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neighbor.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-* 
#-* 
#-*
#Z* -------------------------------------------------------------------

import copy

class Neighbor:

   def __init__(self,vect_list,spacing):
      self.voxel = {}
      self.neighbor = None
      self.spacing = spacing
      c = 0
      voxel = self.voxel
      for v in vect_list:
         k = self.address(v)
         if not voxel.has_key(k):
            voxel[k] = [c]
         else:
            voxel[k].append(c)
         c = c + 1

   def optimize(self):
      self.neighbor = {}
      voxel = self.voxel
      for k in voxel.keys():
         lst = self.neighbor[k]
         for a in (k[0]-1,k[0],k[0]+1):
            for b in (k[1]-1,k[1],k[1]+1):
               for c in (k[2]-1,k[2],k[2]+1):
                  k2 = (a,b,c)
                  if voxel.has_key(k2):
                     lst.extend(voxel[k2])

   def address(self,vect):
      return (int(vect[0]/self.spacing),
              int(vect[1]/self.spacing),
              int(vect[2]/self.spacing))

   def get_voxel(self,vect):
      k = self.address(vect)
      if self.voxel.has_key(k):
         return self.voxel[k]
      else:
         return []
      
   def get_neighbors(self,vect):
      if self.neighbor:
         k = self.address(vect)
         if self.neighbor.has_key(k):
            return self.neighbor[k]
         else:
            return []
      else:
         voxel = self.voxel
         k = self.address(vect)
         lst = []
         for a in (k[0]-1,k[0],k[0]+1):
            for b in (k[1]-1,k[1],k[1]+1):
               for c in (k[2]-1,k[2],k[2]+1):
                  k2 = (a,b,c)
                  if voxel.has_key(k2):
                     lst.extend(voxel[k2])
         return lst
         
         

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