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assign.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* -------------------------------------------------------------------

tmp_sele1 = "assign_tmp1"
tmp_sele2 = "assign_tmp2"

from chempy import champ
from chempy.champ import Champ
from pymol import cmd

def missing_c_termini(selection="(all)",quiet=0):

   # assumes that hydogens are not present!
   
   sele_list = []
   ch=Champ()
   model = cmd.get_model(selection)
   model_pat = ch.insert_model(model)
   assn_pat = ch.insert_pattern_string("[N+0+1]C[C;D2]<0>(=O)")
   ch.pattern_clear_tags(model_pat)
   if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
      result = ch.pattern_get_ext_indices_with_tags(model_pat)
      for atom_tag in result[0]: # just iterate over atom tags
         if len(atom_tag[1])==1: # one and only one match
            if atom_tag[1][0]==0:
               sele_list.append(atom_tag[0])
   cmd.select_list(tmp_sele1,selection,sele_list)
   while cmd.pop(tmp_sele2,tmp_sele1)>0: # complete the carboxy terminus
      cmd.edit(tmp_sele2)
      cmd.attach("O",1,1,"OXT",quiet=1)
      cmd.unpick()
   cmd.delete(tmp_sele1)
   
   
def formal_charges(selection="(all)",quiet=0):
   result = 1
   # assumes that hydogens are not present!
   
   # first, set all formal charges to zero
   
   cmd.alter(selection,"formal_charge=0")

   # next, flag all atoms so that we'll be able to detect what we miss
   
   cmd.flag(23,selection,'set')

   # get the residue dictionary for formal charges
   
   if not hasattr(champ,'formal_charge_dict'):
      from chempy.champ.formal_charges import formal_charge_dict
      champ.formal_charge_dict = formal_charge_dict


   # iterate through the residue dictionary matching each residue based on chemistry
   # and generating the expressions for reassigning formal charges
   
   alter_list = []
   for resn in champ.formal_charge_dict.keys():
      if cmd.select(tmp_sele1,"(%s) and resn %s"%(selection,resn))>0:
         entry = champ.formal_charge_dict[resn]
         for rule in entry:
            model = cmd.get_model(tmp_sele1)
            ch = Champ()
            model_pat = ch.insert_model(model)         
            assn_pat = ch.insert_pattern_string(rule[0])
            ch.pattern_clear_tags(model_pat)
            if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
               result = ch.pattern_get_ext_indices_with_tags(model_pat)
               for atom_tag in result[0]: # just iterate over atom tags
                  if len(atom_tag[1])==1: # one and only one match
                     tag = atom_tag[1][0]
                     formal_charge = rule[1][tag]
                     # the following expression both changes the formal charge and resets flag 23
                     alter_list.append([atom_tag[0],
                                        "formal_charge=%d;flags=flags&0x-8388609"%formal_charge])

   if 1: # n-terminal amine
      # non-proline 
      ch=Champ()
      model = cmd.get_model(selection)
      model_pat = ch.insert_model(model)
      assn_pat = ch.insert_pattern_string("[N;D1]<0>CC(=O)")
      ch.pattern_clear_tags(model_pat)
      if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
            result = ch.pattern_get_ext_indices_with_tags(model_pat)
            for atom_tag in result[0]: # just iterate over atom tags
               if len(atom_tag[1])==1: # one and only one match
                  if atom_tag[1][0]==0:
                     # the following expression both changes the formal charge and resets flag 23
                     alter_list.append([atom_tag[0],
                                        "formal_charge=1;flags=flags&-8388609"])
      # proline residues
      ch=Champ()
      model = cmd.get_model(selection)
      model_pat = ch.insert_model(model)
      assn_pat = ch.insert_pattern_string("C1CC[N;D2]<0>C1C(=O)")
      ch.pattern_clear_tags(model_pat)
      if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
            result = ch.pattern_get_ext_indices_with_tags(model_pat)
            for atom_tag in result[0]: # just iterate over atom tags
               if len(atom_tag[1])==1: # one and only one match
                  if atom_tag[1][0]==0:
                     # the following expression both changes the formal charge and resets flag 23
                     alter_list.append([atom_tag[0],
                                        "formal_charge=1;flags=flags&-8388609"])
      
                     
   if 1: # c-terminal acid
      ch=Champ()
      model = cmd.get_model(selection)
      model_pat = ch.insert_model(model)
      assn_pat = ch.insert_pattern_string("NCC(=O<0>)[O;D1]<1>")
      ch.pattern_clear_tags(model_pat)
      if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
            result = ch.pattern_get_ext_indices_with_tags(model_pat)
            for atom_tag in result[0]: # just iterate over atom tags
               if len(atom_tag[1])==1: # one and only one match
                  if atom_tag[1][0]==1:
                     # the following expression both changes the formal charge and resets flag 23
                     alter_list.append([atom_tag[0],
                                        "formal_charge=-1;flags=flags&-8388609"])
      
   # now evaluate all of these expressions efficiently en-masse 
   cmd.alter_list(selection,alter_list)

   # see if we missed any atoms
   missed_count = cmd.count_atoms("("+selection+") and flag 23")

   if missed_count>0:
      if not quiet:
         # looks like we did, so alter the user
         print " WARNING: %d atoms did not have formal charges assigned"%missed_count
      result = 0
   # remove the temporary selection we used to select appropriate residues
   
   cmd.delete(tmp_sele1)
   
   return result

def amber99(selection="(all)",quiet=0):
   result = 1
   # first, set all parameters to zero

   cmd.alter(selection,"name=''")
   cmd.alter(selection,"partial_charge=0")
   cmd.alter(selection,"bohr=0.0")
   cmd.alter(selection,"text_type=''")

   # next, flag all atoms so that we'll be able to detect what we miss
   
   cmd.flag(23,selection,'set')

   # get the amber99 dictionary
   
   if not hasattr(champ,'amber99_dict'):
      from chempy.champ.amber99 import amber99_dict
      champ.amber99_dict = amber99_dict

   # iterate through the residue dictionary matching each residue based on chemistry
   # and generating the expressions for reassigning formal charges
   
   alter_list = []
   for resn in champ.amber99_dict.keys():
      if cmd.select(tmp_sele1,"(%s) and resn %s"%(selection,resn))>0:
         entry = champ.amber99_dict[resn]
         for rule in entry:
            model = cmd.get_model(tmp_sele1)
            ch = Champ()
            model_pat = ch.insert_model(model)
            ch.pattern_detect_chirality(model_pat)
            assn_pat = ch.insert_pattern_string(rule[0])
            ch.pattern_clear_tags(model_pat)
            if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
               result = ch.pattern_get_ext_indices_with_tags(model_pat)
               for atom_tag in result[0]: # just iterate over atom tags
                  if len(atom_tag[1])==1: # one and only one match
                     tag = atom_tag[1][0]
                     prop_list = rule[1][tag]
                     # the following expression both changes the formal charge and resets flag 23
                     alter_list.append([atom_tag[0],
         "name='''%s''';text_type='''%s''';partial_charge=%f;bohr=%f;flags=flags&-8388609"%prop_list])

   # now evaluate all of these expressions efficiently en-masse 
   cmd.alter_list(selection,alter_list)

   # see if we missed any atoms
   missed_count = cmd.count_atoms("("+selection+") and flag 23")

   if missed_count>0:
      if not quiet:
         # looks like we did, so alter the user
         print " WARNING: %d atoms did not have properties assigned"%missed_count
      result = 0

   # remove the temporary selection we used to select appropriate residues
   
   cmd.delete(tmp_sele1)

   return result

   

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