rdkit-data 201603.5-2 / usr / share / RDKit / Contrib / mmpa / cansmirk.py

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# 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
from __future__ import print_function
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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