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If you have a molecule with a lactam, where the amide nitrogen is a ring bridgehead, then Chem.AssignStereochemistry incorrectly assigns the amide nitrogen as "_ChiralityPossible" even though it's flat.
To Reproduce
from rdkit import Chem
rdmol=Chem.MolFromSmiles("O=C1CCCCC[C@@H]2CN1CCO2")
Chem.AssignStereochemistry(rdmol, force=True, flagPossibleStereoCenters=True)
for atom_idx, atom in enumerate(rdmol.GetAtoms()):
if atom.GetChiralTag() == Chem.ChiralType.CHI_UNSPECIFIED and atom.HasProp(
"_ChiralityPossible"
):
print(atom_idx)
Expected behavior
The nitrogen is not marked as potentially chiral, as it's flat.
Configuration (please complete the following information):
RDKit version: 2022.09.03
Additional context
This is causing issues in OpenFF, which checks that the chirality of the molecule is fully specified and refused to proceed unless it is.
The text was updated successfully, but these errors were encountered:
greglandrum
changed the title
Molecule has planar amide nitrogen incorrectly flagged as _ChiralityPossible
Planar amide nitrogen incorrectly flagged as _ChiralityPossible
May 16, 2024
If you have a molecule with a lactam, where the amide nitrogen is a ring bridgehead, then Chem.AssignStereochemistry incorrectly assigns the amide nitrogen as "_ChiralityPossible" even though it's flat.
To Reproduce
Expected behavior
The nitrogen is not marked as potentially chiral, as it's flat.
Configuration (please complete the following information):
Additional context
This is causing issues in OpenFF, which checks that the chirality of the molecule is fully specified and refused to proceed unless it is.
The text was updated successfully, but these errors were encountered: