def _get_angle_type(self, atom_types, warn=False):
"""Get a particular angle_type between `atom_types` from this ForceField"""
if len(atom_types) != 3:
raise ValueError(
f"AngleType potential can only "
f"be extracted for three atoms. Provided {len(atom_types)}")
forward = FF_TOKENS_SEPARATOR.join(atom_types)
reverse = FF_TOKENS_SEPARATOR.join(reversed(atom_types))
match = None
if forward in self.angle_types:
match = self.angle_types[forward]
if reverse in self.angle_types:
match = self.angle_types[reverse]
msg = f"AngleType between atoms {atom_types[0]}, {atom_types[1]} " \
f"and {atom_types[2]} is missing from the ForceField"
if match:
return match
elif warn:
warnings.warn(msg)
return None
else:
raise MissingPotentialError(msg)
def _get_improper_type(self, atom_types, warn=False):
"""Get a particular improper_type between `atom_types` from this ForceField."""
if len(atom_types) != 4:
raise ValueError(
f"ImproperType potential can only "
f"be extracted for four atoms. Provided {len(atom_types)}"
)
forward = FF_TOKENS_SEPARATOR.join(atom_types)
reverse = FF_TOKENS_SEPARATOR.join(
[atom_types[0], atom_types[2], atom_types[1], atom_types[3]]
)
if forward is self.improper_types:
return self.improper_types[forward]
if reverse in self.improper_types:
return self.improper_types[reverse]
match = None
for i in range(1, 5):
forward_patterns = mask_with(atom_types, i)
reverse_patterns = mask_with(
[atom_types[0], atom_types[2], atom_types[1], atom_types[3]], i
)
for forward_pattern, reverse_pattern in zip(
forward_patterns, reverse_patterns
):
forward_match_key = FF_TOKENS_SEPARATOR.join(forward_pattern)
reverse_match_key = FF_TOKENS_SEPARATOR.join(reverse_pattern)
if forward_match_key in self.dihedral_types:
match = self.dihedral_types[forward_match_key]
break
if reverse_match_key in self.dihedral_types:
match = self.dihedral_types[reverse_match_key]
break
if match:
break
msg = (
f"ImproperType between atoms {atom_types[0]}, {atom_types[1]}, "
f"{atom_types[2]} and {atom_types[3]} is missing from the ForceField."
)
if match:
return match
elif warn:
warnings.warn(msg)
return None
else:
raise MissingPotentialError(msg)
def _get_atom_type(self, atom_type, warn=False):
"""Get a particular atom_type with given `atom_type` from this ForceField"""
if isinstance(atom_type, list):
atom_type = atom_type[0]
if not self.atom_types.get(atom_type):
msg = f"AtomType {atom_type} is not present in the ForceField"
if warn:
warnings.warn(msg)
else:
raise MissingPotentialError(msg)
return self.atom_types.get(atom_type)
def _get_bond_type(self, atom_types, warn=False):
"""Get a particular bond_type between `atom_types` from this ForceField"""
if len(atom_types) != 2:
raise ValueError(
f"BondType potential can only "
f"be extracted for two atoms. Provided {len(atom_types)}")
forward = FF_TOKENS_SEPARATOR.join(atom_types)
reverse = FF_TOKENS_SEPARATOR.join(reversed(atom_types))
if forward in self.bond_types:
return self.bond_types[forward]
if reverse in self.bond_types:
return self.bond_types[reverse]
msg = f"BondType between atoms {atom_types[0]} and {atom_types[1]} " \
f"is missing from the ForceField"
if warn:
warnings.warn(msg)
return None
else:
raise MissingPotentialError(msg)