def _write_bonds(lmp_file: IO, openff_sys: Interchange):
"""Write the Bonds section of a LAMMPS data file"""
lmp_file.write("\nBonds\n\n")
bond_handler = openff_sys["Bonds"]
bond_type_map = dict(enumerate(bond_handler.potentials))
bond_type_map_inv = dict({v: k for k, v in bond_type_map.items()})
for bond_idx, bond in enumerate(openff_sys.topology.mdtop.bonds):
# These are "topology indices"
indices = (
bond.atom1.index,
bond.atom2.index,
)
top_key = TopologyKey(atom_indices=indices)
if top_key in bond_handler.slot_map:
pot_key = bond_handler.slot_map[top_key]
else:
top_key = TopologyKey(atom_indices=indices[::-1])
pot_key = bond_handler.slot_map[top_key]
bond_type = bond_type_map_inv[pot_key]
lmp_file.write(
"{:d}\t{:d}\t{:d}\t{:d}\n".format(
bond_idx + 1,
bond_type + 1,
indices[0] + 1,
indices[1] + 1,
)
)
def _process_single_dihedral(
dihedral: "pmd.Dihedral",
dihedral_type: "pmd.DihedralType",
handler: Union["SMIRNOFFImproperTorsionHandler",
"SMIRNOFFProperTorsionHandler"],
mult: Optional[int] = None,
):
atom1 = dihedral.atom1
atom2 = dihedral.atom2
atom3 = dihedral.atom3
atom4 = dihedral.atom4
k = dihedral_type.phi_k * kcal_mol_rad2
periodicity = dihedral_type.per * unit.dimensionless
phase = dihedral_type.phase * unit.degree
if dihedral.improper:
# ParmEd stores the central atom _third_ (AMBER style)
# SMIRNOFF stores the central atom _second_
# https://parmed.github.io/ParmEd/html/topobj/parmed.topologyobjects.Dihedral.html#parmed-topologyobjects-dihedral
# https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html#impropertorsions
top_key = TopologyKey(
atom_indices=(atom1.idx, atom2.idx, atom2.idx, atom4.idx),
mult=mult,
)
pot_key = PotentialKey(
id=f"{atom1.idx}-{atom3.idx}-{atom2.idx}-{atom4.idx}",
mult=mult,
)
pot = Potential(parameters={
"k": k,
"periodicity": periodicity,
"phase": phase
})
if pot_key in handler.potentials:
raise Exception("fudging dihedral indices")
handler.slot_map.update({top_key: pot_key})
handler.potentials.update({pot_key: pot})
else:
top_key = TopologyKey(
atom_indices=(atom1.idx, atom2.idx, atom3.idx, atom4.idx),
mult=1,
)
pot_key = PotentialKey(
id=f"{atom1.idx}-{atom2.idx}-{atom3.idx}-{atom4.idx}",
mult=1,
)
pot = Potential(parameters={
"k": k,
"periodicity": periodicity,
"phase": phase
})
while pot_key in handler.potentials:
pot_key.mult += 1 # type: ignore[operator]
top_key.mult += 1 # type: ignore[operator]
handler.slot_map.update({top_key: pot_key})
handler.potentials.update({pot_key: pot})
def test_store_improper_torsion_matches(self):
formaldehyde: Molecule = Molecule.from_mapped_smiles(
"[H:3][C:1]([H:4])=[O:2]")
parameter_handler = ImproperTorsionHandler(version=0.3)
parameter_handler.add_parameter(
parameter=ImproperTorsionHandler.ImproperTorsionType(
smirks="[*:1]~[#6X3:2](~[*:3])~[*:4]",
periodicity1=2,
phase1=180.0 * simtk_unit.degree,
k1=1.1 * simtk_unit.kilocalorie_per_mole,
))
potential_handler = SMIRNOFFImproperTorsionHandler()
potential_handler.store_matches(parameter_handler,
formaldehyde.to_topology())
assert len(potential_handler.slot_map) == 3
assert (TopologyKey(atom_indices=(0, 1, 2, 3), mult=0)
in potential_handler.slot_map)
assert (TopologyKey(atom_indices=(0, 2, 3, 1), mult=0)
in potential_handler.slot_map)
assert (TopologyKey(atom_indices=(0, 3, 1, 2), mult=0)
in potential_handler.slot_map)
def store_matches(
self,
parameter_handler: Union["ElectrostaticsHandlerType",
List["ElectrostaticsHandlerType"]],
topology: Union["Topology", "OFFBioTop"],
) -> None:
"""
Populate self.slot_map with key-val pairs of slots
and unique potential identifiers
"""
# Reshape the parameter handlers into a dictionary for easier referencing.
parameter_handlers = {
handler._TAGNAME: handler
for handler in (parameter_handler if isinstance(
parameter_handler, list) else [parameter_handler])
}
self.potentials = dict()
self.slot_map = dict()
reference_molecules = [*topology.reference_molecules]
for reference_molecule in reference_molecules:
matches, potentials = self._find_reference_matches(
parameter_handlers, reference_molecule)
match_mults = defaultdict(set)
for top_key in matches:
match_mults[top_key.atom_indices].add(top_key.mult)
self.potentials.update(potentials)
for top_mol in topology._reference_molecule_to_topology_molecules[
reference_molecule]:
for topology_particle in top_mol.atoms:
reference_index = topology_particle.atom.molecule_particle_index
topology_index = topology_particle.topology_particle_index
for mult in match_mults[(reference_index, )]:
top_key = TopologyKey(atom_indices=(topology_index, ),
mult=mult)
self.slot_map[top_key] = matches[TopologyKey(
atom_indices=(reference_index, ), mult=mult)]
def _write_angles(lmp_file: IO, openff_sys: Interchange):
"""Write the Angles section of a LAMMPS data file"""
from openff.interchange.components.mdtraj import (
_iterate_angles,
_store_bond_partners,
)
_store_bond_partners(openff_sys.topology.mdtop)
lmp_file.write("\nAngles\n\n")
angle_handler = openff_sys["Angles"]
angle_type_map = dict(enumerate(angle_handler.potentials))
angle_type_map_inv = dict({v: k for k, v in angle_type_map.items()})
for angle_idx, angle in enumerate(_iterate_angles(openff_sys.topology.mdtop)):
# These are "topology indices"
indices = tuple(a.index for a in angle)
top_key = TopologyKey(atom_indices=indices)
pot_key = angle_handler.slot_map[top_key]
angle_type = angle_type_map_inv[pot_key]
lmp_file.write(
"{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n".format(
angle_idx + 1,
angle_type + 1,
indices[0] + 1,
indices[1] + 1,
indices[2] + 1,
)
)
def _convert_periodic_torsion_force(force):
