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OpenFF Toolkit 0.7.0 Compatability #31

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Jun 23, 2020
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OpenFF Toolkit 0.7.0 Compatability #31

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14 changes: 11 additions & 3 deletions nonbonded/library/curation/components/filtering.py
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Original file line number Diff line number Diff line change
Expand Up @@ -642,6 +642,9 @@ class FilterByCharged(Component):
def _apply(
cls, data_frame: pandas.DataFrame, schema: FilterByChargedSchema, n_processes
) -> pandas.DataFrame:

from simtk import unit as simtk_unit

def filter_function(data_row):

n_components = data_row["N Components"]
Expand All @@ -651,10 +654,15 @@ def filter_function(data_row):
smiles = data_row[f"Component {index + 1}"]
molecule = Molecule.from_smiles(smiles, allow_undefined_stereo=True)

if numpy.isclose(
sum([atom.formal_charge for atom in molecule.atoms]), 0.0
):
# noinspection PyUnresolvedReferences
atom_charges = [
atom.formal_charge
if isinstance(atom.formal_charge, int)
else atom.formal_charge.value_in_unit(simtk_unit.elementary_charge)
for atom in molecule.atoms
]

if numpy.isclose(sum(atom_charges), 0.0):
continue

return False
Expand Down