bug fixing

app.py

@@ -1038,7 +1038,7 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False,
                  show_segment_details=False, generate_3d=False, use_uff=False):
     """Process input and create visualizations using PeptideAnalyzer"""
     analyzer = PeptideAnalyzer()
-    structure_files = []
+    structure_files = None
     
     # Handle direct SMILES input
     if smiles_input:
@@ -1059,28 +1059,21 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False,
                 generator = PeptideStructureGenerator()
                 
                 try:
+                    # Create a list to store file tuples (name, data)
+                    files_list = []
+                    
                     # Generate ETKDG structure
                     mol_etkdg = generator.generate_structure_etkdg(smiles)
                     etkdg_bytes = generator.mol_to_sdf_bytes(mol_etkdg)
-                    
-                    # Create temporary file path for ETKDG structure
-                    etkdg_file = {
-                        "name": "structure_etkdg.sdf",
-                        "data": etkdg_bytes
-                    }
-                    structure_files.append(etkdg_file)
+                    files_list.append(("structure_etkdg.sdf", etkdg_bytes))
                     
                     # Generate UFF structure if requested
                     if use_uff:
                         mol_uff = generator.generate_structure_uff(smiles)
                         uff_bytes = generator.mol_to_sdf_bytes(mol_uff)
-                        
-                        # Create temporary file path for UFF structure
-                        uff_file = {
-                            "name": "structure_uff.sdf",
-                            "data": uff_bytes
-                        }
-                        structure_files.append(uff_file)
+                        files_list.append(("structure_uff.sdf", uff_bytes))
+                    
+                    structure_files = files_list if files_list else None
                 
                 except Exception as e:
                     return f"Error generating 3D structures: {str(e)}", None, None, []
@@ -1155,8 +1148,8 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False,
             
             if structure_files:
                 summary += "\n3D Structures Generated:\n"
-                for file_info in structure_files:
-                    summary += f"- {file_info['name']}\n"
+                for filename, _ in structure_files:
+                    summary += f"- {filename}\n"
             
             return summary + output_text, img_cyclic, img_linear, structure_files