/usr/share/RDKit/Contrib/fraggle/atomcontrib.py

# 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
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#     * Redistributions in binary form must reproduce the above
#       copyright notice, this list of conditions and the following
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#       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.
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# 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
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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# Created by Jameed Hussain, May 2013

import sys
from optparse import OptionParser
from rdkit import Chem
from rdkit import DataStructs
from collections import defaultdict

#input format
#query_substructs,query_smiles,SMILES,ID,Tversky_sim

#algorithm
#read in query_substructs and smiles
#feed to atomcontrib function to return generalised_SMILES
#use Tanimoto to compare generalised_SMILES with query smiles to give fraggle similarity

from rdkit.Chem.Fraggle import FraggleSim

parser = OptionParser(description="Program to post-process Tversky search results as part of Fraggle",
                    epilog="Format of input file: query_frag_smiles,query_smiles,query_id,retrieved_smi,retrieved_id,tversky_sim\t"
                    "Output: SMILES,ID,QuerySMI,QueryID,Fraggle_Similarity,RDK5_Similarity")
parser.add_option('-c','--cutoff',action='store', dest='cutoff', type='float', default=0.7,
                  help="Cutoff for fraggle similarity. Only results with similarity greater than the cutoff will be output. DEFAULT = 0.7")
parser.add_option('-p','--pfp',action='store', dest='pfp', type='float', default=0.8,
                  help="Cutoff for partial fp similarity. DEFAULT = 0.8")

if __name__ == '__main__':
    #parse the command line options
    (options, args) = parser.parse_args()

    if( (options.cutoff >= 0) and (options.cutoff <= 1) ):
        fraggle_cutoff = options.cutoff
    else:
        print "Fraggle cutoff must be in range 0-1"
        sys.exit(1)


    print "SMILES,ID,QuerySMI,QueryID,Fraggle_Similarity,RDK5_Similarity"

    #create some data structure to store results
    id_to_smi = {}
    day_sim = {}
    frag_sim = {}
    query_size = {}
    query_mols = {}

    #generate dummy mol object which generates empty fp
    emptyMol = Chem.MolFromSmiles('*')

    #read the STDIN
    for line in sys.stdin:
        line = line.rstrip()
        qSubs,qSmi,qID,inSmi,id_,tversky = line.split(",")

        #add query to id_to_smi
        id_to_smi[qID] = qSmi
        id_to_smi[id_] = inSmi

        #add query to data structures
        frag_sim.setdefault(qID, defaultdict(float))
        day_sim.setdefault(qID, {})

        if(qID not in query_size):
            qMol = Chem.MolFromSmiles(qSmi)
            if(qMol == None):
                sys.stderr.write("Can't generate mol for: %s\n" % (qSmi) )
                continue
            query_mols[qID] = qMol
            query_size[qID] = qMol.GetNumAtoms()

        iMol = Chem.MolFromSmiles(inSmi)

        if(iMol == None):
            sys.stderr.write("Can't generate mol for: %s\n" % (inSmi) )
            continue

        #discard based on atom size
        if(iMol.GetNumAtoms() < query_size[qID]-3):
            #sys.stderr.write("Too small: %s\n" % (inSmi) )
            continue;

        if(iMol.GetNumAtoms() > query_size[qID]+4):
            #sys.stderr.write("Too large: %s\n" % (inSmi) )
            continue;
        
        #print '>>>',id_
        rdkit_sim,fraggle_sim = FraggleSim.compute_fraggle_similarity_for_subs(iMol,query_mols[qID],qSmi,qSubs,
                                                                               options.pfp)
        day_sim[qID][id_] = rdkit_sim
        frag_sim[qID][id_] = max(frag_sim[qID][id_],fraggle_sim)

        #check if you have the fp for the modified query
        #and generate if need to



    #right, print out the results for the query
    #Format: SMILES,ID,QuerySMI,QueryID,Fraggle_Similarity,Daylight_Similarity
    for qID in frag_sim:
        for id_ in frag_sim[qID]:
            if(frag_sim[qID][id_] >= fraggle_cutoff):
                print "%s,%s,%s,%s,%s,%s" % (id_to_smi[id_],id_,id_to_smi[qID],qID,frag_sim[qID][id_],day_sim[qID][id_])
rdkit-data 201309-1 / usr / share / RDKit / Contrib / fraggle / atomcontrib.py
