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8892fb160a
* make sure that we can build without boost iostreams or seralization adds some "private" variables on the python side to check for these compilation flags * get out minimal cmake version correct * get minimallib js building installs an up-to-date cmake also updates the version of boost being used for the minimallib adds extra argument to allow the repo to be specified
740 lines
30 KiB
Python
740 lines
30 KiB
Python
# Copyright (C) 2017-2021 Novartis Institute of BioMedical Research
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# and other RDKit contributors
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#
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# All Rights Reserved
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are
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# met:
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#
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above
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# copyright notice, this list of conditions and the following
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# disclaimer in the documentation and/or other materials provided
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# with the distribution.
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# * Neither the name of Novartis Institutes for BioMedical Research Inc.
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# nor the names of its contributors may be used to endorse or promote
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# products derived from this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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""" This is a rough coverage test of the python wrapper for the SubstructLibrary
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it is intended to be shallow but broad.
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"""
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import doctest
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import logging
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import os
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import sys
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import unittest
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from rdkit import RDConfig, RDLogger, rdBase
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from rdkit.RDLogger import logger
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logger = logger()
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import pickle
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import tempfile
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import time
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from rdkit import Chem
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from rdkit.Chem import rdSubstructLibrary, rdGeneralizedSubstruct, rdTautomerQuery
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def load_tests(loader, tests, ignore):
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tests.addTests(doctest.DocTestSuite(rdSubstructLibrary))
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return tests
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def makeStereoExamples():
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el = "NO"
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mols = []
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for e in el:
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for e2 in el:
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if e != e2:
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smi = "C1CCO[C@@](%s)(%s)1" % (e, e2)
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m = Chem.MolFromSmiles(smi)
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if m:
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mols.append(m)
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smi = "C1CCO[C@](%s)(%s)1" % (e, e2)
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m = Chem.MolFromSmiles(smi)
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if m:
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mols.append(m)
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return mols
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class TestCase(unittest.TestCase):
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def setUp(self):
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pass
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def test0SubstructLibrary(self):
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for keyholderCls in [None, rdSubstructLibrary.KeyFromPropHolder]:
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for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
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for holder in [
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rdSubstructLibrary.MolHolder(),
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rdSubstructLibrary.CachedMolHolder(),
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rdSubstructLibrary.CachedSmilesMolHolder()
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]:
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if fpholderCls:
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fpholder = fpholderCls()
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else:
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fpholder = None
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if keyholderCls:
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keyholder = keyholderCls()
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self.assertEqual(keyholder.GetPropName(), "_Name")
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else:
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keyholder = None
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slib_ = rdSubstructLibrary.SubstructLibrary(holder, fpholder, keyholder)
