diff --git a/devtools/data/gen-serialized-results.py b/devtools/data/gen_serialized_results.py similarity index 93% rename from devtools/data/gen-serialized-results.py rename to devtools/data/gen_serialized_results.py index e402b8af..45546827 100644 --- a/devtools/data/gen-serialized-results.py +++ b/devtools/data/gen_serialized_results.py @@ -76,20 +76,25 @@ def execute_and_serialize(dag, protocol, simname): json.dump(outdict, zipfile, cls=JSON_HANDLER.encoder) -def generate_md_json(smc): +def generate_md_settings(): settings = PlainMDProtocol.default_settings() settings.simulation_settings.equilibration_length_nvt = 0.01 * unit.nanosecond settings.simulation_settings.equilibration_length = 0.01 * unit.nanosecond settings.simulation_settings.production_length = 0.01 * unit.nanosecond settings.forcefield_settings.nonbonded_method = "nocutoff" - protocol = PlainMDProtocol(settings=settings) + + return settings + + +def generate_md_json(smc): + protocol = PlainMDProtocol(settings=generate_md_settings()) system = openfe.ChemicalSystem({"ligand": smc}) dag = protocol.create(stateA=system, stateB=system, mapping=None) execute_and_serialize(dag, protocol, "MDProtocol") -def generate_ahfe_json(smc): +def generate_ahfe_settings(): settings = AbsoluteSolvationProtocol.default_settings() settings.solvent_equil_simulation_settings.equilibration_length_nvt = 10 * unit.picosecond settings.solvent_equil_simulation_settings.equilibration_length = 10 * unit.picosecond @@ -114,7 +119,11 @@ def generate_ahfe_json(smc): settings.vacuum_engine_settings.compute_platform = 'CPU' settings.solvent_engine_settings.compute_platform = 'CUDA' - protocol = AbsoluteSolvationProtocol(settings=settings) + return settings + + +def generate_ahfe_json(smc): + protocol = AbsoluteSolvationProtocol(settings=generate_ahfe_settings()) sysA = openfe.ChemicalSystem( {"ligand": smc, "solvent": openfe.SolventComponent()} ) @@ -127,12 +136,17 @@ def generate_ahfe_json(smc): execute_and_serialize(dag, protocol, "AHFEProtocol") -def generate_rfe_json(smcA, smcB): +def generate_rfe_settings(): settings = RelativeHybridTopologyProtocol.default_settings() settings.simulation_settings.equilibration_length = 10 * unit.picosecond settings.simulation_settings.production_length = 250 * unit.picosecond settings.forcefield_settings.nonbonded_method = "nocutoff" - protocol = RelativeHybridTopologyProtocol(settings=settings) + + return settings + + +def generate_rfe_json(smcA, smcB): + protocol = RelativeHybridTopologyProtocol(settings=generate_rfe_settings()) a_smcB = align_mol_shape(smcB, ref_mol=smcA) mapper = KartografAtomMapper(atom_map_hydrogens=True) diff --git a/openfe/tests/protocols/test_solvation_afe_tokenization.py b/openfe/tests/protocols/test_solvation_afe_tokenization.py index 0a2dd7f7..ebaf0399 100644 --- a/openfe/tests/protocols/test_solvation_afe_tokenization.py +++ b/openfe/tests/protocols/test_solvation_afe_tokenization.py @@ -49,7 +49,7 @@ def protocol_result(afe_solv_transformation_json): class TestAbsoluteSolvationProtocol(GufeTokenizableTestsMixin): cls = openmm_afe.AbsoluteSolvationProtocol - key = "AbsoluteSolvationProtocol-929d9a7e355abe8068bdf642cfc115fd" + key = "AbsoluteSolvationProtocol-ba5b74537c4cd1c039a603a9211c2617" repr = f"<{key}>" @pytest.fixture()