Bugfix: avoid double counting for O-O oxonium

xiaoruiDong · Nov 2, 2023 · 60b2f91 · 60b2f91
1 parent d456a7f
commit 60b2f91
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/rdmc/fix.py b/rdmc/fix.py
@@ -390,7 +390,11 @@ def fix_oxonium_bonds(
 
     mol = mol.Copy()
     for miss_bond in oxonium_bonds:
-        mol.AddBond(*miss_bond, order=BondType.SINGLE)
+        try:
+            mol.AddBond(*miss_bond, order=BondType.SINGLE)
+        except RuntimeError:
+            # Oxygen may get double counted
+            continue
 
         # Usually the connected atom is a radical site
         # So, update the number of radical electrons afterward