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cc1.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* -------------------------------------------------------------------

from chempy.models import Indexed
from chempy import Storage,Atom,Bond

import string

class CC1(Storage): # ChemDraw3D 5.0 std., cartesian coordinates

   def fromList(self,molList):

      model = Indexed()

      # read header information
      nAtom = int(molList[0][0:3])

      # read atoms and bonds
      id_dict = {}
      irec = 1
      cnt = 0
      for a in range(nAtom):
         at = Atom()
         at.index = cnt
         id_dict[string.strip(molList[irec][3:8])] = at.index
         at.coord = [float(molList[irec][8:20]), 
            float(molList[irec][20:32]),float(molList[irec][32:44])]
         at.symbol = string.strip(molList[irec][0:3])
         at.numeric_type = int(molList[irec][44:49])
         lst = string.split(string.strip(molList[irec][49:]))
         at.bonds = lst
         irec = irec + 1
         cnt = cnt + 1
         model.atom.append(at)
         
      # interpret bonds
      cnt = 0
      for a in model.atom:
         lst = a.bonds
         del a.bonds
         for b in lst:
            if a.index<id_dict[b]:
               bnd = Bond()
               bnd.index = [ a.index,id_dict[b]]
               model.bond.append(bnd)

      # obtain formal charges from M  CHG record
      return model

#------------------------------------------------------------------------------
   def toList(self,model):

      return []

      # not implemented yet


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