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for i in range(100):
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m = Chem.MolFromSmiles("c1ccccc1")
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m.SetProp("_Name", str(i))
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self.assertEqual(slib_.AddMol(m), i)
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libs = [slib_]
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if rdSubstructLibrary.SubstructLibraryCanSerialize():
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serialized1 = pickle.loads(pickle.dumps(slib_))
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serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
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libs.append(serialized1)
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libs.append(serialized2)
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for slib in libs:
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res = slib.GetMatches(m)
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if keyholderCls:
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for idx in res:
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self.assertEqual(str(idx), slib.GetKeyHolder().GetKey(idx))
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self.assertEqual([str(idx) for idx in res], list(slib.GetKeyHolder().GetKeys(res)))
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t2 = time.time()
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self.assertTrue(len(res) == 100)
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res = slib.GetMatches(m)
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self.assertEqual(len(res), 100)
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self.assertTrue(set(res) == set(list(range(100))))
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res = slib.GetMatches(m, maxResults=100)
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self.assertEqual(len(res), 100)
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self.assertEqual(len(slib.GetMatches(m, startIdx=0, endIdx=100)), 100)
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self.assertTrue(slib.HasMatch(m))
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self.assertEqual(slib.CountMatches(m), 100)
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def test1SubstructLibrary(self):
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for keyholderCls in [None, rdSubstructLibrary.KeyFromPropHolder]:
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for fpholderCls in [None, rdSubstructLibrary.PatternHolder]:
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for holder in [
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rdSubstructLibrary.MolHolder(),
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rdSubstructLibrary.CachedMolHolder(),
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rdSubstructLibrary.CachedSmilesMolHolder()
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]:
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if fpholderCls:
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fpholder = fpholderCls()
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else:
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fpholder = None
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if keyholderCls:
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keyholder = keyholderCls()
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self.assertEqual(keyholder.GetPropName(), "_Name")
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else:
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keyholder = None
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slib_ = rdSubstructLibrary.SubstructLibrary(holder, fpholder, keyholder)
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mols = []
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for i in range(100):
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m = Chem.MolFromSmiles("c1ccccc1")
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m.SetProp("_Name", str(i * 2))
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self.assertEqual(slib_.AddMol(m), i * 2)
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mols.append(m)
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m2 = Chem.MolFromSmiles("CCCC")
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m2.SetProp("_Name", str(i * 2 + 1))
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self.assertEqual(slib_.AddMol(m2), i * 2 + 1)
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mols.append(m2)
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libs = [slib_]
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if rdSubstructLibrary.SubstructLibraryCanSerialize():
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serialized1 = pickle.loads(pickle.dumps(slib_))
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serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
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libs.append(serialized1)
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libs.append(serialized2)
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for slib in libs:
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res = slib.GetMatches(m)
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self.assertEqual(len(res), 100)
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self.assertEqual(set(res), set(list(range(0, 200, 2))))
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if keyholderCls:
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self.assertEqual([str(idx) for idx in res], [str(idx) for idx in range(0, 200, 2)])
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res = slib.GetMatches(m2)
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self.assertEqual(len(res), 100)
