/usr/share/RDKit/Contrib/mmpa/cansmirk.py is in rdkit-data 201403-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 | # Copyright (c) 2012, GlaxoSmithKline Research & Development Ltd.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of GlaxoSmithKline Research & Development Ltd.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# 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)
|