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# 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 "}"
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