Parser uses RMG if RDKit fails to get structure

ReactionMechanismGenerator · Sep 24, 2024 · 94a39b7 · 94a39b7
1 parent 2784fc2
commit 94a39b7
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/src/Parse.jl b/src/Parse.jl
@@ -168,7 +168,12 @@ function getatomdictsmiles(smiles)
         mol.assign_representative_molecule()
         getatomdictfromrmg(mol.mol_repr)
     else
-        getatomdictfromrdkit(Chem.AddHs(Chem.MolFromSmiles(smiles)))
+        try
+            return getatomdictfromrdkit(Chem.AddHs(Chem.MolFromSmiles(smiles)))
+        catch e
+            println("RDKit parsing failed, using RMG instead", e)
+            return getatomdictfromrmg(molecule.Molecule().from_smiles(smiles))
+        end
     end
 end