BugFix: xyz2mol non-robust behavior if resonance generation fails

There are cases ResonanceMolSupplier returns None, causing error in downstream. This commit makes sure, if nothing meaningful is created, at least the mol created previously will be returned.
xiaoruiDong · Nov 1, 2023 · b981120 · b981120
1 parent 209bdf1
commit b981120
Showing 1 changed file with 8 additions and 2 deletions.
diff --git a/rdmc/external/xyz2mol.py b/rdmc/external/xyz2mol.py
@@ -528,8 +528,14 @@ def AC2mol(mol, AC, atoms, charge, allow_charged_fragments=True,
         return []
 
     # BO2mol returns an arbitrary resonance form. Let's make the rest
-    mols = rdchem.ResonanceMolSupplier(mol, Chem.UNCONSTRAINED_CATIONS, Chem.UNCONSTRAINED_ANIONS)
-    mols = [mol for mol in mols]
+    mols = [mol for mol in rdchem.ResonanceMolSupplier(
+        mol,
+        Chem.ALLOW_INCOMPLETE_OCTETS | Chem.UNCONSTRAINED_CATIONS | Chem.UNCONSTRAINED_ANIONS,
+    ) if mol is not None]
+
+    if not mols:
+        mols = [mol]  # For some cases, resonance structure supplier creates Nones
+
 
     return mols