def get_all_torsions(
bond: Tuple[int, int],
molecule: Molecule) -> List[Tuple[int, int, int, int]]:
"""
Get all torsions that pass through the central bond to generate smirks patterns.
Parameters:
bond: The bond which we want all torsions for.
molecule: The molecule which the bond corresponds to.
Returns:
A list of all of the torsion tuples passing through this central bond.
"""
torsions = []
central_bond = molecule.get_bond_between(*bond)
atom1, atom2 = central_bond.atom1, central_bond.atom2
for atom in atom1.bonded_atoms:
for end_atom in atom2.bonded_atoms:
if atom != atom2 and end_atom != atom1:
dihedral = (
atom.molecule_atom_index,
atom1.molecule_atom_index,
atom2.molecule_atom_index,
end_atom.molecule_atom_index,
)
torsions.append(dihedral)
else:
continue
return torsions
def check_general_connection(
connected_atoms: List[int], molecule: off.Molecule
) -> List[int]:
"""
Check that the list of atoms are all connected in order by explicit bonds in the given molecule.
Parameters:
connected_atoms: A list of the atom indices that should be connected in order.
molecule: The molecule that should be checked for connected atoms.
Raises:
AtomConnectionError: If any two of the given list of atoms are not connected.
Returns:
The list of validated connected atom indices.
"""
for i in range(len(connected_atoms) - 1):
# get the atoms to be checked
atoms = [connected_atoms[i], connected_atoms[i + 1]]
try:
_ = molecule.get_bond_between(*atoms)
except (off.topology.NotBondedError, IndexError):
# catch both notbonded errors and tags on atoms not in the molecule
raise AtomConnectionError(
f"The set of atoms {connected_atoms} was not valid for the molecule {molecule}, as there is no bond between atoms {atoms}.",
atoms=atoms,
)
return connected_atoms