def _compute_partial_charges(cls, molecule: Molecule,
method: str) -> unit.Quantity:
"""Call out to the toolkit's toolkit wrappers to generate partial charges"""
molecule = copy.deepcopy(molecule)
molecule.assign_partial_charges(method)
return from_simtk(molecule.partial_charges)
def label_function(molecule: Molecule) -> Dict[str, torch.Tensor]:
"""Generates a set of train / val / test labels for a given molecule."""
from simtk import unit
# Generate a set of ELF10 conformers.
molecule.generate_conformers(n_conformers=800,
rms_cutoff=0.05 * unit.angstrom)
molecule.apply_elf_conformer_selection()
partial_charges = []
for conformer in molecule.conformers:
molecule.assign_partial_charges("am1-mulliken",
use_conformers=[conformer])
partial_charges.append(
molecule.partial_charges.value_in_unit(unit.elementary_charge))
return {
"am1-charges":
torch.from_numpy(numpy.mean(partial_charges, axis=0)).float()
}
