fix 1583 by kekulizing before reperceiving aromaticity, update releas…

…enotes (#1591)
openforcefield · Apr 26, 2023 · cee85d1 · cee85d1
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diff --git a/docs/releasehistory.md b/docs/releasehistory.md
@@ -17,6 +17,7 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 ### Bugfixes
 - [PR #1589](https://github.com/openforcefield/openff-toolkit/pull/1589): Fixes [Issue #1579](https://github.com/openforcefield/openff-toolkit/issues/1579), where Molecule.from_polymer_pdb could not handle NH2 caps at C termini.  
+- [PR #1591](https://github.com/openforcefield/openff-toolkit/pull/1591): Fixes [#1563](https://github.com/openforcefield/openff-toolkit/issues/1563), where `from_rdkit` would sometimes raise an error about radicals if a molecule using a non-MDL aromaticity model was provided. 
 
 ### Improved documentation and warnings
 

diff --git a/openff/toolkit/tests/test_toolkits.py b/openff/toolkit/tests/test_toolkits.py
@@ -2527,6 +2527,15 @@ def test_from_rdkit_radical(self):
         with pytest.raises(RadicalsNotSupportedError):
             RDKitToolkitWrapper().from_rdkit(rdmol)
 
+    def test_from_rdkit_incompatible_aromaticity(self):
+        """Test loading an rdmol where the aromaticity was set by a model that disagrees with MDL"""
+        from rdkit import Chem
+
+        smi = "c2scnc2C"
+        rdmol = Chem.MolFromSmiles(smi)
+        Chem.SetAromaticity(rdmol, Chem.AromaticityModel.AROMATICITY_RDKIT)
+        Molecule.from_rdkit(rdmol)
+
     def test_from_rdkit_transition_metal_radical(self):
         """Test that parsing an rdmol with a transition metal radical works."""
         from rdkit import Chem

diff --git a/openff/toolkit/utils/rdkit_wrapper.py b/openff/toolkit/utils/rdkit_wrapper.py
@@ -1790,7 +1790,6 @@ def from_rdkit(
                 ^ Chem.SANITIZE_SETAROMATICITY
                 ^ Chem.SANITIZE_ADJUSTHS
                 ^ Chem.SANITIZE_CLEANUPCHIRALITY
-                ^ Chem.SANITIZE_KEKULIZE
             ),
         )
         Chem.SetAromaticity(rdmol, Chem.AromaticityModel.AROMATICITY_MDL)