From 94a39b75ebd50b58e66f779ffeb8d40f90fa20c9 Mon Sep 17 00:00:00 2001
From: ssun30 <sun.su@northeastern.edu>
Date: Tue, 6 Aug 2024 15:12:43 -0400
Subject: [PATCH] Parser uses RMG if RDKit fails to get structure

---
 src/Parse.jl | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/Parse.jl b/src/Parse.jl
index 3698081f..37585171 100644
--- 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