Merge pull request #272 from rwxayheee/catch_prepare_err_in_cli

Catch prepare errors without interrupting batch processing
forlilab · Dec 9, 2024 · a4e45d7 · a4e45d7
2 parents 4554056 + 41ef572
commit a4e45d7
Showing 1 changed file with 9 additions and 1 deletion.
diff --git a/meeko/cli/mk_prepare_ligand.py b/meeko/cli/mk_prepare_ligand.py
@@ -637,7 +637,15 @@ def main():
                         print(error_msg, file=sys.stderr)
 
         else:
-            molsetups = preparator.prepare(mol, rename_atoms=args.rename_atoms)
+            try: 
+                molsetups = preparator.prepare(mol, rename_atoms=args.rename_atoms)
+            except Exception as error_msg: 
+                nr_failures += 1
+                this_mol_had_failure = True
+                print(error_msg, file=sys.stderr)
+                input_mol_with_failure += int(this_mol_had_failure)
+                continue
+
             if len(molsetups) > 1:
                 output.is_multimol = True
             suffixes = output.get_suffixes(molsetups)