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self.assertTrue(set(res) == set(list(range(1, 200, 2))))
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if keyholderCls:
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self.assertEqual([str(idx) for idx in res], [str(idx) for idx in range(1, 200, 2)])
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res = slib.GetMatches(m)
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self.assertEqual(len(res), 100)
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res = slib.GetMatches(m, maxResults=100)
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self.assertEqual(len(res), 100)
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self.assertEqual(len(slib.GetMatches(m, startIdx=0, endIdx=50 * 2)), 50)
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self.assertEqual(len(slib.GetMatches(m2, startIdx=1, endIdx=50 * 2 + 1)), 50)
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self.assertTrue(slib.HasMatch(m))
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self.assertTrue(slib.HasMatch(m2))
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self.assertEqual(slib.CountMatches(m), 100)
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self.assertEqual(slib.CountMatches(m2), 100)
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def testOptions(self):
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mols = makeStereoExamples() * 10
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for holderCls in [
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rdSubstructLibrary.MolHolder,
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rdSubstructLibrary.CachedMolHolder,
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rdSubstructLibrary.CachedSmilesMolHolder,
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rdSubstructLibrary.CachedTrustedSmilesMolHolder,
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]:
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holder = holderCls()
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slib_ = rdSubstructLibrary.SubstructLibrary(holder, None)
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for mol in mols:
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slib_.AddMol(mol)
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libs = [slib_]
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if rdSubstructLibrary.SubstructLibraryCanSerialize():
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serialized1 = pickle.loads(pickle.dumps(slib_))
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serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
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libs.append(serialized1)
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libs.append(serialized2)
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for slib in libs:
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
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core.SetProp("core", "core")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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def testSmilesCache(self):
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mols = makeStereoExamples() * 10
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holder = rdSubstructLibrary.CachedSmilesMolHolder()
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slib_ = rdSubstructLibrary.SubstructLibrary(holder, None)
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for mol in mols:
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holder.AddSmiles(Chem.MolToSmiles(mol, isomericSmiles=True))
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libs = [slib_]
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if rdSubstructLibrary.SubstructLibraryCanSerialize():
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serialized1 = pickle.loads(pickle.dumps(slib_))
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serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
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libs.append(serialized1)
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libs.append(serialized2)
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for slib in libs:
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
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core.SetProp("core", "core")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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def testTrustedSmilesCache(self):
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mols = makeStereoExamples() * 10
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holder = rdSubstructLibrary.CachedTrustedSmilesMolHolder()
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slib_ = rdSubstructLibrary.SubstructLibrary(holder, None)
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for mol in mols:
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holder.AddSmiles(Chem.MolToSmiles(mol, isomericSmiles=True))
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libs = [slib_]
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if rdSubstructLibrary.SubstructLibraryCanSerialize():
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serialized1 = pickle.loads(pickle.dumps(slib_))
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serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
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libs.append(serialized1)
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libs.append(serialized2)
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for slib in libs:
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
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core.SetProp("core", "core")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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def testBinaryCache(self):
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mols = makeStereoExamples() * 10
