bug fixing

app.py

@@ -10,7 +10,7 @@ from PIL import Image, ImageDraw, ImageFont
 import matplotlib.pyplot as plt
 import matplotlib.patches as patches
 from io import BytesIO
-
+import tempfile
 import re
 from rdkit import Chem
 
@@ -1038,7 +1038,8 @@ 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 = None
+    temp_dir = tempfile.mkdtemp() if generate_3d else None
+    structure_files = []
     
     # Handle direct SMILES input
     if smiles_input:
@@ -1059,24 +1060,25 @@ 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)
-                    files_list.append(("structure_etkdg.sdf", etkdg_bytes))
+                    etkdg_path = os.path.join(temp_dir, "structure_etkdg.sdf")
+                    writer = Chem.SDWriter(etkdg_path)
+                    writer.write(mol_etkdg)
+                    writer.close()
+                    structure_files.append(etkdg_path)
                     
                     # Generate UFF structure if requested
                     if use_uff:
                         mol_uff = generator.generate_structure_uff(smiles)
-                        uff_bytes = generator.mol_to_sdf_bytes(mol_uff)
-                        files_list.append(("structure_uff.sdf", uff_bytes))
-                    
-                    structure_files = files_list if files_list else None
+                        uff_path = os.path.join(temp_dir, "structure_uff.sdf")
+                        writer = Chem.SDWriter(uff_path)
+                        writer.write(mol_uff)
+                        writer.close()
+                        structure_files.append(uff_path)
                 
                 except Exception as e:
-                    return f"Error generating 3D structures: {str(e)}", None, None, []
+                    return f"Error generating 3D structures: {str(e)}", None, None, None
                 
             # Use analyzer to get sequence
             segments = analyzer.split_on_bonds(smiles)
@@ -1148,13 +1150,13 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False,
             
             if structure_files:
                 summary += "\n3D Structures Generated:\n"
-                for filename, _ in structure_files:
-                    summary += f"- {filename}\n"
+                for filepath in structure_files:
+                    summary += f"- {os.path.basename(filepath)}\n"
             
-            return summary + output_text, img_cyclic, img_linear, structure_files
+            return summary + output_text, img_cyclic, img_linear, structure_files if structure_files else None
             
         except Exception as e:
-            return f"Error processing SMILES: {str(e)}", None, None
+            return f"Error processing SMILES: {str(e)}", None, None, None
     
     # Handle file input
     if file_obj is not None: