def test_angle_potential_handler(self):
top = OFFBioTop.from_molecules(Molecule.from_smiles("CCC"))
angle_handler = AngleHandler(version=0.3)
angle_parameter = AngleHandler.AngleType(
smirks="[*:1]~[*:2]~[*:3]",
k=2.5 * simtk_unit.kilocalorie_per_mole / simtk_unit.radian**2,
angle=100 * simtk_unit.degree,
id="b1000",
)
angle_handler.add_parameter(angle_parameter.to_dict())
forcefield = ForceField()
forcefield.register_parameter_handler(angle_handler)
angle_potentials = SMIRNOFFAngleHandler._from_toolkit(
parameter_handler=forcefield["Angles"],
topology=top,
)
top_key = TopologyKey(atom_indices=(0, 1, 2))
pot_key = angle_potentials.slot_map[top_key]
assert pot_key.associated_handler == "Angles"
pot = angle_potentials.potentials[pot_key]
kcal_mol_rad2 = unit.Unit("kilocalorie / (mole * radian ** 2)")
assert pot.parameters["k"].to(
kcal_mol_rad2).magnitude == pytest.approx(2.5)
def store_matches(self, parameter_handler: AngleHandler,
topology: Topology) -> None:
"""
Populate self.slot_map with key-val pairs of slots
and unique potential identifiers
"""
matches = parameter_handler.find_matches(topology)
for key, val in matches.items():
key = str(key)
self.slot_map[key] = val.parameter_type.smirks
def store_matches(self, parameter_handler: AngleHandler,
topology: Topology) -> None:
"""
Populate self.slot_map with key-val pairs of slots
and unique potential identifiers
"""
matches = parameter_handler.find_matches(topology)
for key, val in matches.items():
topology_key = TopologyKey(atom_indices=key)
potential_key = PotentialKey(id=val.parameter_type.smirks)
self.slot_map[topology_key] = potential_key
def test_angle_potential_handler(self):
top = Topology.from_molecules(Molecule.from_smiles("CCC"))
angle_handler = AngleHandler(version=0.3)
angle_parameter = AngleHandler.AngleType(
smirks="[*:1]~[*:2]~[*:3]",
k=2.5 * omm_unit.kilocalorie_per_mole / omm_unit.radian**2,
angle=100 * omm_unit.degree,
id="b1000",
)
angle_handler.add_parameter(angle_parameter.to_dict())
from openff.system.stubs import ForceField
forcefield = ForceField()
forcefield.register_parameter_handler(angle_handler)
angle_potentials = forcefield["Angles"].create_potential(top)
top_key = TopologyKey(atom_indices=(0, 1, 2))
pot = angle_potentials.potentials[angle_potentials.slot_map[top_key]]
kcal_mol_rad2 = unit.Unit("kilocalorie / (mole * radian ** 2)")
assert pot.parameters["k"].to(
kcal_mol_rad2).magnitude == pytest.approx(2.5)
def store_potentials(self, parameter_handler: AngleHandler) -> None:
"""
Populate self.potentials with key-val pairs of unique potential
identifiers and their associated Potential objects
"""
for smirks in self.slot_map.values():
# ParameterHandler.get_parameter returns a list, although this
# should only ever be length 1
parameter_type = parameter_handler.get_parameter(
{"smirks": smirks})[0]
potential = Potential(parameters={
"k": parameter_type.k,
"angle": parameter_type.angle,
}, )
self.potentials[smirks] = potential
def test_allowed_parameter_handler_types(self):
class DummyParameterHandler(ParameterHandler):
pass
class DummySMIRNOFFHandler(SMIRNOFFPotentialHandler):
type = "Bonds"
expression = "1+1"
@classmethod
def allowed_parameter_handlers(cls):
return [DummyParameterHandler]
@classmethod
def supported_parameters(cls):
return list()
dummy_handler = DummySMIRNOFFHandler()
angle_Handler = AngleHandler(version=0.3)
assert DummyParameterHandler in dummy_handler.allowed_parameter_handlers(
)
assert AngleHandler not in dummy_handler.allowed_parameter_handlers()
assert (DummyParameterHandler
not in SMIRNOFFAngleHandler.allowed_parameter_handlers())
dummy_handler = DummyParameterHandler(version=0.3)
with pytest.raises(InvalidParameterHandlerError):
SMIRNOFFAngleHandler._from_toolkit(
parameter_handler=dummy_handler,
topology=Topology(),
)
with pytest.raises(InvalidParameterHandlerError):
DummySMIRNOFFHandler._from_toolkit(
parameter_handler=angle_Handler,
topology=Topology(),
)