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24f1737839
* remove all of the "from __future__" imports * remove the first batch of rdkit.six imports/uses * next step of rdkit.six removal * removing xrange, range, and some maps * next round of removals * next round of cleanups * fix inchi test * last bits of "from rdkit.six" are gone * and the last of the six stuff is gone * strange importlib problem
133 lines
4.9 KiB
Python
133 lines
4.9 KiB
Python
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are
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# met:
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#
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above
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# copyright notice, this list of conditions and the following
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# disclaimer in the documentation and/or other materials provided
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# with the distribution.
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# * Neither the name of GlaxoSmithKline Research & Development Ltd.
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# nor the names of its contributors may be used to endorse or promote
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# products derived from this software without specific prior written
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# permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Created by Jameed Hussain, May 2013
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import sys
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from optparse import OptionParser
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from rdkit import Chem
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from rdkit import DataStructs
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from collections import defaultdict
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#input format
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#query_substructs,query_smiles,SMILES,ID,Tversky_sim
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#algorithm
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#read in query_substructs and smiles
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#feed to atomcontrib function to return generalised_SMILES
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#use Tanimoto to compare generalised_SMILES with query smiles to give fraggle similarity
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from rdkit.Chem.Fraggle import FraggleSim
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parser = OptionParser(
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description="Program to post-process Tversky search results as part of Fraggle",
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epilog="Format of input file: query_frag_smiles,query_smiles,query_id,retrieved_smi,retrieved_id,tversky_sim\t"
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"Output: SMILES,ID,QuerySMI,QueryID,Fraggle_Similarity,RDK5_Similarity")
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parser.add_option(
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'-c', '--cutoff', action='store', dest='cutoff', type='float', default=0.7,
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help="Cutoff for fraggle similarity. Only results with similarity greater than the cutoff will be output. DEFAULT = 0.7")
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parser.add_option('-p', '--pfp', action='store', dest='pfp', type='float', default=0.8,
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help="Cutoff for partial fp similarity. DEFAULT = 0.8")
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if __name__ == '__main__':
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#parse the command line options
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(options, args) = parser.parse_args()
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if ((options.cutoff >= 0) and (options.cutoff <= 1)):
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fraggle_cutoff = options.cutoff
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else:
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print("Fraggle cutoff must be in range 0-1")
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sys.exit(1)
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print("SMILES,ID,QuerySMI,QueryID,Fraggle_Similarity,RDK5_Similarity")
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#create some data structure to store results
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id_to_smi = {}
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day_sim = {}
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frag_sim = {}
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query_size = {}
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query_mols = {}
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#generate dummy mol object which generates empty fp
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emptyMol = Chem.MolFromSmiles('*')
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#read the STDIN
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for line in sys.stdin:
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line = line.rstrip()
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qSubs, qSmi, qID, inSmi, id_, tversky = line.split(",")
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#add query to id_to_smi
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id_to_smi[qID] = qSmi
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id_to_smi[id_] = inSmi
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#add query to data structures
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frag_sim.setdefault(qID, defaultdict(float))
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day_sim.setdefault(qID, {})
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if (qID not in query_size):
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qMol = Chem.MolFromSmiles(qSmi)
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if (qMol == None):
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sys.stderr.write("Can't generate mol for: %s\n" % (qSmi))
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continue
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query_mols[qID] = qMol
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query_size[qID] = qMol.GetNumAtoms()
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iMol = Chem.MolFromSmiles(inSmi)
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if (iMol == None):
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sys.stderr.write("Can't generate mol for: %s\n" % (inSmi))
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continue
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#discard based on atom size
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if (iMol.GetNumAtoms() < query_size[qID] - 3):
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#sys.stderr.write("Too small: %s\n" % (inSmi) )
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continue
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if (iMol.GetNumAtoms() > query_size[qID] + 4):
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#sys.stderr.write("Too large: %s\n" % (inSmi) )
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continue
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#print '>>>',id_
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rdkit_sim, fraggle_sim = FraggleSim.compute_fraggle_similarity_for_subs(
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iMol, query_mols[qID], qSmi, qSubs, options.pfp)
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day_sim[qID][id_] = rdkit_sim
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frag_sim[qID][id_] = max(frag_sim[qID][id_], fraggle_sim)
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#check if you have the fp for the modified query
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#and generate if need to
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#right, print out the results for the query
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#Format: SMILES,ID,QuerySMI,QueryID,Fraggle_Similarity,Daylight_Similarity
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for qID in frag_sim:
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for id_ in frag_sim[qID]:
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if (frag_sim[qID][id_] >= fraggle_cutoff):
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print("%s,%s,%s,%s,%s,%s" %
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(id_to_smi[id_], id_, id_to_smi[qID], qID, frag_sim[qID][id_], day_sim[qID][id_]))
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