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