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Tests: Extended perception test
To allow another SMILES string. Actually, the test isn't great, the multiplicity cannot be 1, it should probably be 2. However, multiplicity 2 gives an even worse result with many radicals: 'OCCC(C(COO)(O[CH2])C)(C[C]1[CH][CH][C]([CH][CH]1)NO)SC' (all carbon atoms on the benzene ring are marked as having a radical). This is out of scope for the current linear TS adapter PR. The fix should be easy (detect a possibly aromatic ring with all radicals, at least for the C-only case, then make it aromatic). Leaving it as is for now since this is indeed a crazy molecule.
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arc/species/perceive_test.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1415,7 +1415,9 @@ def test_a_collection_of_molecules_from_various_arc_tests(self):
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(-5.67928065, 0.23893607, 2.30792673), (-1.02113438, 2.82848721, 1.61108522),
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(-2.77629877, 2.75649408, 1.89754068), (-1.71528969, 1.64716863, 2.70183805))}
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mol = perceive_molecule_from_xyz(xyz_crazy, charge=0, multiplicity=1, n_fragments=1)
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self.assertIn(mol.to_smiles(), ['OCCC(C(COO)(O[CH2])C)(Cc1ccc(cc1)NO)SC', 'OCCC(C(COO)(O[CH2])C)(CC1=C[CH]C(=C[CH]1)NO)SC'])
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self.assertIn(mol.to_smiles(), ['OCCC(C(COO)(O[CH2])C)(Cc1ccc(cc1)NO)SC',
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'OCCC(C(COO)(O[CH2])C)(CC1=C[CH]C(=C[CH]1)NO)SC',
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'OCCC(C(COO)(O[CH2])C)(C[C]1C=C[C](C=C1)NO)SC'])
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xyz_nhfcl = """N -0.14626256 0.12816405 0.30745256
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F -0.94719775 -0.91910939 -0.09669786

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