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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, October 2013
from __future__ import print_function
import sys
import re
from optparse import OptionParser
from rdkit import Chem
from rdkit import DataStructs
parser = OptionParser(
description="Program to Tversky search results as part of Fraggle",
epilog="Format of input file: whole mol smiles,ID,fraggle split smiles\t\t"
"Output: query_frag_smiles,query_smiles,query_id,retrieved_smi,retrieved_id,tversky_sim")
parser.add_option('-f', '--frags', dest='f_file', type='string',
help="File containing the query fragmentations from Fraggle")
parser.add_option(
'-c', '--cutoff', dest='cutoff', type='float', default=0.8,
help="Cutoff for Tversy similarity. Only Tversky results with similarity greater than the cutoff will be output. DEFAULT = 0.8")
#parse the command line options
(options, args) = parser.parse_args()
if (options.f_file is None):
print("Please specify the file containing the Fraggle fragmentations")
sys.exit(1)
if ((options.cutoff < 0) or (options.cutoff > 1)):
print("Please specify a Tversky cut-off between 0-1")
sys.exit(1)
#sys.exit(1)
queries = []
query_info = []
q_split_input = open(options.f_file, "r")
for line in q_split_input:
info = line.rstrip().split(",")
qmol = Chem.MolFromSmiles(info[2])
#print info[2]
if qmol is None:
sys.stderr.write("Can't generate mol for: %s\n" % (info[2]))
continue
#generate fp of query_substructs
qfp = Chem.RDKFingerprint(qmol, maxPath=5, fpSize=1024, nBitsPerHash=2)
queries.append(qfp)
query_info.append((info[0], info[1], info[2]))
fragments = len(query_info)
for line in sys.stdin:
line = line.rstrip()
smi, id = re.split('\s|,', line)
#print smi,id
mol = Chem.MolFromSmiles(smi)
if mol is None:
sys.stderr.write("Can't generate mol for: %s\n" % (smi))
continue
mfp = Chem.RDKFingerprint(mol, maxPath=5, fpSize=1024, nBitsPerHash=2)
#print smi
res = DataStructs.BulkTverskySimilarity(mfp, queries, 0, 1, False)
#query_frag_smiles,query_smiles,query_id,retrieved_smi,retrieved_id,tversky_sim
for i in range(fragments):
if (res[i] >= options.cutoff):
print("%s,%s,%s,%s,%s,%s" %
(query_info[i][2], query_info[i][0], query_info[i][1], smi, id, res[i]))
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