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https://github.com/rdkit/rdkit.git
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ef90a4bedf
* extra SSS match functions for atoms/bonds initial implementation and testing * add baseline to test * add a functor for matching atom coords * support the extra checks in python * refactor the way the python callbacks are handled * test tolerances * expose the AtomCoordsMatcher to python * allow the extra checks to override the default matching --------- Co-authored-by: = <=>
119 lines
3.6 KiB
Python
119 lines
3.6 KiB
Python
#
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# Copyright (C) 2025 Greg Landrum
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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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#
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#
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import unittest
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from rdkit import Chem
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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 testExtraAtomMatch(self):
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"""Test setting extra atom matching functions """
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mol = Chem.MolFromSmiles('CCCC')
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mol.GetAtomWithIdx(1).SetIntProp('foo', 1)
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mol.GetAtomWithIdx(2).SetIntProp('foo', 2)
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patt = Chem.MolFromSmiles('CC')
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patt.GetAtomWithIdx(0).SetIntProp('bar', 2)
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patt.GetAtomWithIdx(1).SetIntProp('bar', 1)
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def atomCheck(qatom, ratom):
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if not qatom.HasProp('bar') or not ratom.HasProp('foo'):
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return False
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return qatom.GetIntProp('bar') == ratom.GetIntProp('foo')
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matches = mol.GetSubstructMatches(patt)
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self.assertEqual(len(matches), 3)
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params = Chem.SubstructMatchParameters()
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params.setExtraAtomCheckFunc(atomCheck)
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matches = mol.GetSubstructMatches(patt, params)
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self.assertEqual(len(matches), 1)
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self.assertEqual(matches[0], (2, 1))
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# override default check
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patt = Chem.MolFromSmiles('CO')
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patt.GetAtomWithIdx(0).SetIntProp('bar', 2)
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patt.GetAtomWithIdx(1).SetIntProp('bar', 1)
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matches = mol.GetSubstructMatches(patt, params)
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self.assertEqual(len(matches), 0)
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params.extraAtomCheckOverridesDefaultCheck = True
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matches = mol.GetSubstructMatches(patt, params)
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self.assertEqual(len(matches), 1)
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self.assertEqual(matches[0], (2, 1))
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def testExtraBondMatch(self):
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"""Test setting extra bond matching functions """
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mol = Chem.MolFromSmiles('CCCC')
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mol.GetBondWithIdx(1).SetIntProp('foo', 1)
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patt = Chem.MolFromSmiles('CC')
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patt.GetBondWithIdx(0).SetIntProp('bar', 1)
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def bondCheck(qbond, rbond):
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if not qbond.HasProp('bar') or not rbond.HasProp('foo'):
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return False
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return qbond.GetIntProp('bar') == rbond.GetIntProp('foo')
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matches = mol.GetSubstructMatches(patt)
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self.assertEqual(len(matches), 3)
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params = Chem.SubstructMatchParameters()
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params.setExtraBondCheckFunc(bondCheck)
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matches = mol.GetSubstructMatches(patt, params)
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self.assertEqual(len(matches), 1)
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self.assertEqual(matches[0], (1, 2))
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# override default check
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patt = Chem.MolFromSmiles('C=C')
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patt.GetBondWithIdx(0).SetIntProp('bar', 1)
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matches = mol.GetSubstructMatches(patt, params)
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self.assertEqual(len(matches), 0)
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params.extraBondCheckOverridesDefaultCheck = True
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matches = mol.GetSubstructMatches(patt, params)
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self.assertEqual(len(matches), 1)
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self.assertEqual(matches[0], (1, 2))
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def testCoordsFunctor(self):
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m = Chem.MolFromSmiles('CCCC |(0,0,0;1,0,0;2,0,0;3,0,0)|')
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patt = Chem.MolFromSmiles('CC |(3,0,0.1;2,0,0)|')
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params = Chem.SubstructMatchParameters()
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coordMatcher = Chem.AtomCoordsMatcher(tol=.11)
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params.setExtraAtomCheckFunc(coordMatcher)
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matches = m.GetSubstructMatches(patt, params)
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self.assertEqual(len(matches), 1)
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self.assertEqual(matches[0], (3, 2))
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# lifetime management 1:
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coordMatcher = None
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matches = m.GetSubstructMatches(patt, params)
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self.assertEqual(len(matches), 1)
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self.assertEqual(matches[0], (3, 2))
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# lifetime management 2:
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params.setExtraAtomCheckFunc(Chem.AtomCoordsMatcher(tol=.11))
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matches = m.GetSubstructMatches(patt, params)
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self.assertEqual(len(matches), 1)
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self.assertEqual(matches[0], (3, 2))
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if __name__ == '__main__':
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unittest.main()
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