# TODO: Can impropers be separated out from a PeriodicTorsionForce?
# Maybe by seeing if a quartet is in mol/top.propers or .impropers
from openff.interchange.components.smirnoff import SMIRNOFFProperTorsionHandler
proper_torsion_handler = SMIRNOFFProperTorsionHandler()
n_parametrized_torsions = force.getNumTorsions()
for idx in range(n_parametrized_torsions):
atom1, atom2, atom3, atom4, per, phase, k = force.getTorsionParameters(
idx)
# TODO: Process layered torsions
top_key = TopologyKey(atom_indices=(atom1, atom2, atom3, atom4),
mult=0)
while top_key in proper_torsion_handler.slot_map:
top_key.mult += 1
pot_key = PotentialKey(id=f"{atom1}-{atom2}-{atom3}-{atom4}",
mult=top_key.mult)
pot = Potential(
parameters={
"periodicity": int(per) * unit.dimensionless,
"phase": from_simtk(phase),
"k": from_simtk(k),
"idivf": 1 * unit.dimensionless,
})
proper_torsion_handler.slot_map.update({top_key: pot_key})
proper_torsion_handler.potentials.update({pot_key: pot})
return proper_torsion_handler
def _write_atoms(lmp_file: IO, openff_sys: Interchange, atom_type_map: Dict):
"""Write the Atoms section of a LAMMPS data file"""
lmp_file.write("\nAtoms\n\n")
atom_type_map_inv = dict({v: k for k, v in atom_type_map.items()})
electrostatics_handler = openff_sys.handlers["Electrostatics"]
vdw_hander = openff_sys.handlers["vdW"]
charges = electrostatics_handler.charges
for atom in openff_sys.topology.mdtop.atoms:
molecule_idx = atom.residue.index
top_key = TopologyKey(atom_indices=(atom.index,))
pot_key = vdw_hander.slot_map[top_key]
atom_type = atom_type_map_inv[pot_key]
charge = charges[top_key].m_as(unit.e)
pos = openff_sys.positions[atom.index].to(unit.angstrom).magnitude
lmp_file.write(
"{:d}\t{:d}\t{:d}\t{:.8g}\t{:.8g}\t{:.8g}\t{:.8g}\n".format(
atom.index + 1,
molecule_idx + 1,
atom_type + 1,
charge,
pos[0],
pos[1],
pos[2],
)
)
def test_bond_potential_handler(self):
top = OFFBioTop.from_molecules(Molecule.from_smiles("O=O"))
bond_handler = BondHandler(version=0.3)
bond_parameter = BondHandler.BondType(
smirks="[*:1]~[*:2]",
k=1.5 * simtk_unit.kilocalorie_per_mole / simtk_unit.angstrom**2,
length=1.5 * simtk_unit.angstrom,
id="b1000",
)
bond_handler.add_parameter(bond_parameter.to_dict())
from openff.toolkit.typing.engines.smirnoff import ForceField
forcefield = ForceField()
forcefield.register_parameter_handler(bond_handler)
bond_potentials = SMIRNOFFBondHandler._from_toolkit(
parameter_handler=forcefield["Bonds"],
topology=top,
)
top_key = TopologyKey(atom_indices=(0, 1))
pot_key = bond_potentials.slot_map[top_key]
assert pot_key.associated_handler == "Bonds"
pot = bond_potentials.potentials[pot_key]
kcal_mol_a2 = unit.Unit("kilocalorie / (angstrom ** 2 * mole)")
assert pot.parameters["k"].to(kcal_mol_a2).magnitude == pytest.approx(
1.5)
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 _charge_increment_to_potentials(
cls,
atom_indices: Tuple[int, ...],
parameter: ChargeIncrementModelHandler.ChargeIncrementType,
) -> Tuple[Dict[TopologyKey, PotentialKey], Dict[PotentialKey, Potential]]:
"""Maps a matched charge increment parameter to a set of potentials."""
matches = {}
potentials = {}
for i, atom_index in enumerate(atom_indices):
topology_key = TopologyKey(atom_indices=(atom_index, ))
potential_key = PotentialKey(
id=parameter.smirks,
mult=i,
associated_handler="ChargeIncrementModel")
