Field Detail

• DEFAULT_FACECENTEROFFSET

  private static final float DEFAULT_FACECENTEROFFSET

  See Also:

  Constant Field Values

• EDGES_NONE

  private static final int EDGES_NONE

  See Also:

  Constant Field Values

• EDGES_ALL

  public static final int EDGES_ALL

  See Also:

  Constant Field Values

• EDGES_FRONT

  public static final int EDGES_FRONT

  See Also:

  Constant Field Values

• MAX_VERTICES

  private static final int MAX_VERTICES

  See Also:

  Constant Field Values

• FACE_COUNT_MAX

  private static final int FACE_COUNT_MAX

  See Also:

  Constant Field Values

• MAX_OTHER

  private static final int MAX_OTHER

  See Also:

  Constant Field Values

• otherAtoms

  private javajs.util.P3[] otherAtoms

• normalsT

  private javajs.util.V3[] normalsT

• planesT

  private int[][] planesT

• randomPoint

  private static final javajs.util.P3 randomPoint

• MODE_BONDING

  private static final int MODE_BONDING

  See Also:

  Constant Field Values

• MODE_POINTS

  private static final int MODE_POINTS

  See Also:

  Constant Field Values

• MODE_RADIUS

  private static final int MODE_RADIUS

  See Also:

  Constant Field Values

• MODE_BITSET

  private static final int MODE_BITSET

  See Also:

  Constant Field Values

• MODE_UNITCELL

  private static final int MODE_UNITCELL

  See Also:

  Constant Field Values

• MODE_INFO

  private static final int MODE_INFO

  See Also:

  Constant Field Values

• DEFAULT_PLANAR_PARAM

  private static final float DEFAULT_PLANAR_PARAM

  a dot product comparison term

  See Also:

  Constant Field Values

• CONVEX_HULL_MAX

  private static final float CONVEX_HULL_MAX

  See Also:

  Constant Field Values

• polyhedronCount

  public int polyhedronCount

• polyhedrons

  public Polyhedron[] polyhedrons

• drawEdges

  public int drawEdges

• radius

  private float radius

• radiusMin

  private float radiusMin

• pointScale

  private float pointScale

• nVertices

  private int nVertices

• faceCenterOffset

  float faceCenterOffset

• isCollapsed

  boolean isCollapsed

• isFull

  boolean isFull

• iHaveCenterBitSet

  private boolean iHaveCenterBitSet

• bondedOnly

  private boolean bondedOnly

• haveBitSetVertices

  private boolean haveBitSetVertices

• centers

  private BS centers

• thisID

  private java.lang.String thisID

• center

  private javajs.util.P3 center

• bsVertices

  private BS bsVertices

• bsVertexCount

  private BS bsVertexCount

• useUnitCell

  private boolean useUnitCell

• nPoints

  private int nPoints

• planarParam

  private float planarParam

• info

  private java.util.Map<java.lang.String,​SV> info

• distanceRef

  private float distanceRef

• modelIndex

  private int modelIndex

• isAuto

  private boolean isAuto

• bsPolys

  private BS bsPolys

• vAB

  private final javajs.util.V3 vAB

• vAC

  private final javajs.util.V3 vAC

• vBC

  private final javajs.util.V3 vBC

• MAX_DISTANCE_TO_PLANE

  private static float MAX_DISTANCE_TO_PLANE

Constructor Detail

• Polyhedra

  public Polyhedra()

Method Detail

• compare

  public int compare​(java.lang.Object[] a,
                     java.lang.Object[] b)

  Specified by:

  compare in interface java.util.Comparator<java.lang.Object[]>

• setProperty

  public void setProperty​(java.lang.String propertyName,
                          java.lang.Object value,
                          BS bs)

  Specified by:

  setProperty in class Shape

• pointsPolyhedra

  private void pointsPolyhedra​(BS bs,
                               float pointScale)

• scalePolyhedra

  private void scalePolyhedra​(float scale)

• offsetPolyhedra

  private void offsetPolyhedra​(javajs.util.P3 value)

• getIndexFromName

  public int getIndexFromName​(java.lang.String id)

  Overrides:

  getIndexFromName in class Shape

  Returns:

  index

• getProperty

  public java.lang.Object getProperty​(java.lang.String property,
                                      int i)

  Overrides:

  getProperty in class Shape

  Returns:

  true if serviced

• getPropertyData

  public boolean getPropertyData​(java.lang.String property,
                                 java.lang.Object[] data)

  Overrides:

  getPropertyData in class Shape

  Returns:

  true if serviced

• checkID

  private boolean checkID​(java.lang.String thisID)

• findPoly

  private Polyhedron findPoly​(java.lang.String id,
                              int iatom,
                              boolean allowCollapsed)

  Parameters:

  id - may be null

  iatom - may be < 0 to (along with id==null) to get matching polyhedron

  allowCollapsed -

  Returns:

  Polyhedron or null

• findPolyBS

  private BS findPolyBS​(BS bsCenters)

• isMatch

  private boolean isMatch​(java.lang.String id)