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holder = rdSubstructLibrary.CachedMolHolder()
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slib_ = rdSubstructLibrary.SubstructLibrary(holder, None)
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for mol in mols:
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holder.AddBinary(mol.ToBinary())
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libs = [slib_]
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if rdSubstructLibrary.SubstructLibraryCanSerialize():
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serialized1 = pickle.loads(pickle.dumps(slib_))
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serialized2 = rdSubstructLibrary.SubstructLibrary(slib_.Serialize())
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libs.append(serialized1)
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libs.append(serialized2)
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for slib in libs:
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-*)(-*)1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-C(-[O])(-[N])1")
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core.SetProp("core", "core")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core, useChirality=False)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=False)]))
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core = Chem.MolFromSmarts("C-1-C-C-O-[C@@](-[O])(-[N])1")
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res = slib.GetMatches(core)
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self.assertEqual(len(res),
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len([x for x in mols if x.HasSubstructMatch(core, useChirality=True)]))
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def testRingSmartsWithTrustedSmiles(self):
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pat = Chem.MolFromSmarts("[C&R1]")
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pat2 = Chem.MolFromSmarts("C@C") # ring bond
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holder = rdSubstructLibrary.CachedTrustedSmilesMolHolder()
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lib = rdSubstructLibrary.SubstructLibrary(holder)
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lib.AddMol(Chem.MolFromSmiles("C1CC1"))
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# make sure we can get an unsanitized molecule that fails (no ring info)
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print("Testing atom rings")
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with self.assertRaises(RuntimeError):
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holder.GetMol(0).HasSubstructMatch(pat)
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print("testing bond rings")
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with self.assertRaises(RuntimeError):
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holder.GetMol(0).HasSubstructMatch(pat2)
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# shouldn't throw
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print("searching atom rings")
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self.assertEqual(len(lib.GetMatches(pat)), 1)
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self.assertEqual(lib.CountMatches(pat), 1)
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print("searching bond rings")
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self.assertEqual(len(lib.GetMatches(pat2)), 1)
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self.assertEqual(lib.CountMatches(pat2), 1)
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print("done")
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@unittest.skipIf(not rdBase._serializationEnabled, "not built with serialization support")
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def test_init_from_and_to_stream(self):
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mols = makeStereoExamples() * 10
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holder = rdSubstructLibrary.CachedSmilesMolHolder()
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# one day I'll fix this, but we need to write text but read binary
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# grrr.... something about the python_streambuf handler.
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slib = rdSubstructLibrary.SubstructLibrary(holder, None)
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for mol in mols:
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holder.AddSmiles(Chem.MolToSmiles(mol, isomericSmiles=True))
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if rdSubstructLibrary.SubstructLibraryCanSerialize():
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fd, path = tempfile.mkstemp()
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with open(path, 'w') as file:
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slib.ToStream(file)
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with open(path, 'rb') as file:
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slib2 = rdSubstructLibrary.SubstructLibrary()
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slib2.InitFromStream(file)
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self.assertEqual(len(slib), len(slib2))
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from io import BytesIO, StringIO
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s = StringIO()
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slib.ToStream(s)
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sb = BytesIO(s.getvalue().encode("ascii"))
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self.assertTrue(len(sb.getvalue()) > 0)
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slib3 = rdSubstructLibrary.SubstructLibrary()
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slib3.InitFromStream(sb)
