Class Polyhedra

Method Details

• compare

  public int compare(Object[] a, Object[] b)

  Specified by:

  compare in interface Comparator<Object[]>

• setProperty

  public void setProperty(String propertyName, Object value, javajs.util.BS bs)

  Specified by:

  setProperty in class Shape

• setDefinedFaces

  private void setDefinedFaces(javajs.util.P3[] points, int[][] faces)

• pointsPolyhedra

  private void pointsPolyhedra(javajs.util.BS bs, float pointScale)

• scalePolyhedra

  private void scalePolyhedra(float scale)

• offsetPolyhedra

  private void offsetPolyhedra(javajs.util.P3 value)

• getIndexFromName

  public int getIndexFromName(String id)

  Overrides:

  getIndexFromName in class Shape

  Returns:

  index

• getProperty

  public Object getProperty(String property, int i)

  Overrides:

  getProperty in class Shape

  Returns:

  true if serviced

• getPropertyData

  public boolean getPropertyData(String property, Object[] data)

  Overrides:

  getPropertyData in class Shape

  Returns:

  true if serviced

• getAtomsWithin

  private javajs.util.BS getAtomsWithin(Polyhedron p, float offset)

• checkID

  private boolean checkID(String thisID)

• findPoly

  private Polyhedron findPoly(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 javajs.util.BS findPolyBS(javajs.util.BS bsCenters)

• isMatch

  private boolean isMatch(String id)

• getShapeDetail

  public Object getShapeDetail()

  Overrides:

  getShapeDetail in class Shape

• andBitSet

  private javajs.util.BS andBitSet(javajs.util.BS bs)

• deletePolyhedra

  private void deletePolyhedra()

• setVisible

  private void setVisible(boolean visible)

• buildPolyhedra

  private void buildPolyhedra()

• setPointsFromBitset

  private void setPointsFromBitset()

• 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)

• fixExplicitFaceWinding

  private int[] fixExplicitFaceWinding(int[] face, int ipt, javajs.util.P3[] points, javajs.util.V3[] normals)

  Check to see that the winding of the explicit face is correct. If not, correct it. Also set the normals.

  Parameters:

  face -

  ipt -

  points -

  normals -

  Returns:

  correctly wound face

• getFaceTriangles

  private int[][] getFaceTriangles(int n, Map<Integer,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, Map<Integer,Object[]> htNormMap, Map<String,Object> htEdgeMap, float planarParam, javajs.util.BS bsTemp, 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 Object addEdge(javajs.util.Lst<int[]> faceEdgeList, Map<String,Object> htEdgeMap, 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, Map<Integer,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(javajs.util.BS bsModels)

  Overrides:

  setModelVisibilityFlags in class Shape

• getShapeState

  public String getShapeState()

  Overrides:

  getShapeState in class AtomShape