# TODO: Handle the cases where n - 1 charge increments have been defined,
# maybe by implementing this in the TK?
charge_increment = getattr(parameter, f"charge_increment{i + 1}")
potential = Potential(
parameters={"charge_increment": from_simtk(charge_increment)})
matches[topology_key] = potential_key
potentials[potential_key] = potential
return matches, potentials
def store_matches(
self,
parameter_handler: ParameterHandler,
topology: Union["Topology", "OFFBioTop"],
) -> None:
"""
Populate self.slot_map with key-val pairs of slots
and unique potential identifiers
"""
parameter_handler_name = getattr(parameter_handler, "_TAGNAME", None)
if self.slot_map:
# TODO: Should the slot_map always be reset, or should we be able to partially
# update it? Also Note the duplicated code in the child classes
self.slot_map = dict()
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,
associated_handler=parameter_handler_name)
self.slot_map[topology_key] = potential_key
if self.__class__.__name__ in [
"SMIRNOFFBondHandler", "SMIRNOFFAngleHandler"
]:
valence_terms = self.valence_terms(topology)
parameter_handler._check_all_valence_terms_assigned(
assigned_terms=matches,
valence_terms=valence_terms,
exception_cls=UnassignedValenceParameterException,
)
def store_matches(
self,
parameter_handler: "ProperTorsionHandler",
topology: "OFFBioTop",
) -> None:
"""
Populate self.slot_map with key-val pairs of slots
and unique potential identifiers
"""
if self.slot_map:
self.slot_map = dict()
matches = parameter_handler.find_matches(topology)
for key, val in matches.items():
n_terms = len(val.parameter_type.k)
for n in range(n_terms):
smirks = val.parameter_type.smirks
topology_key = TopologyKey(atom_indices=key, mult=n)
potential_key = PotentialKey(
id=smirks, mult=n, associated_handler="ProperTorsions")
self.slot_map[topology_key] = potential_key
parameter_handler._check_all_valence_terms_assigned(
assigned_terms=matches,
valence_terms=list(topology.propers),
exception_cls=UnassignedProperTorsionParameterException,
)
def _find_am1_matches(
cls,
parameter_handler: Union["ToolkitAM1BCCHandler",
ChargeIncrementModelHandler],
reference_molecule: Molecule,
) -> Tuple[Dict[TopologyKey, PotentialKey], Dict[PotentialKey, Potential]]:
"""Constructs a slot and potential map for a charge model based parameter handler."""
reference_molecule = copy.deepcopy(reference_molecule)
reference_smiles = reference_molecule.to_smiles(
isomeric=True, explicit_hydrogens=True, mapped=True)
method = getattr(parameter_handler, "partial_charge_method", "am1bcc")
partial_charges = cls._compute_partial_charges(reference_molecule,
method=method)
matches = {}
potentials = {}
for i, partial_charge in enumerate(partial_charges):
potential_key = PotentialKey(id=reference_smiles,
mult=i,
associated_handler="ToolkitAM1BCC")
potentials[potential_key] = Potential(
parameters={"charge": partial_charge})
matches[TopologyKey(atom_indices=(i, ))] = potential_key
return matches, potentials
def _get_lj_parameters(openff_sys: "Interchange", atom_idx: int) -> Dict:
vdw_hander = openff_sys.handlers["vdW"]
atom_key = TopologyKey(atom_indices=(atom_idx, ))
identifier = vdw_hander.slot_map[atom_key]
potential = vdw_hander.potentials[identifier]
parameters = potential.parameters
return parameters
def _get_buck_parameters(openff_sys: "Interchange", atom_idx: int) -> Dict:
buck_hander = openff_sys.handlers["Buckingham-6"]
atom_key = TopologyKey(atom_indices=(atom_idx, ))
identifier = buck_hander.slot_map[atom_key]
potential = buck_hander.potentials[identifier]
parameters = potential.parameters
return parameters
def store_constraints(
self,
parameter_handlers: Any,
topology: "OFFBioTop",
) -> None:
if self.slot_map:
self.slot_map = dict()
constraint_handler = [
p for p in parameter_handlers if type(p) == ConstraintHandler
][0]
constraint_matches = constraint_handler.find_matches(topology)
if any([type(p) == BondHandler for p in parameter_handlers]):
bond_handler = [
p for p in parameter_handlers if type(p) == BondHandler
][0]
bonds = SMIRNOFFBondHandler._from_toolkit(
parameter_handler=bond_handler,
topology=topology,
)
else:
bond_handler = None
bonds = None
for key, match in constraint_matches.items():
topology_key = TopologyKey(atom_indices=key)
smirks = match.parameter_type.smirks
distance = match.parameter_type.distance
if distance is not None:
# This constraint parameter is fully specified
potential_key = PotentialKey(id=smirks,
associated_handler="Constraints")
distance = match.parameter_type.distance
else:
# This constraint parameter depends on the BondHandler ...
if bond_handler is None:
from openff.interchange.exceptions import MissingParametersError
raise MissingParametersError(
f"Constraint with SMIRKS pattern {smirks} found with no distance "
"specified, and no corresponding bond parameters were found. The distance "
"of this constraint is not specified.")
