fixes openfe OpenFreeEnergy#278

related to off tk #1563
hmacdope · Apr 27, 2023 · a0744ca · a0744ca
1 parent 7de1283
commit a0744ca
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/gufe/components/smallmoleculecomponent.py b/gufe/components/smallmoleculecomponent.py
@@ -175,8 +175,13 @@ def _from_sdf_supplier(cls, supp):
     def to_openff(self):
         """OpenFF Toolkit representation of this molecule"""
         from openff.toolkit.topology import Molecule as OFFMolecule
+        m = self.to_rdkit()
 
-        m = OFFMolecule(self._rdkit, allow_undefined_stereo=True)
+        # see openfe #278 / openff tk #1563
+        Chem.Kekulize(m)
+        Chem.SetAromaticity(m, Chem.AromaticityModel.AROMATICITY_MDL)
+
+        m = OFFMolecule(m, allow_undefined_stereo=True)
         m.name = self.name
 
         return m