mirror of
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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
150 lines
7.1 KiB
Python
150 lines
7.1 KiB
Python
#
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# Copyright (C) 2023 Greg Landrum and other RDKit contributors
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# @@ All Rights Reserved @@
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#
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# This file is part of the RDKit.
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# The contents are covered by the terms of the BSD license
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# which is included in the file license.txt, found at the root
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# of the RDKit source tree.
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import unittest
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from rdkit import Chem
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from rdkit.Chem import rdGeneralizedSubstruct
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from rdkit import rdBase
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@unittest.skipIf(not rdBase._serializationEnabled, "not built with serialization support")
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class TestCase(unittest.TestCase):
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def test1CreationAndSubstruct(self):
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m = Chem.MolFromSmiles('COCc1n[nH]c(F)c1 |LN:1:1.3|')
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xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(m)
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mol = Chem.MolFromSmiles('COOCc1n[nH]c(F)c1')
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matches = rdGeneralizedSubstruct.MolGetSubstructMatches(mol, xqm)
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self.assertEqual(len(matches), 1)
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self.assertEqual(tuple(matches[0]), (0, 1, 2, 3, 4, 5, 9, 6, 7, 8))
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match = rdGeneralizedSubstruct.MolGetSubstructMatch(mol, xqm)
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self.assertEqual(tuple(match), (0, 1, 2, 3, 4, 5, 9, 6, 7, 8))
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self.assertTrue(rdGeneralizedSubstruct.MolHasSubstructMatch(mol, xqm))
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def test2Params(self):
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m = Chem.MolFromSmiles('COCc1n[nH]c(F)c1[C@H](F)Cl |LN:1:1.3|')
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xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(m)
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mol1 = Chem.MolFromSmiles('COOCc1n[nH]c(F)c1[C@H](F)Cl')
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mol2 = Chem.MolFromSmiles('COOCc1n[nH]c(F)c1[C@@H](F)Cl')
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm)), 1)
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params = Chem.SubstructMatchParameters()
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params.useChirality = True
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm, params)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm, params)), 0)
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def test3MultipleResults(self):
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m = Chem.MolFromSmiles('COC |LN:1:1.3|')
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xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(m)
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mol1 = Chem.MolFromSmiles('COOCC')
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mol2 = Chem.MolFromSmiles('COCC')
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params = Chem.SubstructMatchParameters()
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params.uniquify = False
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm, params)), 2)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm, params)), 2)
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def test4AdjustQueryProperties(self):
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m = Chem.MolFromSmiles('COCc1n[nH]cc1 |LN:1:1.3|')
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xqm1 = rdGeneralizedSubstruct.CreateExtendedQueryMol(m)
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xqm2 = rdGeneralizedSubstruct.CreateExtendedQueryMol(m, adjustQueryProperties=True)
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nops = Chem.AdjustQueryParameters.NoAdjustments()
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xqm3 = rdGeneralizedSubstruct.CreateExtendedQueryMol(m, adjustQueryProperties=True,
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adjustQueryParameters=nops)
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mol1 = Chem.MolFromSmiles('COCc1n[nH]cc1')
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mol2 = Chem.MolFromSmiles('COCc1n[nH]c(F)c1')
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm1)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm2)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm3)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm1)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm2)), 0)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm3)), 1)
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def test5ControlSteps(self):
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m = Chem.MolFromSmiles('COCC1OC(N)=N1 |LN:1:1.3|')
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xqm1 = rdGeneralizedSubstruct.CreateExtendedQueryMol(m)
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xqm2 = rdGeneralizedSubstruct.CreateExtendedQueryMol(m, doEnumeration=False)
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xqm3 = rdGeneralizedSubstruct.CreateExtendedQueryMol(m, doTautomers=False)
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xqm4 = rdGeneralizedSubstruct.CreateExtendedQueryMol(m, doEnumeration=False, doTautomers=False)
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mol1 = Chem.MolFromSmiles('COCC1OC(N)=N1')
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm1)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm2)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm3)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol1, xqm4)), 1)
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mol2 = Chem.MolFromSmiles('COCC1OC(=N)N1')
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self.assertEqual(len(mol2.GetSubstructMatches(m)), 0)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm1)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm2)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm3)), 0)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol2, xqm4)), 0)
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mol3 = Chem.MolFromSmiles('COOCC1OC(N)=N1')
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol3, xqm1)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol3, xqm2)), 0)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol3, xqm3)), 1)
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self.assertEqual(len(rdGeneralizedSubstruct.MolGetSubstructMatches(mol3, xqm4)), 0)
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def test6Serialization(self):
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m = Chem.MolFromSmiles('COCc1n[nH]c(F)c1 |LN:1:1.3|')
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xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(m)
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mol = Chem.MolFromSmiles('COOCc1n[nH]c(F)c1')
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matches = rdGeneralizedSubstruct.MolGetSubstructMatches(mol, xqm)
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self.assertEqual(len(matches), 1)
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self.assertEqual(tuple(matches[0]), (0, 1, 2, 3, 4, 5, 9, 6, 7, 8))
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xqm2 = rdGeneralizedSubstruct.ExtendedQueryMol(xqm.ToBinary())
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matches = rdGeneralizedSubstruct.MolGetSubstructMatches(mol, xqm2)
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self.assertEqual(len(matches), 1)
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def test7GenericMatchers(self):
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m = Chem.MolFromSmiles('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|')
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qps = Chem.AdjustQueryParameters.NoAdjustments()
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qps.makeDummiesQueries = True
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m = Chem.AdjustQueryProperties(m, qps)
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Chem.SetGenericQueriesFromProperties(m)
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ps = Chem.SubstructMatchParameters()
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ps.useGenericMatchers = True
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mol1 = Chem.MolFromSmiles('COC1=NNC(C=C)=C1')
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mol2 = Chem.MolFromSmiles('COC1=NNC(CC)=C1')
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mol3 = Chem.MolFromSmiles('COOC1=NNC(C=C)=C1')
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mol4 = Chem.MolFromSmiles('COOC1=NNC(CC)=C1')
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self.assertTrue(mol1.HasSubstructMatch(m, ps))
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self.assertFalse(mol2.HasSubstructMatch(m, ps))
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self.assertFalse(mol3.HasSubstructMatch(m, ps))
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self.assertFalse(mol4.HasSubstructMatch(m, ps))
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xqm = rdGeneralizedSubstruct.CreateExtendedQueryMol(m)
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self.assertTrue(rdGeneralizedSubstruct.MolHasSubstructMatch(mol1, xqm, ps))
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self.assertFalse(rdGeneralizedSubstruct.MolHasSubstructMatch(mol2, xqm, ps))
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self.assertTrue(rdGeneralizedSubstruct.MolHasSubstructMatch(mol3, xqm, ps))
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self.assertFalse(rdGeneralizedSubstruct.MolHasSubstructMatch(mol4, xqm, ps))
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xqm2 = rdGeneralizedSubstruct.ExtendedQueryMol(xqm.ToBinary())
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self.assertTrue(rdGeneralizedSubstruct.MolHasSubstructMatch(mol1, xqm2, ps))
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self.assertFalse(rdGeneralizedSubstruct.MolHasSubstructMatch(mol2, xqm2, ps))
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self.assertTrue(rdGeneralizedSubstruct.MolHasSubstructMatch(mol3, xqm2, ps))
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self.assertFalse(rdGeneralizedSubstruct.MolHasSubstructMatch(mol4, xqm2, ps))
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if __name__ == '__main__': # pragma: nocover
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unittest.main()
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