# ... so use the same PotentialKey instance as the BondHandler to look up the distance
potential_key = bonds.slot_map[topology_key]
self.slot_map[topology_key] = potential_key
distance = bonds.potentials[potential_key].parameters["length"]
potential = Potential(parameters={
"distance": distance,
})
self.constraints[
potential_key] = potential # type: ignore[assignment]
def test_argon_buck(self):
"""Test that Buckingham potentials are supported and can be exported"""
from openff.interchange.components.smirnoff import SMIRNOFFElectrostaticsHandler
mol = Molecule.from_smiles("[#18]")
top = OFFBioTop.from_molecules([mol, mol])
top.mdtop = md.Topology.from_openmm(top.to_openmm())
# http://www.sklogwiki.org/SklogWiki/index.php/Argon#Buckingham_potential
erg_mol = unit.erg / unit.mol * float(unit.avogadro_number)
A = 1.69e-8 * erg_mol
B = 1 / (0.273 * unit.angstrom)
C = 102e-12 * erg_mol * unit.angstrom**6
r = 0.3 * unit.nanometer
buck = BuckinghamvdWHandler()
coul = SMIRNOFFElectrostaticsHandler(method="pme")
pot_key = PotentialKey(id="[#18]")
pot = Potential(parameters={"A": A, "B": B, "C": C})
for atom in top.mdtop.atoms:
top_key = TopologyKey(atom_indices=(atom.index, ))
buck.slot_map.update({top_key: pot_key})
coul.slot_map.update({top_key: pot_key})
coul.potentials.update({
pot_key:
Potential(parameters={"charge": 0 * unit.elementary_charge})
})
buck.potentials[pot_key] = pot
out = Interchange()
out.handlers["Buckingham-6"] = buck
out.handlers["Electrostatics"] = coul
out.topology = top
out.box = [10, 10, 10] * unit.nanometer
out.positions = [[0, 0, 0], [0.3, 0, 0]] * unit.nanometer
out.to_gro("out.gro", writer="internal")
out.to_top("out.top", writer="internal")
omm_energies = get_openmm_energies(out)
by_hand = A * exp(-B * r) - C * r**-6
resid = omm_energies.energies["Nonbonded"] - by_hand
assert resid < 1e-5 * unit.kilojoule / unit.mol
# TODO: Add back comparison to GROMACS energies once GROMACS 2020+
# supports Buckingham potentials
with pytest.raises(GMXMdrunError):
get_gromacs_energies(out, mdp="cutoff_buck")
def store_matches(
self,
force_field: "Forcefield",
topology: "OFFBioTop",
) -> None:
"""Populate slotmap with key-val pairs of slots and unique potential Identifiers"""
from foyer.atomtyper import find_atomtypes
top_graph = TopologyGraph.from_openff_topology(
openff_topology=topology)
type_map = find_atomtypes(top_graph, forcefield=force_field)
for key, val in type_map.items():
top_key = TopologyKey(atom_indices=(key, ))
self.slot_map[top_key] = PotentialKey(id=val["atomtype"])
def __add__(self, other):
"""Combine two Interchange objects. This method is unstable and likely unsafe."""
import mdtraj as md
from openff.interchange.models import TopologyKey
warnings.warn(
"Iterchange object combination is experimental and likely to produce "
"strange results. Use with caution!")
