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# Copyright (c) 2013, 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, July 2013
from __future__ import print_function
import sys
import re
from optparse import OptionParser
from rdkit import Chem
from rdkit.Chem import AllChem
def smiles_to_smarts(smi):
mol = Chem.MolFromSmiles(smi)
if (mol is None):
sys.stderr.write("Can't generate mol for: %s\n" % (smi))
return None
#change the isotope to 42
for atom in mol.GetAtoms():
atom.SetIsotope(42)
#preint out the smiles - all the atom attributes will be fully specified
smarts = Chem.MolToSmiles(mol, isomericSmiles=True)
#remove the 42 isotope labels
smarts = re.sub(r'\[42', "[", smarts)
#now have a fully specified SMARTS - simples!
return smarts
if __name__ == '__main__':
parser = OptionParser(
description="Program to apply transformations to a set of input molecules",
epilog="Example command: mol_transform.py -t TRANSFORM_FILE <SMILES_FILE\t\t"
"Format of smiles file: SMILES ID <space or comma separated>\t\t\t"
"Format of transform file: transform <one per line>\t\t\t"
"Output: SMILES,ID,Transfrom,Modified_SMILES")
parser.add_option('-f', '--file', action='store', dest='transform_file', type='string',
help='The file containing the transforms to apply to your input SMILES')
(options, args) = parser.parse_args()
#print options.transform_file
if (options.transform_file == None):
print("Please specify the transform file.")
sys.exit(1)
smiles = []
#read the STDIN
for line in sys.stdin:
line = line.rstrip()
smi, id = re.split('\s|,', line)
#print smiles,id
smiles.append((smi, id))
#read the transform file
#all the transform must come from BioDig to guarantee they have been cansmirk'ed
infile = open(options.transform_file, 'r')
print("Input_SMILES,ID,RG-Transform,RG-transformedSMILES")
for transform in infile:
transform = transform.rstrip()
#need to conver the smiles to smart to get rid of any potential issues
lhs, rhs = transform.split(">>")
if (lhs == "[*:1][H]"):
lhs = "[*;!H0:1]"
else:
lhs = smiles_to_smarts(lhs)
if (rhs == "[*:1][H]"):
rhs = "[*:1]"
else:
rhs = smiles_to_smarts(rhs)
rdkit_transform = "%s>>%s" % (lhs, rhs)
rxn = AllChem.ReactionFromSmarts(rdkit_transform)
#rxn = AllChem.ReactionFromSmarts(transform)
for x in smiles:
mol = Chem.MolFromSmiles(x[0])
ps = rxn.RunReactants([mol])
products = set()
for y in range(len(ps)):
for z in range(len(ps[y])):
p = ps[y][z]
Chem.SanitizeMol(p)
products.add(Chem.MolToSmiles(p, isomericSmiles=True))
for p in products:
print("%s,%s,%s,%s" % (x[0], x[1], transform, p))
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