVertices
boolean iHaveCenterBitSet
short[] normixesT = new short[MAX_VERTICES]
int nVertices
Point3f[] otherAtoms = new Point3f[MAX_VERTICES + 1]
byte[] planesT = new byte[MAX_VERTICES * 3]
float radius
final Vector3f vAB = new Vector3f()
final Vector3f vAC = new Vector3f()

Static Private Attributes

static final float DEFAULT_DISTANCE_FACTOR = 1.85f
static final float DEFAULT_FACECENTEROFFSET = 0.25f
static final int EDGES_NONE = 0
static final int FACE_COUNT_MAX = MAX_VERTICES - 3
static final int MAX_VERTICES = 150
static float minDistanceForPlanarity = 0.1f
static final Point3f randomPoint = new Point3f(3141f, 2718f, 1414f)

Detailed Description

Definition at line 45 of file Polyhedra.java.

The documentation for this class was generated from the following file:

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