bug fixing

app.py

@@ -1025,11 +1025,14 @@ class PeptideStructureGenerator:
     @staticmethod
     def mol_to_sdf_bytes(mol):
         """Convert RDKit molecule to SDF file bytes"""
-        sio = BytesIO()
+        # First write to StringIO in text mode
+        sio = StringIO()
         writer = Chem.SDWriter(sio)
         writer.write(mol)
         writer.close()
-        return sio.getvalue()
+        
+        # Convert the string to bytes
+        return sio.getvalue().encode('utf-8')
 
 def process_input(smiles_input=None, file_obj=None, show_linear=False, 
                  show_segment_details=False, generate_3d=False, use_uff=False):
@@ -1109,7 +1112,12 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False,
             
             # Check if cyclic using analyzer's method
             is_cyclic, peptide_cycles, aromatic_cycles = analyzer.is_cyclic(smiles)
-            sequence = f"cyclo({'-'.join(sequence_parts)})" if is_cyclic else '-'.join(sequence_parts)
+            three_letter = '-'.join(sequence_parts)
+            one_letter = ''.join(analyzer.three_to_one.get(aa.split('(')[0], 'X') for aa in sequence_parts)
+        
+            if is_cyclic:
+                three_letter = f"cyclo({three_letter})"
+                one_letter = f"cyclo({one_letter})"
             
             # Create cyclic structure visualization
             img_cyclic = annotate_cyclic_structure(mol, sequence)
@@ -1123,13 +1131,14 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False,
                 buf.seek(0)
                 img_linear = Image.open(buf)
                 plt.close(fig_linear)
-            
+
             # Add summary to output
             summary = "Summary:\n"
-            summary += f"Sequence: {sequence}\n"
+            summary += f"Sequence: {three_letter}\n"
+            summary += f"One-letter code: {one_letter}\n"
             summary += f"Is Cyclic: {'Yes' if is_cyclic else 'No'}\n"
-            if is_cyclic:
-                summary += f"Peptide Cycles: {', '.join(peptide_cycles)}\n"
+            #if is_cyclic:
+                #summary += f"Peptide Cycles: {', '.join(peptide_cycles)}\n"
                 #summary += f"Aromatic Cycles: {', '.join(aromatic_cycles)}\n"
             
             return summary + output_text, img_cyclic, img_linear, structure_files