rdkit-data 201603.5-2 / usr / share / RDKit / Contrib / fraggle / rdkit_tversky.py

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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 xrange(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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