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#! /usr/bin/env jython
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
# 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 GlaxoSmithKline Research & Development Ltd.
# 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 Jameed Hussain, July 2013
from __future__ import print_function
import sys
import re
import array
from chemaxon.util import MolHandler
from chemaxon.struc import Molecule
from chemaxon.descriptors import ChemicalFingerprint
from chemaxon.descriptors import CFParameters
from chemaxon.descriptors import SimilarityCalculatorFactory
def desalt(mol):
parmol = mol
smi = mol.toFormat("smiles")
parcount = 0
msmi = smi.split('.')
for smi in msmi:
mol = MolHandler(smi).getMolecule()
count = mol.getAtomCount()
if count > parcount:
parcount = count
parmol = mol
return parmol
cfp = CFParameters(
"<?xml version=\"1.0\" encoding=\"UTF-8\"?><ChemicalFingerprintConfiguration Version =\"0.3\" schemaLocation=\"cfp.xsd\"> <Parameters Length=\"1024\" BondCount=\"7\" BitCount=\"4\"/> <StandardizerConfiguration Version =\"0.1\"><Actions><Action ID=\"aromatize\" Act=\"aromatize\"/> </Actions> </StandardizerConfiguration><ScreeningConfiguration><ParametrizedMetrics><ParametrizedMetric Name=\"Tversky\" ActiveFamily=\"Generic\" Metric=\"Tversky\" Threshold=\"0.5\" TverskyAlpha=\"0.1\" TverskyBeta=\"0.9\"/></ParametrizedMetrics></ScreeningConfiguration></ChemicalFingerprintConfiguration>")
cfp.setLength(1024)
cfp.setBondCount(7)
cfp.setBitCount(4)
#output needs to look like this:
#qSubs,qSmi,qID,inSmi,id,tversky
#first read in queries
q_split_input = open("frag_q_split_out", 'r')
queries = []
for line in q_split_input:
info = line.rstrip().split(",")
#print info
#generate fp for query
#print info[2]
mol = MolHandler(info[2]).getMolecule()
mol.aromatize(Molecule.AROM_GENERAL)
qfp = ChemicalFingerprint(cfp)
qfp.generate(mol)
qintfp = array.array('i', list(map(int, qfp.toFloatArray())))
queries.append((qintfp, info[0], info[1], info[2]))
#print queries
for line in sys.stdin:
line_fields = re.split('\s|,', line)
dbsmi = line_fields[0]
dbid = line_fields[1]
mol = MolHandler(dbsmi).getMolecule()
mol_desalted = desalt(mol)
mol_desalted.aromatize(Molecule.AROM_GENERAL)
#print mol_desalted.toFormat("smiles")
fp = ChemicalFingerprint(cfp)
fp.generate(mol)
intfp = array.array('i', list(map(int, fp.toFloatArray())))
for q in queries:
qsmi = q[1]
qid = q[2]
qsub = q[3]
sc = SimilarityCalculatorFactory.create("Tversky;0.95;0.05")
sc.setQueryFingerprint(q[0])
tversky = sc.getSimilarity(intfp)
if (tversky >= 0.9):
print("%s,%s,%s,%s,%s,%s" % (qsub, qsmi, qid, dbsmi, dbid, tversky))
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