def check_linear_torsions(
torsion: Tuple[int, int, int, int], molecule: off.Molecule
) -> Tuple[int, int, int, int]:
"""
Check that the torsion supplied is not for a linear bond.
Parameters:
torsion: The indices of the atoms in the selected torsion.
molecule: The molecule which should be checked.
Raises:
LinearTorsionError: If the given torsion involves driving a linear bond.
"""
# this is based on the past submissions to QCarchive which have failed
# highlight the central bond of a linear torsion
linear_smarts = "[*!D1:1]~[$(*#*)&D2,$(C=*)&D2:2]"
matches = molecule.chemical_environment_matches(linear_smarts)
if torsion[1:3] in matches or torsion[2:0:-1] in matches:
raise LinearTorsionError(
f"The dihedral {torsion} in molecule {molecule} highlights a linear bond."
)
return torsion
def improper_torsion_indices(offmol: Molecule) -> np.ndarray:
""""[*:1]~[X3:2](~[*:3])~[*:4]" matches (_all_improper_torsion_indices returns "[*:1]~[*:2](~[*:3])~[*:4]" matches)
Notes
-----
Motivation: offmol.impropers returns a large number of impropers, and we may wish to restrict this number.
May update this filter definition based on discussion in https://github.com/openforcefield/openforcefield/issues/746
"""
improper_smarts = "[*:1]~[X3:2](~[*:3])~[*:4]"
return np.array(offmol.chemical_environment_matches(improper_smarts))
def _detect_linear_torsions(self, molecule: off.Molecule) -> List:
"""
Try and find any linear bonds in the molecule with torsions that should not be driven.
Parameters:
molecule: An openforcefield molecule instance
Returns:
A list of the central bond tuples in the molecule which should not be driven, this can then be compared
against the torsions which have been selected.
"""
# this is based on the past submissions to QCarchive which have failed
# highlight the central bond of a linear torsion
linear_smarts = "[*!D1:1]~[$(*#*)&D2,$(C=*)&D2:2]"
matches = molecule.chemical_environment_matches(linear_smarts)
return matches