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#
# 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()
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