# # Copyright (C) 2020 Greg Landrum and T5 Informatics GmbH # @@ 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 rdAbbreviations class TestCase(unittest.TestCase): def setUp(self): self.defaultAbbrevs = rdAbbreviations.GetDefaultAbbreviations() self.defaultLinkers = rdAbbreviations.GetDefaultLinkers() self.customLinkers = rdAbbreviations.ParseLinkers('''PEG3 *OCCOCCOCC* PEG3 Pent *CCCCC* Cy *C1CCC(*)CC1 Cy''') self.parseMapping = lambda mapping: tuple(map(int, mapping.strip('[],').split(','))) def testParsingAbbrevs(self): defn = '''CO2Et C(=O)OCC COOEt C(=O)OCC OiBu OCC(C)C tBu C(C)(C)C''' abbrevs = rdAbbreviations.ParseAbbreviations(defn) m = Chem.MolFromSmiles('CCC(=O)OCC') nm = rdAbbreviations.CondenseMolAbbreviations(m, abbrevs, maxCoverage=1.0) self.assertEqual(Chem.MolToCXSmiles(nm), '*CC |$CO2Et;;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (0, 1, 2)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (0, 1)) def testCondense(self): m = Chem.MolFromSmiles('FC(F)(F)CC(=O)O') nm = rdAbbreviations.CondenseMolAbbreviations(m, self.defaultAbbrevs, maxCoverage=1.0) self.assertEqual(Chem.MolToCXSmiles(nm), '*C* |$CF3;;CO2H$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (1, 4, 5)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (3, 4)) m = Chem.MolFromSmiles('CCC(F)(F)F') nm = rdAbbreviations.CondenseMolAbbreviations(m, self.defaultAbbrevs) self.assertEqual(Chem.MolToCXSmiles(nm), '*C(F)(F)F |$Et;;;;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (1, 2, 3, 4, 5)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (1, 2, 3, 4)) # make sure we don't mess up chirality m = Chem.MolFromSmiles('FC(F)(F)[C@](Cl)(F)I') nm = rdAbbreviations.CondenseMolAbbreviations(m, self.defaultAbbrevs, maxCoverage=1.0) self.assertEqual(Chem.MolToCXSmiles(nm), '*[C@@](F)(Cl)I |$CF3;;;;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (1, 4, 5, 6, 7)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (3, 4, 5, 6)) def testLabel(self): m = Chem.MolFromSmiles('CC(C)CC(F)(F)F') nm = rdAbbreviations.LabelMolAbbreviations(m, self.defaultAbbrevs, maxCoverage=1.0) sgs = Chem.GetMolSubstanceGroups(nm) self.assertEqual(len(sgs), 2) self.assertEqual(sgs[0].GetProp('TYPE'), "SUP") self.assertEqual(sgs[0].GetProp('LABEL'), "iPr") self.assertEqual(list(sgs[0].GetAtoms()), [1, 0, 2]) self.assertEqual(list(sgs[0].GetBonds()), [2]) aps = sgs[0].GetAttachPoints() self.assertEqual(len(aps), 1) self.assertEqual(aps[0].aIdx, 1) self.assertEqual(aps[0].lvIdx, 3) self.assertEqual(sgs[1].GetProp('TYPE'), "SUP") self.assertEqual(sgs[1].GetProp('LABEL'), "CF3") self.assertEqual(list(sgs[1].GetAtoms()), [4, 5, 6, 7]) self.assertEqual(list(sgs[1].GetBonds()), [3]) aps = sgs[1].GetAttachPoints() self.assertEqual(len(aps), 1) self.assertEqual(aps[0].aIdx, 4) self.assertEqual(aps[0].lvIdx, 3) def testCondenseLinkers(self): m = Chem.MolFromSmiles('FCOCCOCCOCCCCCCCCCCl') nm = rdAbbreviations.CondenseMolAbbreviations(m, self.defaultLinkers, maxCoverage=1.0) self.assertEqual(Chem.MolToCXSmiles(nm), 'FC**Cl |$;;PEG3;Hept;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (0, 