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self.assertEqual(len(slib), len(slib2))
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def test_addpatterns(self):
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pdb_ligands = [
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"CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1",
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"COc1ccc(S(=O)(=O)NCC2CC2)cc1Nc1ncc(-c2cccc(-c3cccnc3)c2)o1",
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"COc1ccc(-c2oc3ncnc(N)c3c2-c2ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cc2)cc1",
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"COC(=O)Nc1nc2ccc(Oc3ccc(NC(=O)Nc4cc(C(F)(F)F)ccc4F)cc3)cc2[nH]1",
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"COc1cc(Nc2ncnc(-c3cccnc3Nc3ccccc3)n2)cc(OC)c1OC",
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"O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1", "O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
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"CNC(=O)c1cc(Oc2ccc3[nH]c(Nc4ccc(Cl)c(C(F)(F)F)c4)nc3c2)ccn1",
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"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
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"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
|
|
"COc1cc2nccc(Oc3ccc4c(c3)OCCN4C(=O)Nc3ccc(Cl)cc3)c2cc1OC",
|
|
"CNC(=O)c1c(C)oc2cc(Oc3cc[nH+]c4cc(OCCN5CCOCC5)ccc34)ccc12",
|
|
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
|
|
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
|
|
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
|
|
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
|
|
"Cc1ccc(C(=O)Nc2cc(CCC[NH+](C)C)cc(C(F)(F)F)c2)cc1Nc1ncccc1-c1ccncn1",
|
|
"COc1cc(Nc2nccc(Nc3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
|
|
"COc1cc(Nc2nccc(N(C)c3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
|
|
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1", "Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
|
|
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
|
|
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
|
|
"CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21", "CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21"
|
|
]
|
|
|
|
for patterns in [
|
|
rdSubstructLibrary.PatternHolder(),
|
|
rdSubstructLibrary.TautomerPatternHolder()
|
|
]:
|
|
mols = [Chem.MolFromSmiles(smi) for smi in pdb_ligands]
|
|
holder = rdSubstructLibrary.CachedMolHolder()
|
|
slib_with_patterns = rdSubstructLibrary.SubstructLibrary(holder, patterns)
|
|
|
|
for mol in mols:
|
|
slib_with_patterns.AddMol(mol)
|
|
|
|
for nthreads in [1, 2, 0]:
|
|
slib_without_patterns = rdSubstructLibrary.SubstructLibrary(holder, None)
|
|
rdSubstructLibrary.AddPatterns(slib_without_patterns, nthreads)
|
|
# check for seg fault
|
|
# were the fingerprints really created
|
|
slib_without_patterns.GetFpHolder().GetFingerprint(0)
|
|
for mol in mols:
|
|
l1 = slib_with_patterns.CountMatches(mol)
|
|
l2 = slib_without_patterns.CountMatches(mol)
|
|
self.assertTrue(l1)
|
|
self.assertEqual(l1, l2)
|
|
|
|
def test_basic_addpatterns(self):
|
|
# add mols
|
|
pdb_ligands = [
|
|
"CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1",
|
|
"COc1ccc(S(=O)(=O)NCC2CC2)cc1Nc1ncc(-c2cccc(-c3cccnc3)c2)o1",
|
|
"COc1ccc(-c2oc3ncnc(N)c3c2-c2ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cc2)cc1",
|
|
"COC(=O)Nc1nc2ccc(Oc3ccc(NC(=O)Nc4cc(C(F)(F)F)ccc4F)cc3)cc2[nH]1",
|
|
"COc1cc(Nc2ncnc(-c3cccnc3Nc3ccccc3)n2)cc(OC)c1OC",
|
|
"O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1", "O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
|
|
"CNC(=O)c1cc(Oc2ccc3[nH]c(Nc4ccc(Cl)c(C(F)(F)F)c4)nc3c2)ccn1",
|
|
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
|
|
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
|
|
"COc1cc2nccc(Oc3ccc4c(c3)OCCN4C(=O)Nc3ccc(Cl)cc3)c2cc1OC",
|
|
"CNC(=O)c1c(C)oc2cc(Oc3cc[nH+]c4cc(OCCN5CCOCC5)ccc34)ccc12",
|
|
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
|
|
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
|
|
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
|
|
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
|
|
"Cc1ccc(C(=O)Nc2cc(CCC[NH+](C)C)cc(C(F)(F)F)c2)cc1Nc1ncccc1-c1ccncn1",
|
|
"COc1cc(Nc2nccc(Nc3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
|
|
"COc1cc(Nc2nccc(N(C)c3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
|
|
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1", "Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
|
|
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
|
|
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
|
|
"CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21", "CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21"
|
|
]
|
|
|
|
for holder in [
|
|
rdSubstructLibrary.CachedSmilesMolHolder(),
|
|
rdSubstructLibrary.CachedTrustedSmilesMolHolder()
|
|
]:
|
|
for smi in pdb_ligands:
|
|
holder.AddSmiles(smi)
|
|
|
|
for patttern in [
|
|
None,
|
|
rdSubstructLibrary.PatternHolder(),
|
|
rdSubstructLibrary.TautomerPatternHolder()
|
|
]:
|
|
lib = rdSubstructLibrary.SubstructLibrary(holder)
|
|
rdSubstructLibrary.AddPatterns(lib, numThreads=-1)
|
|
self.assertEqual(len(lib.GetMolHolder()), len(lib.GetFpHolder()))
|
|
for smi in pdb_ligands:
|
|
self.assertTrue(lib.CountMatches(Chem.MolFromSmiles(smi)))
|
|
|
|
def test_PatternHolder(self):
|
|
for holder in [rdSubstructLibrary.PatternHolder, rdSubstructLibrary.TautomerPatternHolder]:
|
|
fname = os.path.join(os.environ["RDBASE"], "Data", "NCI", "first_5K.smi")
|
|
suppl = Chem.SmilesMolSupplier(fname, delimiter="\t", titleLine=False)
|
|
mols1 = rdSubstructLibrary.CachedTrustedSmilesMolHolder()
|
|
fps1 = holder(2048)
|
|
ssslib1 = rdSubstructLibrary.SubstructLibrary(mols1, fps1)
|
|
mols2 = rdSubstructLibrary.CachedTrustedSmilesMolHolder()
|
|
fps2 = holder()
|
|
ssslib2 = rdSubstructLibrary.SubstructLibrary(mols2, fps2)
