def test_topology_virtualsites_atom_indexing(self):
"""
Add multiple instances of the same molecule, but in a different
order, and ensure that virtual site particles are indexed correctly
"""
topology = Topology()
topology.add_molecule(create_ethanol())
topology.add_molecule(create_ethanol())
topology.add_molecule(create_reversed_ethanol())
# Add a virtualsite to the reference ethanol
for ref_mol in topology.reference_molecules:
atoms = [ref_mol.atoms[i] for i in [0, 1]]
ref_mol._add_bond_charge_virtual_site(
atoms,
0.5 * unit.angstrom,
)
virtual_site_topology_atom_indices = [(0, 1), (9, 10), (26, 25)]
for top_vs, expected_indices in zip(
topology.topology_virtual_sites,
virtual_site_topology_atom_indices):
assert (tuple([at.topology_particle_index
for at in top_vs.atoms]) == expected_indices)
assert top_vs.atom(
0).topology_particle_index == expected_indices[0]
assert top_vs.atom(
1).topology_particle_index == expected_indices[1]
def test_unsupported_mixing_rule():
molecules = [create_ethanol()]
pdbfile = app.PDBFile(get_data_file_path("systems/test_systems/1_ethanol.pdb"))
topology = OFFBioTop.from_openmm(pdbfile.topology, unique_molecules=molecules)
topology.mdtop = md.Topology.from_openmm(topology.to_openmm())
forcefield = ForceField("test_forcefields/test_forcefield.offxml")
openff_sys = Interchange.from_smirnoff(force_field=forcefield, topology=topology)
openff_sys["vdW"].mixing_rule = "geometric"
with pytest.raises(UnsupportedExportError, match="default NonbondedForce"):
openff_sys.to_openmm(combine_nonbonded_forces=True)
def test_to_file_multi_molecule_different_order(self):
"""
Checks for the following if Topology.to_write maintains the order of atoms
for the same molecule with different indexing
"""
from tempfile import NamedTemporaryFile
from openff.toolkit.tests.test_forcefield import (
create_ethanol,
create_reversed_ethanol,
)
from openff.toolkit.topology import Molecule, Topology
topology = Topology()
topology.add_molecule(create_ethanol())
topology.add_molecule(create_reversed_ethanol())
mol = Molecule.from_pdb_and_smiles(
get_data_file_path("systems/test_systems/1_ethanol.pdb"), "CCO")
positions = mol.conformers[0]
# Make up coordinates for the second ethanol by translating the first by 10 angstroms
# (note that this will still be a gibberish conformation, since the atom order in the second molecule is different)
positions = np.concatenate(
[positions, positions + 10.0 * unit.angstrom])
element_order = []
with NamedTemporaryFile(suffix=".pdb") as iofile:
topology.to_file(iofile.name, positions)
data = open(iofile.name).readlines()
for line in data:
if line.startswith("HETATM"):
element_order.append(line.strip()[-1])
assert element_order == [
"C",
"C",
"O",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"O",
"C",
"C",
]
def test_from_openmm_missing_reference(self):
"""Test creation of an OpenFF Topology object from an OpenMM Topology when missing a unique molecule"""
from simtk.openmm import app
pdbfile = app.PDBFile(
get_data_file_path(
"systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb"))
molecules = [create_ethanol()]
with pytest.raises(
ValueError,
match="No match found for molecule C6H12") as excinfo:
topology = Topology.from_openmm(pdbfile.topology,
unique_molecules=molecules)
def test_openmm_nonbonded_methods(inputs):
"""See test_nonbonded_method_resolution in openff/toolkit/tests/test_forcefield.py"""
vdw_method = inputs["vdw_method"]
electrostatics_method = inputs["electrostatics_method"]
periodic = inputs["periodic"]
result = inputs["result"]
molecules = [create_ethanol()]
forcefield = ForceField("test_forcefields/test_forcefield.offxml")
pdbfile = app.PDBFile(get_data_file_path("systems/test_systems/1_ethanol.pdb"))
topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules)
if not periodic:
topology.box_vectors = None
if type(result) == int:
nonbonded_method = result
# The method is validated and may raise an exception if it's not supported.
forcefield.get_parameter_handler("vdW", {}).method = vdw_method
forcefield.get_parameter_handler(
"Electrostatics", {}
).method = electrostatics_method
openff_interchange = Interchange.from_smirnoff(
force_field=forcefield, topology=topology
)
openmm_system = openff_interchange.to_openmm(combine_nonbonded_forces=True)
for force in openmm_system.getForces():
if isinstance(force, openmm.NonbondedForce):
assert force.getNonbondedMethod() == nonbonded_method
break
else:
raise Exception
elif issubclass(result, (BaseException, Exception)):
exception = result
forcefield.get_parameter_handler("vdW", {}).method = vdw_method
forcefield.get_parameter_handler(
"Electrostatics", {}
).method = electrostatics_method
openff_interchange = Interchange.from_smirnoff(
force_field=forcefield, topology=topology
)
with pytest.raises(exception):
openff_interchange.to_openmm(combine_nonbonded_forces=True)
else:
raise Exception("uh oh")
def test_from_openmm(self):
"""Test creation of an OpenFF Topology object from an OpenMM Topology and component molecules"""
from simtk.openmm import app
pdbfile = app.PDBFile(
get_data_file_path(
"systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb"))
with pytest.raises(MissingUniqueMoleculesError,
match="requires a list of Molecule objects"):
Topology.from_openmm(pdbfile.topology)
molecules = [create_ethanol(), create_cyclohexane()]
topology = Topology.from_openmm(pdbfile.topology,
unique_molecules=molecules)
assert topology.n_reference_molecules == 2
assert topology.n_topology_molecules == 239