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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 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: Name<tab>SMARTS<tab>Note
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))
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