|
|
|
|
RDLogger.DisableLog('rdApp.error')
|
|
for i in range(0, 1000, 10):
|
|
try:
|
|
mol = suppl[i]
|
|
except Exception:
|
|
continue
|
|
if (not mol):
|
|
continue
|
|
mols1.AddSmiles(Chem.MolToSmiles(mol))
|
|
fps1.AddFingerprint(fps1.MakeFingerprint(mol))
|
|
ssslib2.AddMol(mol)
|
|
RDLogger.EnableLog('rdApp.error')
|
|
query = Chem.MolFromSmarts("N")
|
|
self.assertIsNotNone(query)
|
|
matches1 = sorted(ssslib1.GetMatches(query))
|
|
matches2 = sorted(ssslib2.GetMatches(query))
|
|
self.assertEqual(len(matches1), len(matches2))
|
|
self.assertTrue(all([m1 == matches2[i] for i, m1 in enumerate(matches1)]))
|
|
|
|
def testMolBundles(self):
|
|
ssl = rdSubstructLibrary.SubstructLibrary()
|
|
for smi in ('CCOC', 'CCNC', 'COOCOO', 'CCNC', 'CCCC'):
|
|
ssl.AddMol(Chem.MolFromSmiles(smi))
|
|
bndl = Chem.MolBundle()
|
|
for smi in ('COC', 'CCC'):
|
|
bndl.AddMol(Chem.MolFromSmiles(smi))
|
|
self.assertEqual(list(ssl.GetMatches(bndl)), [0, 4])
|
|
bndl.AddMol(Chem.MolFromSmiles('CN'))
|
|
self.assertEqual(list(sorted(ssl.GetMatches(bndl))), [0, 1, 3, 4])
|
|
|
|
def testSubstructParameters(self):
|
|
ssl = rdSubstructLibrary.SubstructLibrary()
|
|
for smi in ('C[C@H](F)Cl', 'C[C@@H](F)Cl', 'CC(F)Cl'):
|
|
ssl.AddMol(Chem.MolFromSmiles(smi))
|
|
bndl = Chem.MolBundle()
|
|
for smi in ('C[C@H](F)Cl', ):
|
|
bndl.AddMol(Chem.MolFromSmiles(smi))
|
|
params = Chem.SubstructMatchParameters()
|
|
self.assertEqual(list(sorted(ssl.GetMatches(bndl, params))), [0, 1, 2])
|
|
|
|
params.useChirality = True
|
|
self.assertEqual(list(sorted(ssl.GetMatches(bndl, params))), [0])
|
|
|
|
def testSearchOrder(self):
|
|
for keyholder in [None, rdSubstructLibrary.KeyFromPropHolder()]:
|
|
ssl = rdSubstructLibrary.SubstructLibrary(rdSubstructLibrary.MolHolder(), keyholder)
|
|
for idx, smi in enumerate(("CCCOC", "CCCCOCC", "CCOC", "COC", "CCCCCOC")):
|
|
m = Chem.MolFromSmiles(smi)
|
|
m.SetProp("_Name", str(idx))
|
|
ssl.AddMol(m)
|
|
|
|
ssl.SetSearchOrder((3, 2, 0, 1, 4))
|
|
self.assertEqual(ssl.GetSearchOrder(), (3, 2, 0, 1, 4))
|
|
qm = Chem.MolFromSmiles('COC')
|
|
self.assertEqual(list(ssl.GetMatches(qm, maxResults=2)), [3, 2])
|
|
self.assertEqual(list(ssl.GetMatches(qm, maxResults=2)), [3, 2])
|
|
if keyholder:
|
|
self.assertEqual(keyholder.GetPropName(), "_Name")
|
|
self.assertEqual(list(ssl.GetKeyHolder().GetKeys(ssl.GetMatches(qm, maxResults=2))),
|
|
['3', '2'])
|
|
|
|
# make sure we can clear the search order:
|
|
ssl.SetSearchOrder(None)
|
|
self.assertEqual(ssl.GetSearchOrder(), ())
|
|
|
|
ssl.SetSearchOrder((3, 2, 0, 1, 4))
|
|
self.assertEqual(ssl.GetSearchOrder(), (3, 2, 0, 1, 4))
|
|
|
|
ssl.SetSearchOrder([])
|
|
self.assertEqual(ssl.GetSearchOrder(), ())
|
|
|
|
def testSearchOrder2(self):
|
|
ssl = rdSubstructLibrary.SubstructLibrary()
|
|
for smi in ("CCCOC", "CCCCOCC", "CCOC", "COC", "CCCCCOC"):
|
|
ssl.AddMol(Chem.MolFromSmiles(smi))
|
|
|
|
def setSearchSmallestFirst(sslib):
|
|
searchOrder = list(range(len(sslib)))
|
|
holder = sslib.GetMolHolder()
|
|
searchOrder.sort(key=lambda x, holder=holder: holder.GetMol(x).GetNumAtoms())
|
|
sslib.SetSearchOrder(searchOrder)
|
|
|
|
setSearchSmallestFirst(ssl)
|
|
qm = Chem.MolFromSmiles('COC')
|
|
self.assertEqual(list(ssl.GetMatches(qm)), [3, 2, 0, 1, 4])
|
|
|
|
def testPropHolder(self):
|
|
for propname in [None, 'foo']:
|
|
if propname is None:
|
|
keyholder = rdSubstructLibrary.KeyFromPropHolder()
|
|
else:
|
|
keyholder = rdSubstructLibrary.KeyFromPropHolder(propname)
|
|
|
|
library = rdSubstructLibrary.SubstructLibrary(rdSubstructLibrary.MolHolder(), keyholder)
|
|
m = Chem.MolFromSmiles('CCC')
|
|
if propname is None:
|
|
self.assertEqual(keyholder.GetPropName(), "_Name")
|
|
else:
|
|
self.assertEqual(keyholder.GetPropName(), propname)
|
|
|
|
if propname:
|
|
m.SetProp(propname, 'Z11234')
|
|
else:
|
|
m.SetProp("_Name", 'Z11234')
|
|
|
|
library.AddMol(m)
|
|
indices = library.GetMatches(m)
|
|
self.assertEqual(['Z11234'], list(library.GetKeyHolder().GetKeys(indices)))
|
|
|
|
def test_bad_smiles(self):
|
|
# add mols
|
|
pdb_ligands = [
|
|
"&CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1",
|
|
"&COc1ccc(S(=O)(=O)NCC2CC2)cc1Nc1ncc(-c2cccc(-c3cccnc3)c2)o1",
|
|
"&COc1ccc(-c2oc3ncnc(N)c3c2-c2ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cc2)cc1",
|
|
"&COC(=O)Nc1nc2ccc(Oc3ccc(NC(=O)Nc4cc(C(F)(F)F)ccc4F)cc3)cc2[nH]1",
|
|
"&COc1cc(Nc2ncnc(-c3cccnc3Nc3ccccc3)n2)cc(OC)c1OC",
|
|
"&O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
|
|
"&O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
|
|
"&CNC(=O)c1cc(Oc2ccc3[nH]c(Nc4ccc(Cl)c(C(F)(F)F)c4)nc3c2)ccn1",
|
|
"&CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
|
|
"&CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
|
|
"&COc1cc2nccc(Oc3ccc4c(c3)OCCN4C(=O)Nc3ccc(Cl)cc3)c2cc1OC",
|
|
"&CNC(=O)c1c(C)oc2cc(Oc3cc[nH+]c4cc(OCCN5CCOCC5)ccc34)ccc12",
|
|
"&COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
|
|
"&COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
|
|
"&COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
|
|
"&COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
|
|
"&Cc1ccc(C(=O)Nc2cc(CCC[NH+](C)C)cc(C(F)(F)F)c2)cc1Nc1ncccc1-c1ccncn1",
|
|
"&COc1cc(Nc2nccc(Nc3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
|
|
"&COc1cc(Nc2nccc(N(C)c3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
|
|
"&Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"&Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"&Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
|
|
"&Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
|
|
"&Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"&Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
|
|
"&O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
|
|
"&O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
|
|
"&CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21", "&CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21"
|
|
]