self_copy = Interchange()
self_copy._inner_data = deepcopy(self._inner_data)
atom_offset = self_copy.topology.mdtop.n_atoms
other_top = deepcopy(other.topology)
for top_mol in other_top.topology_molecules:
self_copy.topology.add_molecule(top_mol.reference_molecule)
self_copy.topology.mdtop = md.Topology.from_openmm(
self_copy.topology.to_openmm())
for handler_name, handler in other.handlers.items():
self_handler = self_copy.handlers[handler_name]
for top_key, pot_key in handler.slot_map.items():
new_atom_indices = tuple(idx + atom_offset
for idx in top_key.atom_indices)
new_top_key = TopologyKey(
atom_indices=new_atom_indices,
mult=top_key.mult,
)
self_handler.slot_map.update({new_top_key: pot_key})
self_handler.potentials.update(
{pot_key: handler.potentials[pot_key]})
new_positions = np.vstack([self_copy.positions, other.positions])
self_copy.positions = new_positions
if not np.all(self_copy.box == other.box):
raise NotImplementedError(
"Combination with unequal box vectors is not curretnly supported"
)
return self_copy
def store_matches(
self,
atom_slots: Dict[TopologyKey, PotentialKey],
topology: "OFFBioTop",
) -> None:
for connection in getattr(topology, self.connection_attribute):
try:
atoms_iterable = connection.atoms
except AttributeError:
atoms_iterable = connection
atoms_indices = tuple(atom.topology_atom_index
for atom in atoms_iterable)
top_key = TopologyKey(atom_indices=atoms_indices)
pot_key_ids = tuple(
_get_potential_key_id(atom_slots, idx)
for idx in atoms_indices)
self.slot_map[top_key] = PotentialKey(
id=POTENTIAL_KEY_SEPARATOR.join(pot_key_ids))
def _convert_harmonic_angle_force(force):
from openff.interchange.components.smirnoff import SMIRNOFFAngleHandler
angle_handler = SMIRNOFFAngleHandler()
n_parametrized_angles = force.getNumAngles()
for idx in range(n_parametrized_angles):
atom1, atom2, atom3, angle, k = force.getAngleParameters(idx)
top_key = TopologyKey(atom_indices=(atom1, atom2, atom3))
pot_key = PotentialKey(id=f"{atom1}-{atom2}-{atom3}")
pot = Potential(parameters={
"angle": from_simtk(angle),
"k": from_simtk(k)
})
angle_handler.slot_map.update({top_key: pot_key})
angle_handler.potentials.update({pot_key: pot})
return angle_handler
def _convert_harmonic_bond_force(force):
from openff.interchange.components.smirnoff import SMIRNOFFBondHandler
bond_handler = SMIRNOFFBondHandler()
n_parametrized_bonds = force.getNumBonds()
for idx in range(n_parametrized_bonds):
atom1, atom2, length, k = force.getBondParameters(idx)
top_key = TopologyKey(atom_indices=(atom1, atom2))
pot_key = PotentialKey(id=f"{atom1}-{atom2}")
pot = Potential(parameters={
"length": from_simtk(length),
"k": from_simtk(k)
})
bond_handler.slot_map.update({top_key: pot_key})
bond_handler.potentials.update({pot_key: pot})
return bond_handler
def _convert_nonbonded_force(force):
from openff.interchange.components.smirnoff import (
SMIRNOFFElectrostaticsHandler,
SMIRNOFFvdWHandler,
)
vdw_handler = SMIRNOFFvdWHandler()
electrostatics = SMIRNOFFElectrostaticsHandler(method="pme")
n_parametrized_particles = force.getNumParticles()
for idx in range(n_parametrized_particles):
charge, sigma, epsilon = force.getParticleParameters(idx)
top_key = TopologyKey(atom_indices=(idx, ))
pot_key = PotentialKey(id=f"{idx}")
pot = Potential(parameters={
"sigma": from_simtk(sigma),
"epsilon": from_simtk(epsilon),
})
vdw_handler.slot_map.update({top_key: pot_key})
vdw_handler.potentials.update({pot_key: pot})
electrostatics.slot_map.update({top_key: pot_key})
electrostatics.potentials.update(
{pot_key: Potential(parameters={"charge": from_simtk(charge)})})
vdw_handler.cutoff = force.getCutoffDistance()
electrostatics.cutoff = force.getCutoffDistance()
if force.getNonbondedMethod() == openmm.NonbondedForce.PME:
electrostatics.method = "pme"
elif force.getNonbondedMethod() in {
openmm.NonbondedForce.CutoffPeriodic,
openmm.NonbondedForce.CutoffNonPeriodic,
}:
# TODO: Store reaction-field dielectric
electrostatics.method = "reactionfield"
elif force.getNonbondedMethod() == openmm.NonbondedForce.NoCutoff:
raise Exception("NonbondedMethod NoCutoff is not supported")
return vdw_handler, electrostatics
def charges(self) -> Dict[TopologyKey, unit.Quantity]:
"""Returns the total partial charge on each particle in the associated interchange."""
