Logo Search packages:      
Sourcecode: pymol version File versions

21export_formal_charges.py

# PyMOL

from pymol import cmd,stored
from chempy.champ import Champ
import re

import string


print '''# NOTE: This file was autogenerated
formal_charge_dict = {
'''

for res in (  'ala','arg','asp','asn','cys','gln','glu','gly','his',
              'hip','hie','hid','ile','leu','lys','met','phe','pro',
              'ser','thr','trp','tyr','val' ):

   stored.fc_dict = {}
   print "'"+string.upper(res)+"': ["
   print "   ("
   
   ch = Champ()
   cmd.fragment(res,"tmp")
   cmd.iterate("tmp","stored.fc_dict[name]=formal_charge",quiet=1)
   cmd.alter("all","formal_charge=0",quiet=1)
   cmd.remove("hydro",quiet=1)
   model = cmd.get_model("tmp")
   cmd.delete("tmp")
   
   m1 = ch.insert_model(model)
   ch.pattern_detect_chirality(m1)
   ch.pattern_orient_bonds(m1)
   pat1 = ch.pattern_get_string_with_names(m1)
   ch.pattern_detect_chirality(m1)
   pat2 = ch.pattern_get_string_with_names(m1)

# confirm that CHAMP handles this pattern well...

   if pat1!=pat2:
      print " Chirality Assignment Error!"
      print pat1
      print pat2
      break
   else:
      pat = pat1

#   print pat1

   clean_pat = re.sub("<[^>]*>","",pat)
   source = ch.insert_pattern_string(clean_pat)
#   print ch.pattern_get_string(source)
#   print ch.pattern_get_string(m1)
   if ch.match_1v1_b(source,m1)==0:
      print " Error: Pattern doesn't match with self!"
      
   pat_isomer = string.replace(pat,"@@","X")
   pat_isomer = string.replace(pat_isomer,"@","@@")
   pat_isomer = string.replace(pat_isomer,"X","@")
   isomer = ch.insert_pattern_string(pat_isomer)
#   if ch.match_1v1_b(isomer,m1)==1:
#      if(res!='gly'):
#         print " Error: Pattern matches the enatiomer"

   pat_racemic = string.replace(pat,"@","")
   racemic = ch.insert_pattern_string(pat_racemic)
   
#   print ch.pattern_get_string(source)
#   print ch.pattern_get_string(isomer)
#   print ch.pattern_get_string(racemic)

   if ch.match_1v1_b(racemic,source)!=1:
      print " Error: Racemic doesn't match source isomer"
   
   if ch.match_1v1_b(racemic,isomer)!=1:
      print " Error: Racemic doesn't match enantiomer"
   
   lst = []
   for a in string.split(pat,'<'):
      for b in string.split(a,'>'):
         lst.append(b)
   
   tag_count = 0
   pat_list = []
   tag_list = []
   flag = 0
   while 1:
      if lst==[]:
         break
      pat_list.append(lst.pop(0))
      if lst==[]:
         break;
      tag_list.append((tag_count,stored.fc_dict[lst.pop(0)]))
      pat_list.append("<%d>"%tag_count)
      tag_count = tag_count+1

   new_pat = string.join(pat_list,'')
   print "      '"+new_pat+"',"

#   np = ch.insert_pattern_string(new_pat)
#   print ch.pattern_get_tags(np)
#   ch.pattern_clear_tags(m1)
#   print ch.match_1v1_map(np,m1,1,1)
#   print ch.pattern_get_ext_indices_with_tags(m1)
   
   print "      {"
   for a in tag_list:
      print "        %2d: %d,"%a
   print "      },"
   print "   ),"
   print "],"

print "}"

   
   

   

Generated by  Doxygen 1.6.0   Back to index