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Save atom hybridization #408

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1966ea3
save the atom hybridization
jthorton Nov 14, 2024
c287bc1
Merge branch 'main' into atom_hybridization
IAlibay Nov 18, 2024
1844c0a
Merge branch 'main' into atom_hybridization
IAlibay Nov 20, 2024
70540f5
use try except for missing hybridization data
jthorton Nov 22, 2024
27bd913
Merge remote-tracking branch 'origin/atom_hybridization' into atom_hy…
jthorton Nov 22, 2024
e4867fc
fix and expand tests
jthorton Nov 22, 2024
adab104
Merge branch 'main' into atom_hybridization
jthorton Nov 25, 2024
1e40b08
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 25, 2024
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17 changes: 16 additions & 1 deletion gufe/components/smallmoleculecomponent.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,20 @@
5: Chem.rdchem.BondStereo.STEREOTRANS}
_BONDSTEREO_TO_INT = {v: k for k, v in _INT_TO_BONDSTEREO.items()}

# following the numbering in rdkit
_INT_TO_HYBRIDIZATION = {
0: Chem.rdchem.HybridizationType.UNSPECIFIED,
1: Chem.rdchem.HybridizationType.S,
2: Chem.rdchem.HybridizationType.SP,
3: Chem.rdchem.HybridizationType.SP2,
4: Chem.rdchem.HybridizationType.SP3,
5: Chem.rdchem.HybridizationType.SP2D,
6: Chem.rdchem.HybridizationType.SP3D,
7: Chem.rdchem.HybridizationType.SP3D2,
8: Chem.rdchem.HybridizationType.OTHER
}
_HYBRIDIZATION_TO_INT = {v: k for k, v in _INT_TO_HYBRIDIZATION.items()}


def _setprops(obj, d: dict) -> None:
# add props onto rdkit "obj" (atom/bond/mol/conformer)
Expand Down Expand Up @@ -213,7 +227,7 @@ def _to_dict(self) -> dict:
atoms.append((
atom.GetAtomicNum(), atom.GetIsotope(), atom.GetFormalCharge(), atom.GetIsAromatic(),
_ATOMCHIRAL_TO_INT[atom.GetChiralTag()], atom.GetAtomMapNum(),
atom.GetPropsAsDict(includePrivate=False),
atom.GetPropsAsDict(includePrivate=False), _HYBRIDIZATION_TO_INT[atom.GetHybridization()]
))
output['atoms'] = atoms

Expand Down Expand Up @@ -247,6 +261,7 @@ def _from_dict(cls, d: dict):
a.SetChiralTag(_INT_TO_ATOMCHIRAL[atom[4]])
a.SetAtomMapNum(atom[5])
_setprops(a, atom[6])
a.SetHybridization(_INT_TO_HYBRIDIZATION[atom[7]])
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em.AddAtom(a)

for bond in d['bonds']:
Expand Down
12 changes: 12 additions & 0 deletions gufe/tests/test_smallmoleculecomponent.py
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Original file line number Diff line number Diff line change
Expand Up @@ -330,6 +330,18 @@ def test_to_dict(self, phenol):

assert isinstance(d, dict)

def test_to_dict_hybridization(self, phenol):
"""
Make sure dict round trip saves the hybridization
<https://github.com/OpenFreeEnergy/gufe/issues/407>
"""
phenol_dict = phenol.to_dict()
TOKENIZABLE_REGISTRY.clear()
new_phenol = SmallMoleculeComponent.from_dict(phenol_dict)
for atom in new_phenol.to_rdkit().GetAtoms():
if atom.GetAtomicNum() == 6:
assert atom.GetHybridization() == Chem.rdchem.HybridizationType.SP2

@pytest.mark.skipif(not HAS_OFFTK, reason="no openff toolkit available")
def test_deserialize_roundtrip(self, toluene, phenol):
roundtrip = SmallMoleculeComponent.from_dict(phenol.to_dict())
Expand Down
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