1, 2, 11, 18)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (0, 1, 10, 17)) m = Chem.MolFromSmiles('COC1CCC(C)CC1') nm = rdAbbreviations.CondenseMolAbbreviations(m, self.customLinkers, maxCoverage=1.0) self.assertEqual(Chem.MolToCXSmiles(nm), 'C*OC |$;Cy;;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (0, 1, 2, 6)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (0, 1, 5)) def testAbbreviationsAndLinkers(self): m = Chem.MolFromSmiles('COC1CCC(C)CC1') # wouldn't normally do this in this order: nm = rdAbbreviations.CondenseMolAbbreviations(m, self.defaultAbbrevs, maxCoverage=1.0) self.assertEqual(Chem.MolToCXSmiles(nm), '*C1CCC(C)CC1 |$OMe;;;;;;;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (1, 2, 3, 4, 5, 6, 7, 8)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (1, 2, 3, 4, 5, 6, 7, 8)) nm = rdAbbreviations.CondenseMolAbbreviations(nm, self.customLinkers, maxCoverage=1.0) self.assertEqual(Chem.MolToCXSmiles(nm), '**C |$OMe;Cy;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (1, 2, 6)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (1, 5)) # This is a more logical order nm = rdAbbreviations.CondenseMolAbbreviations(m, self.customLinkers, maxCoverage=1.0) self.assertEqual(Chem.MolToCXSmiles(nm), 'C*OC |$;Cy;;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (0, 1, 2, 6)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (0, 1, 5)) nm = rdAbbreviations.CondenseMolAbbreviations(nm, self.defaultAbbrevs, maxCoverage=1.0) self.assertEqual(Chem.MolToCXSmiles(nm), 'C*OC |$;Cy;;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (0, 1, 2, 6)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (0, 1, 5)) def testAbbreviationsSubstanceGroups(self): m = Chem.MolFromMolBlock(''' Mrv2014 09152006492D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 7 7 1 0 0 M V30 BEGIN ATOM M V30 1 C 5.25 -5.9858 0 0 M V30 2 C 4.48 -7.3196 0 0 M V30 3 C 6.02 -7.3196 0 0 M V30 4 F 8.6873 -8.8596 0 0 M V30 5 C 7.3537 -8.0896 0 0 M V30 6 F 6.02 -8.8596 0 0 M V30 7 F 7.3537 -6.5496 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 3 1 M V30 3 1 2 3 M V30 4 1 3 5 M V30 5 1 4 5 M V30 6 1 5 6 M V30 7 1 5 7 M V30 END BOND M V30 BEGIN SGROUP M V30 1 SUP 0 ATOMS=(4 4 5 6 7) SAP=(3 5 3 1) XBONDS=(1 4) LABEL=CF3 M V30 END SGROUP M V30 END CTAB M END''') nm = rdAbbreviations.CondenseAbbreviationSubstanceGroups(m) nm.RemoveAllConformers() # avoid coords in CXSMILES self.assertEqual(Chem.MolToCXSmiles(nm), '*C1CC1 |$CF3;;;$|') self.assertTrue(nm.HasProp('_origAtomMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origAtomMapping')), (0, 1, 2, 4)) self.assertTrue(nm.HasProp('_origBondMapping')) self.assertEqual(self.parseMapping(nm.GetProp('_origBondMapping')), (0, 1, 2, 3)) def testGithub3692(self): defaults = rdAbbreviations.GetDefaultAbbreviations() self.assertIsNotNone(defaults[0].mol) lbls = [x.label for x in defaults] self.assertIn('CO2Et', lbls) idx = lbls.index('CO2Et') self.assertEqual(Chem.MolToSmiles(defaults[idx].mol), '*C(=O)OCC') if __name__ == '__main__': # pragma: nocover unittest.main()