charges = defaultdict(lambda: 0.0 * unit.e)
for topology_key, potential_key in self.slot_map.items():
potential = self.potentials[potential_key]
for parameter_key, parameter_value in potential.parameters.items():
if parameter_key != "charge" and parameter_key != "charge_increment":
raise NotImplementedError()
charge = parameter_value
charges[topology_key.atom_indices[0]] += charge
return {
TopologyKey(atom_indices=(index, )): charge
for index, charge in charges.items()
}
def store_matches(
self,
parameter_handler: ParameterHandler,
topology: Union["Topology", "OFFBioTop"],
) -> None:
"""
Populate self.slot_map with key-val pairs of slots
and unique potential identifiers
"""
parameter_handler_name = getattr(parameter_handler, "_TAGNAME", None)
if self.slot_map:
# TODO: Should the slot_map always be reset, or should we be able to partially
# update it? Also Note the duplicated code in the child classes
self.slot_map = dict()
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,
associated_handler=parameter_handler_name)
self.slot_map[topology_key] = potential_key
def _library_charge_to_potentials(
cls,
atom_indices: Tuple[int, ...],
parameter: LibraryChargeHandler.LibraryChargeType,
) -> Tuple[Dict[TopologyKey, PotentialKey], Dict[PotentialKey, Potential]]:
"""Maps a matched library charge parameter to a set of potentials."""
matches = {}
potentials = {}
for i, (atom_index,
charge) in enumerate(zip(atom_indices, parameter.charge)):
topology_key = TopologyKey(atom_indices=(atom_index, ))
potential_key = PotentialKey(id=parameter.smirks,
mult=i,
associated_handler="LibraryCharges")
potential = Potential(parameters={"charge": from_simtk(charge)})
matches[topology_key] = potential_key
potentials[potential_key] = potential
return matches, potentials
def store_matches(self, parameter_handler: "ImproperTorsionHandler",
topology: "OFFBioTop") -> None:
"""
Populate self.slot_map with key-val pairs of slots
and unique potential identifiers
"""
if self.slot_map:
self.slot_map = dict()
matches = parameter_handler.find_matches(topology)
for key, val in matches.items():
parameter_handler._assert_correct_connectivity(
val,
[
(0, 1),
(1, 2),
(1, 3),
],
)
n_terms = len(val.parameter_type.k)
for n in range(n_terms):
smirks = val.parameter_type.smirks
non_central_indices = [key[0], key[2], key[3]]
for permuted_key in [(
non_central_indices[i],
non_central_indices[j],
non_central_indices[k],
) for (i, j, k) in [(0, 1, 2), (1, 2, 0), (2, 0, 1)]]:
topology_key = TopologyKey(atom_indices=(key[1],
*permuted_key),
mult=n)
potential_key = PotentialKey(
id=smirks,
mult=n,
associated_handler="ImproperTorsions")
self.slot_map[topology_key] = potential_key
def ethanol_with_rb_torsions(self):
mol = Molecule.from_smiles("CC")
mol.generate_conformers(n_conformers=1)
top = mol.to_topology()
parsley = ForceField("openff-1.0.0.offxml")
out = Interchange.from_smirnoff(parsley, top)
out.box = [4, 4, 4]
out.positions = mol.conformers[0]
out.positions = np.round(out.positions, 2)
rb_torsions = RBTorsionHandler()
smirks = "[#1:1]-[#6X4:2]-[#6X4:3]-[#1:4]"
pot_key = PotentialKey(id=smirks)
for proper in top.propers:
top_key = TopologyKey(
