# # 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 BRICS import sys, cPickle, re inF = file(sys.argv[1], 'r') inLs = inF.readlines() delim = ' ' # definitions of the functional groups to look for and flag. # format is: NameSMARTSNote fgData = """AcidChloride C(=O)Cl Acid Chloride CarboxylicAcid C(=O)[O;H,-] Carboxylic acid SulfonylChloride [$(S-!@[#6])](=O)(=O)(Cl) Sulfonyl Chloride Amine [N;!H0;$(N-[#6]);!$(N-[!#6]);!$(N-C=[O,N,S])] Amine BoronicAcid [$(B-!@[#6])](O)(O) Boronic Acid Isocyanate [$(N-!@[#6])](=!@C=!@O) Isocyanate Alcohol [O;H1;$(O-!@[#6;!$(C=!@[O,N,S])])] Alcohol Aldehyde [CH;D2;!$(C-[!#6])]=O Aldehyde Halogen [$([Cl,Br,I]-!@[#6]);!$([Cl,Br,I]-!@C-!@[F,Cl,Br,I]);!$([Cl,Br,I]-[C,S](=[O,S,N]))] Halogen""" fglines = [re.split(r'\t+', x.strip()) for x in fgData.split('\n')] hLabels = [x[0] for x in fglines] patts = [Chem.MolFromSmarts(x[1]) for x in fglines] labels = inLs[0].strip().split(delim) + hLabels + ['HasBRICSBond?'] print(delim.join(labels)) for line in inLs[1:]: splitL = line.strip().split(delim) mol = Chem.MolFromSmiles(splitL[1]) for fg in patts: if mol.HasSubstructMatch(fg): splitL.append('True') else: splitL.append('False') bricsRes = BRICS.BRICSDecompose(mol) if len(bricsRes) > 1: splitL.append('True') else: splitL.append('False') print(delim.join(splitL))