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O2 perception (#756)
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Fixes an issue with perceiving O2 as a triplet from xyz
test added
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@calvinp0
calvinp0 authored Jul 9, 2024
2 parents 8b3b841 + b9b3304 commit 0d16383
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Showing 2 changed files with 39 additions and 28 deletions.
7 changes: 7 additions & 0 deletions arc/species/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1380,6 +1380,13 @@ def molecules_from_xyz(xyz: Optional[Union[dict, str]],
return None, None
xyz = check_xyz_dict(xyz)

if xyz['symbols'] == ('O', 'O') and multiplicity != 1:
coords = np.asarray(xyz['coords'], dtype=np.float32)
vector = coords[0] - coords[1]
if float(np.dot(vector, vector) ** 0.5) < 1.4:
# Special case for O2 triplet
return Molecule(smiles='[O][O]'), Molecule(smiles='[O][O]')

# 1. Generate a molecule with no bond order information with atoms ordered as in xyz.
mol_graph = MolGraph(symbols=xyz['symbols'], coords=xyz['coords'])
inferred_connections = mol_graph.infer_connections()
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60 changes: 32 additions & 28 deletions arc/species/converter_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3481,37 +3481,37 @@ def test_xyz_to_smiles(self):
C 0.00000000 0.00000000 -0.50136500
H 0.00000000 0.00000000 -1.57173600"""

# xyz9 = """S -0.00866000 -0.60254900 0.00000000
# N -0.96878800 0.63275900 0.00000000
# N 1.01229100 0.58298500 0.00000000"""
#
# xyz10 = """O -0.79494500 -0.93969200 0.00000000
# O -0.32753500 1.24003800 0.00000000
# O 1.28811400 -0.24729000 0.00000000
# N 0.14143500 0.11571500 0.00000000
# H -1.65602000 -0.48026800 0.00000000"""
#
# xyz11 = """O 1.64973000 -0.57433600 0.02610800
# O 0.49836300 1.28744800 -0.18806200
# N -0.57621600 -0.65116600 0.24595200
# N -1.78357200 -0.10211200 -0.14953800
# N 0.61460400 0.08152700 -0.00952700
# H -0.42001200 -1.61494900 -0.03311600
# H -1.72480300 0.33507600 -1.06884500
# H -2.07362100 0.59363400 0.53038600"""
xyz9 = """S -0.00866000 -0.60254900 0.00000000
N -0.96878800 0.63275900 0.00000000
N 1.01229100 0.58298500 0.00000000"""

xyz10 = """O -0.79494500 -0.93969200 0.00000000
O -0.32753500 1.24003800 0.00000000
O 1.28811400 -0.24729000 0.00000000
N 0.14143500 0.11571500 0.00000000
H -1.65602000 -0.48026800 0.00000000"""

xyz11 = """O 1.64973000 -0.57433600 0.02610800
O 0.49836300 1.28744800 -0.18806200
N -0.57621600 -0.65116600 0.24595200
N -1.78357200 -0.10211200 -0.14953800
N 0.61460400 0.08152700 -0.00952700
H -0.42001200 -1.61494900 -0.03311600
H -1.72480300 0.33507600 -1.06884500
H -2.07362100 0.59363400 0.53038600"""

xyz12 = """O 1.10621000 0.00000000 -0.13455300
O -1.10621000 0.00000000 -0.13455300
N 0.00000000 0.00000000 0.33490500"""

# xyz13 = """O -0.37723000 -1.27051900 0.00000000
# N -0.12115000 -0.04252600 0.00000000
# N -0.95339100 0.91468300 0.00000000
# C 1.31648000 0.33217600 0.00000000
# H 1.76422500 -0.11051900 -0.89038300
# H 1.76422500 -0.11051900 0.89038300
# H 1.40045900 1.41618100 0.00000000
# H -1.88127600 0.47189500 0.00000000"""
xyz13 = """O -0.37723000 -1.27051900 0.00000000
N -0.12115000 -0.04252600 0.00000000
N -0.95339100 0.91468300 0.00000000
C 1.31648000 0.33217600 0.00000000
H 1.76422500 -0.11051900 -0.89038300
H 1.76422500 -0.11051900 0.89038300
H 1.40045900 1.41618100 0.00000000
H -1.88127600 0.47189500 0.00000000"""

xyz14 = """S -0.12942800 0.11104800 0.22427200
O 0.98591500 -1.00752300 -0.31179100
Expand Down Expand Up @@ -3576,7 +3576,7 @@ def test_xyz_to_smiles(self):
mol6 = converter.molecules_from_xyz(converter.str_to_xyz(xyz6), multiplicity=1)[1]
mol7 = converter.molecules_from_xyz(converter.str_to_xyz(xyz7), multiplicity=1)[1]
mol8 = converter.molecules_from_xyz(converter.str_to_xyz(xyz8))[1]
# mol9 = converter.molecules_from_xyz(converter.str_to_xyz(xyz9), multiplicity=1)[1]
mol9 = converter.molecules_from_xyz(converter.str_to_xyz(xyz9), multiplicity=1)[1]
# mol10 = converter.molecules_from_xyz(converter.str_to_xyz(xyz10))[1]
# mol11 = converter.molecules_from_xyz(converter.str_to_xyz(xyz11))[1]
mol12 = converter.molecules_from_xyz(converter.str_to_xyz(xyz12))[1]
Expand All @@ -3588,6 +3588,8 @@ def test_xyz_to_smiles(self):
mol18 = converter.molecules_from_xyz(converter.str_to_xyz(xyz18))[1]
mol19 = converter.molecules_from_xyz(converter.str_to_xyz(xyz19))[1]
mol20 = converter.molecules_from_xyz(converter.str_to_xyz(xyz20))[1]
mol21 = converter.molecules_from_xyz("""O 0.0000000 0.0000000 0.6076340
O 0.0000000 0.0000000 -0.6076340""")[1]

self.assertEqual(mol1.to_smiles(), '[NH-][S+](=O)(O)C')
self.assertIn(mol2.to_smiles(), ['COC1=C(CO)C=C([C](C)C)C=C1', 'COC1C=CC(=CC=1CO)[C](C)C'])
Expand All @@ -3597,7 +3599,7 @@ def test_xyz_to_smiles(self):
self.assertEqual(mol6.to_smiles(), 'N#S')
self.assertEqual(mol7.to_smiles(), '[N-]=[NH2+]')
self.assertEqual(mol8.to_smiles(), 'C#N')
# self.assertEqual(mol9.to_smiles(), '[N-]=[S+]#N') # gives [N]S#N, multiplicity 3
self.assertEqual(mol9.to_smiles(), '[N-]=[S+]#N') # gives [N]S#N, multiplicity 3
# self.assertEqual(mol10.to_smiles(), '[N+](=O)(O)[O-]') # gives None
# self.assertEqual(mol11.to_smiles(), 'N(N)[N+](=O)[O-]') # gives None
self.assertEqual(mol12.to_smiles(), '[O]N=O')
Expand All @@ -3618,6 +3620,8 @@ def test_xyz_to_smiles(self):
8 H u0 p0 c0 {5,S}
""") # cannot read SMILES 'c1ncc[n]1' (but can generate them)
self.assertEqual(mol20.to_smiles(), 'C=C[CH]C=CC')
self.assertEqual(mol21.to_smiles(), '[O][O]')
self.assertEqual(mol21.multiplicity, 3)

def test_to_rdkit_mol(self):
"""Test converting an RMG Molecule object to an RDKit Molecule object"""
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