diff --git a/devtools/data/gen-serialized-results.py b/devtools/data/gen-serialized-results.py index ccc5d728..bd74a01f 100644 --- a/devtools/data/gen-serialized-results.py +++ b/devtools/data/gen-serialized-results.py @@ -14,7 +14,12 @@ import json import logging import pathlib import tempfile -from openff.toolkit import Molecule +from openff.toolkit import ( + Molecule, RDKitToolkitWrapper, AmberToolsToolkitWrapper +) +from openff.toolkit.utils.toolkit_registry import ( + toolkit_registry_manager, ToolkitRegistry +) from openff.units import unit from kartograf.atom_aligner import align_mol_shape from kartograf import KartografAtomMapper @@ -31,11 +36,16 @@ logger = logging.getLogger(__name__) LIGA = "[H]C([H])([H])C([H])([H])C(=O)C([H])([H])C([H])([H])[H]" LIGB = "[H]C([H])([H])C(=O)C([H])([H])C([H])([H])C([H])([H])[H]" +amber_rdkit = ToolkitRegistry( + [RDKitToolkitWrapper(), AmberToolsToolkitWrapper()] +) + def get_molecule(smi, name): - m = Molecule.from_smiles(smi) - m.generate_conformers() - m.assign_partial_charges(partial_charge_method="am1bcc") + with toolkit_registry_manager(amber_rdkit): + m = Molecule.from_smiles(smi) + m.generate_conformers() + m.assign_partial_charges(partial_charge_method="am1bcc") return openfe.SmallMoleculeComponent.from_openff(m, name=name) diff --git a/openfe/tests/data/openmm_rfe/RHFEProtocol_json_results.gz b/openfe/tests/data/openmm_rfe/RHFEProtocol_json_results.gz index a5c27be5..6504e381 100644 Binary files a/openfe/tests/data/openmm_rfe/RHFEProtocol_json_results.gz and b/openfe/tests/data/openmm_rfe/RHFEProtocol_json_results.gz differ diff --git a/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py b/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py index 75b77c91..e404783b 100644 --- a/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py +++ b/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py @@ -1407,7 +1407,7 @@ class TestProtocolResult: est = protocolresult.get_estimate() assert est - assert est.m == pytest.approx(15.71, abs=0.3) + assert est.m == pytest.approx(16.85, abs=0.3) assert isinstance(est, unit.Quantity) assert est.is_compatible_with(unit.kilojoule_per_mole) @@ -1415,7 +1415,7 @@ class TestProtocolResult: est = protocolresult.get_uncertainty() assert est - assert est.m == pytest.approx(0.1, abs=0.1) + assert est.m == pytest.approx(0.1, abs=0.2) assert isinstance(est, unit.Quantity) assert est.is_compatible_with(unit.kilojoule_per_mole)