# # 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