atom_indices=tuple(a.topology_atom_index for a in proper)
)
rb_torsions.slot_map.update({top_key: pot_key})
# Values from HC-CT-CT-HC RB torsion
# https://github.com/mosdef-hub/foyer/blob/7816bf53a127502520a18d76c81510f96adfdbed/foyer/forcefields/xml/oplsaa.xml#L2585
pot = Potential(
parameters={
"C0": 0.6276 * kj_mol,
"C1": 1.8828 * kj_mol,
"C2": 0.0 * kj_mol,
"C3": -2.5104 * kj_mol,
"C4": 0.0 * kj_mol,
"C5": 0.0 * kj_mol,
}
)
rb_torsions.potentials.update({pot_key: pot})
out.handlers.update({"RBTorsions": rb_torsions})
out.handlers.pop("ProperTorsions")
return out
def _find_reference_matches(
cls,
parameter_handlers: Dict[str, "ElectrostaticsHandlerType"],
reference_molecule: Molecule,
) -> Tuple[Dict[TopologyKey, PotentialKey], Dict[PotentialKey, Potential]]:
"""Constructs a slot and potential map for a particular reference molecule
and set of parameter handlers."""
matches = {}
potentials = {}
expected_matches = {i for i in range(reference_molecule.n_atoms)}
for handler_type in cls.charge_precedence():
if handler_type not in parameter_handlers:
continue
parameter_handler = parameter_handlers[handler_type]
slot_matches, slot_potentials = None, {}
am1_matches, am1_potentials = None, {}
if handler_type in ["LibraryCharges", "ChargeIncrementModel"]:
slot_matches, slot_potentials = cls._find_slot_matches(
parameter_handler, reference_molecule)
if handler_type in ["ToolkitAM1BCC", "ChargeIncrementModel"]:
am1_matches, am1_potentials = cls._find_am1_matches(
parameter_handler, reference_molecule)
if slot_matches is None and am1_matches is None:
raise NotImplementedError()
elif slot_matches is not None and am1_matches is not None:
am1_matches = {
TopologyKey(atom_indices=topology_key.atom_indices,
mult=0): potential_key
for topology_key, potential_key in am1_matches.items()
}
slot_matches = {
TopologyKey(atom_indices=topology_key.atom_indices,
mult=1): potential_key
for topology_key, potential_key in slot_matches.items()
}
matched_atom_indices = {
index
for key in slot_matches for index in key.atom_indices
}
matched_atom_indices.intersection_update({
index
for key in am1_matches for index in key.atom_indices
})
elif slot_matches is not None:
matched_atom_indices = {
index
for key in slot_matches for index in key.atom_indices
}
else:
matched_atom_indices = {
index
for key in am1_matches for index in key.atom_indices
}
if matched_atom_indices != expected_matches:
# Handle the case where a handler could not fully assign the charges
# to the whole molecule.
continue
matches.update(slot_matches if slot_matches is not None else {})
matches.update(am1_matches if am1_matches is not None else {})
potentials.update(slot_potentials)
potentials.update(am1_potentials)
break
found_matches = {
index
for key in matches for index in key.atom_indices
}
if found_matches != expected_matches:
raise RuntimeError(
f"{reference_molecule.to_smiles(explicit_hydrogens=False)} could "
f"not be fully assigned charges.")
return matches, potentials
def _get_potential_key_id(atom_slots: Dict[TopologyKey, PotentialKey], idx):
"""From a dictionary of TopologyKey: PotentialKey, get the PotentialKey id"""
top_key = TopologyKey(atom_indices=(idx, ))
return atom_slots[top_key].id
