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Use utility functions in jsonutils to fix #151 #257

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merged 3 commits into from
Dec 4, 2024
Merged

Use utility functions in jsonutils to fix #151 #257

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5874160
use utility functions in jsonutils: string_to_tuple
rwxayheee Nov 30, 2024
638c4f4
remove unnecessary print
rwxayheee Nov 30, 2024
4b08a31
add test for dihedral JSON (de)serialization
diogomart Dec 4, 2024
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12 changes: 6 additions & 6 deletions meeko/molsetup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1377,7 +1377,7 @@ def from_json(obj):
obj["ring_closure_info"]["bonds_removed"],
obj["ring_closure_info"]["pseudos_by_atom"],
)
molsetup.rotamers = obj["rotamers"]
molsetup.rotamers = [{string_to_tuple(k, element_type=int): v for k,v in rotamer.items()} for rotamer in obj["rotamers"]]
molsetup.atom_params = obj["atom_params"]
molsetup.restraints = [Restraint.from_json(x) for x in obj["restraints"]]
molsetup.flexibility_model = obj["flexibility_model"]
Expand Down Expand Up @@ -2147,8 +2147,8 @@ def from_json(obj):
]
# TODO: Dihedral decoding may need another look
rdkit_molsetup.dihedral_interactions = obj["dihedral_interactions"]
rdkit_molsetup.dihedral_partaking_atoms = obj["dihedral_partaking_atoms"]
rdkit_molsetup.dihedral_labels = obj["dihedral_labels"]
rdkit_molsetup.dihedral_partaking_atoms = {string_to_tuple(k, element_type=int): v for k,v in obj["dihedral_partaking_atoms"].items()}
rdkit_molsetup.dihedral_labels = {string_to_tuple(k, element_type=int): v for k,v in obj["dihedral_labels"].items()}
rdkit_molsetup.atom_to_ring_id = {
int(k): [string_to_tuple(t) for t in v]
for k, v in obj["atom_to_ring_id"].items()
Expand Down Expand Up @@ -2332,7 +2332,7 @@ def default(self, obj):
for k, v in obj.rings.items()
},
"ring_closure_info": obj.ring_closure_info.__dict__,
"rotamers": obj.rotamers,
"rotamers": [{tuple_to_string(k): v for k, v in rotamer.items()} for rotamer in obj.rotamers],
"atom_params": obj.atom_params,
"restraints": [
self.restraint_encoder.default(x) for x in obj.restraints
Expand All @@ -2358,8 +2358,8 @@ def default(self, obj):
output_dict["mol"] = rdMolInterchange.MolToJSON(obj.mol)
output_dict["modified_atom_positions"] = obj.modified_atom_positions
output_dict["dihedral_interactions"] = obj.dihedral_interactions
output_dict["dihedral_partaking_atoms"] = obj.dihedral_partaking_atoms
output_dict["dihedral_labels"] = obj.dihedral_labels
output_dict["dihedral_partaking_atoms"] = {tuple_to_string(k): v for k,v in obj.dihedral_partaking_atoms.items()}
output_dict["dihedral_labels"] = {tuple_to_string(k): v for k,v in obj.dihedral_labels.items()}
output_dict["atom_to_ring_id"] = obj.atom_to_ring_id
output_dict["ring_corners"] = obj.ring_corners
output_dict["rmsd_symmetry_indices"] = obj.rmsd_symmetry_indices
Expand Down
24 changes: 24 additions & 0 deletions test/json_serialization_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,12 @@

from meeko.utils.pdbutils import PDBAtomInfo

try:
import openforcefields
_got_openff = True
except ImportError as err:
_got_openff = False

# from ..meeko.utils.pdbutils import PDBAtomInfo

pkgdir = pathlib.Path(meeko.__file__).parents[1]
Expand Down Expand Up @@ -413,6 +419,11 @@ def check_molsetup_equality(decoded_obj: MoleculeSetup, starting_obj: MoleculeSe
decoded_obj.restraints[idx], starting_obj.restraints[idx]
)

# dihedrals
assert decoded_obj.dihedral_partaking_atoms == starting_obj.dihedral_partaking_atoms
assert decoded_obj.dihedral_interactions == starting_obj.dihedral_interactions
assert decoded_obj.dihedral_labels == starting_obj.dihedral_labels

# Checking flexibility model
for key in starting_obj.flexibility_model:
assert key in decoded_obj.flexibility_model
Expand Down Expand Up @@ -763,5 +774,18 @@ def check_polymer_equality(
assert decoded_obj.log == starting_obj.log
return

@pytest.mark.skipif(not _got_openff, reason="requires openff-forcefields")
def test_dihedral_equality():
mk_prep = MoleculePreparation(
merge_these_atom_types=(),
dihedral_model="openff",
)
fn = str(pkgdir/"test"/"flexibility_data"/"non_sequential_atom_ordering_01.mol")
mol = Chem.MolFromMolFile(fn, removeHs=False)
starting_molsetup = mk_prep(mol)[0]
json_str = json.dumps(starting_molsetup, cls=MoleculeSetupEncoder)
decoded_molsetup = json.loads(json_str, object_hook=RDKitMoleculeSetup.from_json)
check_molsetup_equality(starting_molsetup, decoded_molsetup)
return

# endregion
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