def test_optimization_submissions_with_constraints(fractal_compute_server):
"""
Make sure that the constraints are added to the optimization and enforced.
"""
client = FractalClient(fractal_compute_server)
ethane = Molecule.from_file(get_data("ethane.sdf"), "sdf")
factory = OptimizationDatasetFactory()
dataset = OptimizationDataset(
dataset_name="Test optimizations with constraint",
description="Test optimization dataset with constraints",
tagline="Testing optimization datasets")
# add just mm spec
dataset.add_qc_spec(method="openff-1.0.0",
basis="smirnoff",
program="openmm",
spec_name="default",
spec_description="mm default spec",
overwrite=True)
# build some constraints
constraints = Constraints()
constraints.add_set_constraint(constraint_type="dihedral",
indices=[2, 0, 1, 5],
value=60,
bonded=True)
constraints.add_freeze_constraint(constraint_type="distance",
indices=[0, 1],
bonded=True)
# add the molecule
attributes = factory.create_cmiles_metadata(ethane)
index = ethane.to_smiles()
dataset.add_molecule(index=index,
molecule=ethane,
attributes=attributes,
constraints=constraints)
# now add a mock url so we can submit the data
dataset.metadata.long_description_url = "https://test.org"
# now submit again
dataset.submit(client=client)
fractal_compute_server.await_results()
# make sure of the results are complete
ds = client.get_collection("OptimizationDataset", dataset.dataset_name)
record = ds.get_record(ds.df.index[0], "default")
assert "constraints" in record.keywords
assert record.status.value == "COMPLETE"
assert record.error is None
assert len(record.trajectory) > 1
# now make sure the constraints worked
final_molecule = record.get_final_molecule()
assert pytest.approx(60, final_molecule.measure((2, 0, 1, 5)))
assert pytest.approx(record.get_initial_molecule().measure((0, 1)),
final_molecule.measure((0, 1)))
def _create_qcsubmit_dataset(self, dataset_name, mols, season):
from openff.qcsubmit.factories import OptimizationDataset, OptimizationDatasetFactory
# create OptimizationDataset with QCSubmit
ds = OptimizationDataset(dataset_name=dataset_name)
factory = OptimizationDatasetFactory()
for mol in mols:
id = self._mol_to_id(mol)
attributes = factory.create_cmiles_metadata(mol)
ds.add_molecule(index=id, molecule=mol, attributes=attributes)
ds.qc_specifications = SEASONS[season]
ds.metadata.long_description_url = "https://localhost.local/null"
# add in known modifications to `OptimizationDataset` defaults
ds.optimization_procedure.coordsys = 'dlc'
ds.optimization_procedure.reset = True
return ds