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charge.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

def __list_sum(the_list):
   return reduce(lambda x,y:x+y,the_list)

def combine_fragments(*arg,**kw):
   '''
   merge_fragments(target,source1,source2,source3,...)
   
   WARNING: This is not how you *should* combine fragments,
   rather this is just a convenient kludge for getting
   something remotely realistic in a big hurry.
   
   NOTE: atom names must be unique throughout -- especially
   including the "capping" atoms used during the ab-initio
   calculations (you can use PyMOL to rename these if they
   happen to coincide).
'''
   
   if kw.has_key('net_charge'):
      net_charge = kw['net_charge']
   else:
      net_charge = None
   if len(arg)<1:
      raise TypeError('invalid arguments')
   dst = copy.deepcopy(arg[0])
   frg_lst = arg[1:]
   n_frg = len(frg_lst)
   n_dst_atm = len(dst.atom)

   # create dictionary/indices for shared atoms
   
   n_tot = 0
   dst_dict = {}
   for a in dst.atom:
      sig = a.name
      dst_dict[sig] = n_tot
      n_tot = n_tot + 1

   # create fragment membership list for destination atoms
   
   members = []
   for a in range(n_tot):
      members.append([])
   
   # create indices for unique atoms

   for fragment in frg_lst:
      c = 0
      for a in fragment.atom:
         sig = a.name
         if dst_dict.has_key(sig):
            a.chg_index = dst_dict[sig]
            members[a.chg_index].append(fragment)
         else:
            # find an attached atom that *is* in the destination structure
            attached_index = None
            for b in fragment.bond:
               attached = None
               if b.index[0]==c:
                  attached = fragment.atom[b.index[1]]
               elif b.index[1]==c:
                  attached = fragment.atom[b.index[0]]
               if attached!=None:
                  if dst_dict.has_key(attached.name):
                     attached_index = dst_dict[attached.name]
                     break
            a.chg_index = n_tot
            if attached_index!=None:
               a.attached_index = attached_index
            n_tot = n_tot + 1
         c = c + 1
            
   # create array for charges
   
   chg = []
   for a in range(n_frg):
      chg.append([0.0] * n_tot)
   
   # now load and count measurements

   cnt = [0] * n_tot
   c = 0
   for fragment in frg_lst:
      for a in fragment.atom:
         index = a.chg_index
         if (index < n_dst_atm):
            chg[c][index] = chg[c][index] + a.partial_charge
            cnt[index] = cnt[index] + 1
         else:
            aindex = a.attached_index
            chg[c][aindex] = chg[c][aindex] + a.partial_charge
      c = c + 1

   # now compute average charges for each destination atom

   avg = []
   for index in range(n_dst_atm):
      if cnt[index]:
         tmp_lst = []
         for a in chg:
            tmp_lst.append(a[index])
         avg.append(__list_sum(tmp_lst)/cnt[index])
      else:
         avg.append(0.0)
      
   # correct total charge

   chg_sum = __list_sum(avg)

   print "chg_sum",chg_sum
   if net_charge != None:
      chg_diff = net_charge - chg_sum
      chg_adjust = chg_diff / n_dst_atm
   else:
      chg_adjust = 0.0
      
   c = 0
   for a in dst.atom:
      a.partial_charge = avg[c] + chg_adjust
      c = c + 1

   return dst


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