• getShapeDetail

  public java.lang.Object getShapeDetail()

  Overrides:

  getShapeDetail in class Shape

• andBitSet

  private BS andBitSet​(BS bs)

• deletePolyhedra

  private void deletePolyhedra()

• setVisible

  private void setVisible​(boolean visible)

• buildPolyhedra

  private void buildPolyhedra()

• addPolyhedron

  private void addPolyhedron​(Polyhedron p)

• constructBondsPolyhedron

  private Polyhedron constructBondsPolyhedron​(Atom atom,
                                              int otherAtomCount)

• constructUnitCellPolygon

  private Polyhedron constructUnitCellPolygon​(Atom atom,
                                              boolean useBondAlgorithm)

• constructBitSetPolyhedron

  private Polyhedron constructBitSetPolyhedron​(Atom atom)

• constructRadiusPolyhedron

  private Polyhedron constructRadiusPolyhedron​(Atom atom,
                                               AtomIndexIterator iter)

• setGap

  private int setGap​(javajs.util.P3 atom,
                     int otherAtomCount)

• validatePolyhedron

  private Polyhedron validatePolyhedron​(javajs.util.P3 atomOrPt,
                                        int vertexCount)

• getFaceTriangles

  private int[][] getFaceTriangles​(int n,
                                   java.util.Map<java.lang.Integer,​java.lang.Object[]> htNormMap,
                                   int triangleCount)

• addFacet

  private void addFacet​(int i,
                        int j,
                        int k,
                        javajs.util.P3 ptRef,
                        javajs.util.P3[] points,
                        javajs.util.V3[] normals,
                        int[][] faces,
                        int planeCount,
                        int nRef,
                        boolean isWindingOK,
                        javajs.util.V3 vTemp)

  Add one of the three "facets" that compose the planes of a "collapsed" polyhedron. A mask of -2 ensures that only the [1-2] edge is marked as an outer edge.

  Parameters:

  i -

  j -

  k -

  ptRef - slightly out from the center; based on centerOffset parameter

  points -

  normals -

  faces -

  planeCount -

  nRef -

  isWindingOK -

  vTemp -

• checkFacet

  private float checkFacet​(javajs.util.P3[] points,
                           int nPoints,
                           int[] t,
                           int index,
                           javajs.util.V3 norm,
                           javajs.util.P4 pTemp,
                           javajs.util.V3 vNorm,
                           javajs.util.V3 vAC,
                           java.util.Map<java.lang.Integer,​java.lang.Object[]> htNormMap,
                           java.util.Map<java.lang.String,​java.lang.Object> htEdgeMap,
                           float planarParam,
                           BS bsTemp,
                           java.lang.Object[] edgeTest)

  Clean out overlapping triangles based on normals and cross products. For now, we use normixes, which are approximations of normals. It is not 100% guaranteed that this will work.

  Parameters:

  points -

  nPoints -

  t -

  index -

  norm -

  pTemp -

  vNorm -

  vAC -

  htNormMap -

  htEdgeMap -

  planarParam -

  bsTemp -

  edgeTest -

  Returns:

  0 if no error or value indicating the error

• addEdge

  private java.lang.Object addEdge​(javajs.util.Lst<int[]> faceEdgeList,
                                   java.util.Map<java.lang.String,​java.lang.Object> htEdgeMap,
                                   java.lang.Integer normix,
                                   int[] p1,
                                   int i,
                                   javajs.util.P3[] points)

  Check each edge to see that (a) it has not been used before (b) it does not have vertex points on both sides of it (c) if it runs opposite another edge, then both edge masks are set properly

  Parameters:

  faceEdgeList -

  htEdgeMap -

  normix -

  p1 -

  i -

  points -

  Returns:

  true if this triangle is OK

• testDiff

  private boolean testDiff​(javajs.util.P3 a1,
                           javajs.util.P3 b1,
                           javajs.util.P3 a2,
                           javajs.util.P3 b2)

• isPlanar

  private boolean isPlanar​(javajs.util.P3 pt1,
                           javajs.util.P3 pt2,
                           javajs.util.P3 pt3,
                           javajs.util.P3 ptX)

• getFaces

  private int[][] getFaces​(int[][] triangles,
                           int triangleCount,
                           java.util.Map<java.lang.Integer,​java.lang.Object[]> htNormMap)

  Face: a CCW loop of edges all (within tolerance) in the same plane. Objective is to find all triangles with *essentially* the same normal and to then group them into a face. But we have to be careful here; not everything is perfect. We can have be so slightly off in a 4- or 6-face, and we still want it to be called a face. We allow a normal dot product (i.e. cos(theta)) to be < 0.05. This empirically seems to work.

  Parameters:

  triangles -

  triangleCount -

  htNormMap -

  Returns:

  array of CCW connecting edges

• setModelVisibilityFlags

  public void setModelVisibilityFlags​(BS bsModels)

  Overrides:

  setModelVisibilityFlags in class Shape

• getShapeState

  public java.lang.String getShapeState()

  Overrides:

  getShapeState in class AtomShape