|
|
# this test is really verbose, so disable the actual output without
|
|
# disabling that logging happens.
|
|
rdBase.LogToPythonLogger()
|
|
pylog = logging.getLogger("rdkit")
|
|
pylog.setLevel(logging.CRITICAL)
|
|
for holder in [
|
|
rdSubstructLibrary.CachedSmilesMolHolder(),
|
|
rdSubstructLibrary.CachedTrustedSmilesMolHolder()
|
|
]:
|
|
for smi in pdb_ligands:
|
|
holder.AddSmiles(smi)
|
|
lib = rdSubstructLibrary.SubstructLibrary(holder)
|
|
# this should excercise the logger
|
|
smi = "CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1"
|
|
self.assertEqual(0, lib.CountMatches(Chem.MolFromSmiles(smi)))
|
|
|
|
# test add patterns
|
|
rdSubstructLibrary.AddPatterns(lib, -1)
|
|
pylog.setLevel(logging.WARN)
|
|
rdBase.LogToCppStreams()
|
|
|
|
@unittest.skipIf(not rdBase._serializationEnabled, "not built with serialization support")
|
|
def test_using_xqms(self):
|
|
smis = ["COCC=O", "COOCC=O", "COOOCC=O", "COOOOCC=O"]
|
|
|
|
for holder in [
|
|
rdSubstructLibrary.CachedSmilesMolHolder(),
|
|
rdSubstructLibrary.CachedTrustedSmilesMolHolder()
|
|
]:
|
|
for smi in smis:
|
|
holder.AddSmiles(smi)
|
|
fph = rdSubstructLibrary.TautomerPatternHolder()
|
|
lib = rdSubstructLibrary.SubstructLibrary(holder)
|
|
|
|
mol = Chem.MolFromSmiles("COCC")
|
|
xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(mol)
|
|
res = lib.GetMatches(xqm)
|
|
self.assertEqual(list(res), [0])
|
|
self.assertTrue(lib.HasMatch(xqm))
|
|
self.assertEqual(lib.CountMatches(xqm), 1)
|
|
|
|
mol = Chem.MolFromSmiles("COC=CO")
|
|
xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(mol)
|
|
res = lib.GetMatches(xqm)
|
|
self.assertEqual(list(res), [0])
|
|
self.assertTrue(lib.HasMatch(xqm))
|
|
self.assertEqual(lib.CountMatches(xqm), 1)
|
|
|
|
mol = Chem.MolFromSmiles("COCC |LN:1:1.3|")
|
|
xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(mol)
|
|
res = lib.GetMatches(xqm)
|
|
self.assertEqual(list(res), [0, 1, 2])
|
|
self.assertTrue(lib.HasMatch(xqm))
|
|
self.assertEqual(lib.CountMatches(xqm), 3)
|
|
|
|
mol = Chem.MolFromSmiles("COC=CO |LN:1:1.3|")
|
|
xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(mol)
|
|
res = lib.GetMatches(xqm)
|
|
self.assertEqual(list(res), [0, 1, 2])
|
|
self.assertTrue(lib.HasMatch(xqm))
|
|
self.assertEqual(lib.CountMatches(xqm), 3)
|
|
|
|
mol = Chem.MolFromSmiles("CNC=CO |LN:1:1.3|")
|
|
xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(mol)
|
|
res = lib.GetMatches(xqm)
|
|
self.assertEqual(list(res), [])
|
|
self.assertFalse(lib.HasMatch(xqm))
|
|
self.assertEqual(lib.CountMatches(xqm), 0)
|
|
|
|
|
|
if __name__ == '__main__':
|
|
unittest.main()
|