/usr/share/RDKit/Contrib/mmpa/cansmirk.py is in rdkit-data 201309-1.
This file is owned by root:root, with mode 0o644.
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# Created by Jameed Hussain, September 2012
import sys
import re
from rdkit import Chem
from indexing import cansmirk
if __name__=='__main__':
if (len(sys.argv) >= 2):
print "Program that canonicalises an input SMIRKS so its in same format as MMP identification program.\n";
print "USAGE: ./cansmirks.py <file_of_smirks\n";
sys.exit(1)
#read the STDIN
for line in sys.stdin:
line = line.rstrip()
line_fields = re.split('\s|,',line)
smirks = line_fields[0]
if(len(line_fields) == 1):
id=""
else:
id=line_fields[1]
lhs,rhs = smirks.split(">>")
l = Chem.MolFromSmiles( lhs )
if(l == None):
sys.stderr.write("Can't generate mol for: %s\n" % (lhs) )
continue
r = Chem.MolFromSmiles( rhs )
if(r == None):
sys.stderr.write("Can't generate mol for: %s\n" % (rhs) )
continue
clhs = Chem.MolToSmiles( l, isomericSmiles=True )
crhs = Chem.MolToSmiles( r, isomericSmiles=True )
#just need to take care of [*H:1]
if(clhs == '[*H:1]'):
clhs = '[*:1][H]'
if(crhs == '[*H:1]'):
crhs = '[*:1][H]'
#print clhs
#print crhs
csmirk,context = cansmirk(clhs,crhs,"")
print "%s %s" % (csmirk,id)
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