21
Better way to calculate Voronoi volume (step 1)
- Find all the vertices associated with an atom.
- Each polyhedra vertex sits at the center of sphere that goes
through 4 atom centers (with no other atom centers being closer). So
using 4 sets of atom center coordinates (x,y,z), solve for the four
unknowns in
(x-a)^2 + (y-b)^2 + (z-c)^2 = r^2 .
- Label each vertex by the indices of the 4 atoms to which it is associated.
- Central atom is atom 0
- Each neighboring atom has an index number (i=1,2,3...)
- Planes are denoted by the indices of the 2
atoms that form them (01)
- Lines are denoted by the indices of 3 atoms (012)
- Vertices are denoted by 4 indices (0123)
Talk on Surfaces and Volumes /
(C) Mark Gerstein (mbg@hyper.stanford.edu) /
May 1996