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#
# Copyright (c) 2009, Novartis Institutes for BioMedical Research Inc.
# 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 Novartis Institutes for BioMedical Research Inc.
# 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 Greg Landrum and Anna Vulpetti, March 2009
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.AtomPairs import Pairs, Torsions
import sys, cPickle
# maxPathLength is the maximum path length in atoms
# maxPathLength=6 corresponds to F-FP-5
# maxPathLength=7 corresponds to F-FP-6
# maxPathLength=8 corresponds to F-FP-7
maxPathLength = 8
# nameField is the name of the property (from the SD file) that has molecule
# names... If the molecules have names in the first row of the file, use "_Name"
nameField = 'Compound_orig'
#nameField = '_Name'
extraQueries = (('SCF3?', Chem.MolFromSmarts('SC(F)(F)F')),
('COCF3?', Chem.MolFromSmarts('C(=O)C(F)(F)F')),
('OCF3?', Chem.MolFromSmarts('OC(F)(F)F')),
('NCF3?', Chem.MolFromSmarts('NC(F)(F)F')),
('CF3?', Chem.MolFromSmarts('C(F)(F)F')), )
def GetMolFingerprint(mol, maxPathLength):
FQuery = Chem.MolFromSmarts('F')
CF3Query = Chem.MolFromSmarts('[$(C(F)(F)F)]')
CF3Rxn = AllChem.ReactionFromSmarts('[*:1]-C(F)(F)F>>[*:1]-F')
hasCF3 = mol.HasSubstructMatch(CF3Query)
if hasCF3:
p = CF3Rxn.RunReactants((mol, ))[0][0]
Chem.SanitizeMol(p)
for nm in mol.GetPropNames():
p.SetProp(nm, mol.GetProp(nm))
mol = p
match = mol.GetSubstructMatch(FQuery)
fp = Torsions.GetHashedTopologicalTorsionFingerprint(mol, nBits=9192, targetSize=maxPathLength,
fromAtoms=match)
for i in range(2, maxPathLength):
nfp = Torsions.GetHashedTopologicalTorsionFingerprint(mol, nBits=9192, targetSize=i,
fromAtoms=match)
for bit, v in nfp.GetNonzeroElements().iteritems():
fp[bit] = fp[bit] + v
return fp
if __name__ == '__main__':
suppl = Chem.SDMolSupplier(sys.argv[1])
outF = file(sys.argv[2], 'w+')
fps = []
for i, mol in enumerate(suppl):
if not mol:
continue
smi = Chem.MolToSmiles(mol, True)
queryMatches = [str(mol.HasSubstructMatch(y)) for x, y in extraQueries]
fp = GetMolFingerprint(mol, maxPathLength)
nm = mol.GetProp(nameField)
fps.append([nm, smi, fp] + queryMatches)
colNames = ['name', 'smiles', 'fp'] + [x for x, y in extraQueries]
cPickle.dump(colNames, outF)
cPickle.dump(fps, outF)
print('name1 smiles1 name2 smiles2 name12 smiles12 environment_id ' + ' '.join(
[x for x, y in extraQueries]))
if 1:
seen = []
smis = []
data = []
for row in fps:
nm = row[0]
smi = row[1]
fp = row[2]
if fp in seen and smi not in smis:
id = seen.index(fp)
onm, osmi = data[id]
print(nm, smi, onm, osmi, nm + '.' + onm, smi + '.' + osmi, id + 1, ' '.join(row[3:]))
else:
seen.append(fp)
smis.append(smi)
data.append((nm, smi))
else:
smis = []
for nm, smi, fp in fps:
if smi not in smis:
pass
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