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 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 _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: "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 _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 _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 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 _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 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_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 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 _from_parmed(cls, structure) -> "Interchange":
import parmed as pmd
out = cls()
if structure.positions:
out.positions = np.asarray(structure.positions._value) * unit.angstrom
if structure.box is not None:
if any(structure.box[3:] != 3 * [90.0]):
raise UnsupportedBoxError(
f"Found box with angles {structure.box[3:]}. Only"
"rectangular boxes are currently supported.")
out.box = structure.box[:3] * unit.angstrom
from openff.toolkit.topology import Molecule
from openff.interchange.components.mdtraj import OFFBioTop
if structure.topology is not None:
mdtop = md.Topology.from_openmm(
structure.topology) # type: ignore[attr-defined]
top = OFFBioTop(mdtop=mdtop)
out.topology = top
else:
# TODO: Remove this case
# This code should not be reached, since a pathway
# OpenFF -> OpenMM -> MDTraj already exists
mdtop = md.Topology() # type: ignore[attr-defined]
main_chain = md.core.topology.Chain(
index=0, topology=mdtop) # type: ignore[attr-defined]
top = OFFBioTop(mdtop=None)
# There is no way to tell if ParmEd residues are connected (cannot be processed
# as separate OFFMols) or disconnected (can be). For now, will have to accept the
# inefficiency of putting everything into on OFFMol ...
mol = Molecule()
mol.name = getattr(structure, "name", "Mol")
for res in structure.residues:
# ... however, MDTraj's Topology class only stores residues, not molecules,
# so this should roughly match up with ParmEd
this_res = md.core.topology.Residue( # type: ignore[attr-defined]
name=res.name,
index=res.idx,
chain=main_chain,
resSeq=0,
)
for atom in res.atoms:
mol.add_atom(atomic_number=atom.atomic_number,
formal_charge=0,
is_aromatic=False)
mdtop.add_atom(
name=atom.name,
element=md.element.Element.getByAtomicNumber(
atom.element), # type: ignore[attr-defined]
residue=this_res,
)
main_chain._residues.append(this_res)
for res in structure.residues:
for atom in res.atoms:
for bond in atom.bonds:
try:
mol.add_bond(
atom1=bond.atom1.idx,
atom2=bond.atom2.idx,
bond_order=int(bond.order),
is_aromatic=False,
)
# TODO: Use a custom exception after
# https://github.com/openforcefield/openff-toolkit/issues/771
except Exception as e:
if "Bond already exists" in str(e):
pass
else:
raise e
mdtop.add_bond(
atom1=mdtop.atom(bond.atom1.idx),
atom2=mdtop.atom(bond.atom2.idx),
order=int(bond.order)
if bond.order is not None else None,
)
# Topology.add_molecule requires a safe .to_smiles() call, so instead
# do a dangerous molecule addition
ref_mol = FrozenMolecule(mol)
# This doesn't work because molecule hashing requires valid SMILES
# top._reference_molecule_to_topology_molecules[ref_mol] = []
# so just tack it on for now
top._reference_mm_molecule = ref_mol
top_mol = TopologyMolecule(reference_molecule=ref_mol, topology=top)
top._topology_molecules.append(top_mol)
# top._reference_molecule_to_topology_molecules[ref_mol].append(top_mol)
mdtop._chains.append(main_chain)
out.topology = top
from openff.interchange.components.smirnoff import (
SMIRNOFFAngleHandler,
SMIRNOFFBondHandler,
SMIRNOFFElectrostaticsHandler,
SMIRNOFFImproperTorsionHandler,
SMIRNOFFProperTorsionHandler,
SMIRNOFFvdWHandler,
)
vdw_handler = SMIRNOFFvdWHandler()
coul_handler = SMIRNOFFElectrostaticsHandler(method="pme")
for atom in structure.atoms:
atom_idx = atom.idx
sigma = atom.sigma * unit.angstrom
epsilon = atom.epsilon * kcal_mol
charge = atom.charge * unit.elementary_charge
top_key = TopologyKey(atom_indices=(atom_idx, ))
pot_key = PotentialKey(id=str(atom_idx))
pot = Potential(parameters={"sigma": sigma, "epsilon": epsilon})
vdw_handler.slot_map.update({top_key: pot_key})
vdw_handler.potentials.update({pot_key: pot})
coul_handler.slot_map.update({top_key: pot_key})
coul_handler.potentials.update(
{pot_key: Potential(parameters={"charge": charge})})
bond_handler = SMIRNOFFBondHandler()
for bond in structure.bonds:
atom1 = bond.atom1
atom2 = bond.atom2
k = bond.type.k * kcal_mol_a2
length = bond.type.req * unit.angstrom
top_key = TopologyKey(atom_indices=(atom1.idx, atom2.idx))
pot_key = PotentialKey(id=f"{atom1.idx}-{atom2.idx}")
pot = Potential(parameters={"k": k * 2, "length": length})
bond_handler.slot_map.update({top_key: pot_key})
bond_handler.potentials.update({pot_key: pot})
out.handlers.update({"vdW": vdw_handler})
out.handlers.update({"Electrostatics": coul_handler})
out.handlers.update({"Bonds": bond_handler})
angle_handler = SMIRNOFFAngleHandler()
for angle in structure.angles:
atom1 = angle.atom1
atom2 = angle.atom2
atom3 = angle.atom3
k = angle.type.k * kcal_mol_rad2
theta = angle.type.theteq * unit.degree
top_key = TopologyKey(atom_indices=(atom1.idx, atom2.idx, atom3.idx))
pot_key = PotentialKey(id=f"{atom1.idx}-{atom2.idx}-{atom3.idx}")
pot = Potential(parameters={"k": k * 2, "angle": theta})
angle_handler.slot_map.update({top_key: pot_key})
angle_handler.potentials.update({pot_key: pot})
proper_torsion_handler = SMIRNOFFProperTorsionHandler()
improper_torsion_handler = SMIRNOFFImproperTorsionHandler()
for dihedral in structure.dihedrals:
if isinstance(dihedral.type, pmd.DihedralType):
if dihedral.improper:
_process_single_dihedral(dihedral, dihedral.type,
improper_torsion_handler, 0)
else:
_process_single_dihedral(dihedral, dihedral.type,
proper_torsion_handler, 0)
elif isinstance(dihedral.type, pmd.DihedralTypeList):
for dih_idx, dihedral_type in enumerate(dihedral.type):
if dihedral.improper:
_process_single_dihedral(dihedral, dihedral_type,
improper_torsion_handler, dih_idx)
else:
_process_single_dihedral(
dihedral,
dihedral_type,
proper_torsion_handler,
dih_idx,
)
out.handlers.update({"Electrostatics": coul_handler})
out.handlers.update({"Bonds": bond_handler})
out.handlers.update({"Angles": angle_handler})
out.handlers.update({"ProperTorsions": proper_torsion_handler})
return out
