def test_from_mdtraj(self):
"""Test construction of an OpenFF Topology from an MDTraj Topology object"""
import mdtraj as md
pdb_path = get_data_file_path(
"systems/test_systems/1_cyclohexane_1_ethanol.pdb")
trj = md.load(pdb_path)
with pytest.raises(MissingUniqueMoleculesError,
match="requires a list of Molecule objects"):
Topology.from_mdtraj(trj.top)
unique_molecules = [
Molecule.from_smiles(mol_name) for mol_name in ["C1CCCCC1", "CCO"]
]
top = Topology.from_mdtraj(trj.top, unique_molecules=unique_molecules)
assert top.n_topology_molecules == 2
assert top.n_topology_bonds == 26
def _atom_indices_by_role(
substance: Substance, coordinate_path: str
) -> Dict[Component.Role, List[int]]:
"""Retrieve the indices of the atoms which belong to components with a
specific role.
"""
import mdtraj
from openff.toolkit.topology import Molecule, Topology
# Split the substance into the components assigned each role.
components_by_role = _components_by_role(substance)
# Create OFF representations of the components
off_molecules = {
component: Molecule.from_smiles(component.smiles)
for components in components_by_role.values()
for component in components
}
# Load in the complex structure.
mdtraj_trajectory: mdtraj.Trajectory = mdtraj.load_pdb(coordinate_path)
off_topology: Topology = Topology.from_mdtraj(
mdtraj_trajectory.topology, off_molecules.values()
)
atom_indices = defaultdict(list)
for component_role in components_by_role:
for component in components_by_role[component_role]:
# Find the indices of all instances of this component.
off_molecule = off_molecules[component]
for topology_molecule in off_topology.topology_molecules:
if (
topology_molecule.reference_molecule.to_smiles()
!= off_molecule.to_smiles()
):
continue
atom_indices[component_role].extend(
[
i + topology_molecule.atom_start_topology_index
for i in range(topology_molecule.n_atoms)
]
)
return atom_indices
def test_compute_gradients(tmpdir, smirks, all_zeros):
# Load a short trajectory.
coordinate_path = get_data_filename("test/trajectories/water.pdb")
trajectory_path = get_data_filename("test/trajectories/water.dcd")
trajectory = mdtraj.load_dcd(trajectory_path, coordinate_path)
observables = ObservableFrame({
"PotentialEnergy":
ObservableArray(
np.zeros(len(trajectory)) * unit.kilojoule / unit.mole)
})
_compute_gradients(
[ParameterGradientKey("vdW", smirks, "epsilon")],
observables,
ForceField("openff-1.2.0.offxml"),
ThermodynamicState(298.15 * unit.kelvin, 1.0 * unit.atmosphere),
Topology.from_mdtraj(trajectory.topology, [Molecule.from_smiles("O")]),
trajectory,
ComputeResources(),
True,
)
assert len(
observables["PotentialEnergy"].gradients[0].value) == len(trajectory)
if all_zeros:
assert np.allclose(
observables["PotentialEnergy"].gradients[0].value,
0.0 * unit.kilojoule / unit.kilocalorie,
)
else:
assert not np.allclose(
observables["PotentialEnergy"].gradients[0].value,
0.0 * unit.kilojoule / unit.kilocalorie,
)
