# # 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 rdkit import Chem from rdkit import DataStructs from CreateFps import GetMolFingerprint from rdkit.RDLogger import logger logger = logger() import sys # 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' # propField is the name of the property (from the SD file) you want to use # as the "activity" propField = 'chemical_shift_1' # similarity threshold for a pair to be considered interesting. # (i.e. pairs with a similiarity below this value will not be # added to the output. similarityThreshold = 0.5 if __name__ == '__main__': suppl = Chem.SDMolSupplier(sys.argv[1]) outF = file(sys.argv[2], 'w+') data = [] logger.info('reading molecules and generating fingeprints') for i, mol in enumerate(suppl): if not mol: continue smi = Chem.MolToSmiles(mol, True) nm = mol.GetProp(nameField) property = float(mol.GetProp(propField)) fp = GetMolFingerprint(mol, maxPathLength) data.append((nm, smi, property, fp)) logger.info(' got %d molecules' % len(data)) logger.info('calculating pairs') pairs = [] for i in range(len(data)): for j in range(i + 1, len(data)): if DataStructs.DiceSimilarity(data[i][-1], data[j][-1]) > similarityThreshold: pairs.append((i, j)) if not (i + 1) % 100: logger.info('Done %d molecules' % (i + 1)) logger.info(' got %d reasonable pairs' % len(pairs)) logger.info('creating output file') print >> outF, 'nameA|nameB|nameAB|smilesA|smilesB|smilesAB|actA|actB|dAct|dist|disparity' for i, j in pairs: if data[i][2] < data[j][2]: i, j = j, i nmi, smii, propi, fpi = data[i] nmj, smij, propj, fpj = data[j] dAct = propi - propj dist = 1. - DataStructs.DiceSimilarity(fpi, fpj) if dist != 0: disparity = dAct / dist else: disparity = 1000 print >> outF, '%s|%s|%s_%s|%s|%s|%s.%s|%f|%f|%f|%f|%f' % ( nmi, nmj, nmi, nmj, smii, smij, smii, smij, propi, propj, dAct, dist, disparity)