bug fixing

app.py

@@ -816,8 +816,14 @@ class PeptideStructureGenerator:
         
         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):
+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()
     temp_dir = tempfile.mkdtemp() if generate_3d else None
@@ -859,77 +865,38 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False,
                 except Exception as e:
                     return f"Error generating 3D structures: {str(e)}", None, None, []
                 
-            segments = analyzer.split_on_bonds(smiles)
+            # Process the structure
+            result = analyzer.analyze_structure(smiles)
             
-            sequence_parts = []
-            output_text = ""
-            
-            # Only include segment analysis in output if requested
-            if show_segment_details:
-                output_text += "Segment Analysis:\n"
-                for i, segment in enumerate(segments):
-                    output_text += f"\nSegment {i}:\n"
-                    output_text += f"Content: {segment['content']}\n"
-                    output_text += f"Bond before: {segment.get('bond_before', 'None')}\n"
-                    output_text += f"Bond after: {segment.get('bond_after', 'None')}\n"
-                    
-                    residue, mods = analyzer.identify_residue(segment)
-                    if residue:
-                        if mods:
-                            sequence_parts.append(f"{residue}({','.join(mods)})")
-                        else:
-                            sequence_parts.append(residue)
-                        output_text += f"Identified as: {residue}\n"
-                        output_text += f"Modifications: {mods}\n"
-                    else:
-                        output_text += f"Warning: Could not identify residue in segment: {segment['content']}\n"
-                output_text += "\n"
-            else:
-                for segment in segments:
-                    residue, mods = analyzer.identify_residue(segment)
-                    if residue:
-                        if mods:
-                            sequence_parts.append(f"{residue}({','.join(mods)})")
-                        else:
-                            sequence_parts.append(residue)
-            
-            is_cyclic, peptide_cycles, aromatic_cycles = analyzer.is_cyclic(smiles)
-            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})"
-            
-            img_cyclic = annotate_cyclic_structure(mol, three_letter)
+            # Create the 2D structure visualization
+            img_cyclic = annotate_cyclic_structure(mol, result['three_letter'])
             
             # Create linear representation if requested
             img_linear = None
             if show_linear:
-                fig_linear = create_enhanced_linear_viz(three_letter, smiles)
+                fig_linear = create_enhanced_linear_viz(result['three_letter'], smiles)
                 buf = BytesIO()
                 fig_linear.savefig(buf, format='png', bbox_inches='tight', dpi=300)
                 buf.seek(0)
                 img_linear = Image.open(buf)
                 plt.close(fig_linear)
-
+            
+            # Prepare the summary text
             summary = "Summary:\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"
-                #summary += f"Aromatic Cycles: {', '.join(aromatic_cycles)}\n"
+            summary += f"Sequence: {result['three_letter']}\n"
+            summary += f"One-letter code: {result['one_letter']}\n"
+            summary += f"Is Cyclic: {'Yes' if result['is_cyclic'] else 'No'}\n"
             
             if structure_files:
                 summary += "\n3D Structures Generated:\n"
                 for filepath in structure_files:
                     summary += f"- {os.path.basename(filepath)}\n"
             
-            return summary + output_text, img_cyclic, img_linear, structure_files if structure_files else None
+            # Return the results
+            return summary, img_cyclic, img_linear, structure_files if structure_files else []
             
         except Exception as e:
-            return f"Error processing SMILES: {str(e)}", None, None, None
+            return f"Error processing SMILES: {str(e)}", None, None, []
     
     # Handle file input
     if file_obj is not None:
@@ -943,46 +910,24 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False,
             output_text = ""
             for line in content.splitlines():
                 smiles = line.strip()
-                if smiles:
-                    if not analyzer.is_peptide(smiles):
-                        output_text += f"Skipping non-peptide SMILES: {smiles}\n"
-                        continue
-                    
-                    segments = analyzer.split_on_bonds(smiles)
-                    sequence_parts = []
-                    
-                    if show_segment_details:
-                        output_text += f"\nSegment Analysis for SMILES: {smiles}\n"
-                        for i, segment in enumerate(segments):
-                            output_text += f"\nSegment {i}:\n"
-                            output_text += f"Content: {segment['content']}\n"
-                            output_text += f"Bond before: {segment.get('bond_before', 'None')}\n"
-                            output_text += f"Bond after: {segment.get('bond_after', 'None')}\n"
-                            residue, mods = analyzer.identify_residue(segment)
-                            if residue:
-                                if mods:
-                                    sequence_parts.append(f"{residue}({','.join(mods)})")
-                                else:
-                                    sequence_parts.append(residue)
-                                output_text += f"Identified as: {residue}\n"
-                                output_text += f"Modifications: {mods}\n"
-                    else:
-                        for segment in segments:
-                            residue, mods = analyzer.identify_residue(segment)
-                            if residue:
-                                if mods:
-                                    sequence_parts.append(f"{residue}({','.join(mods)})")
-                                else:
-                                    sequence_parts.append(residue)
-                    
-                    is_cyclic, peptide_cycles, aromatic_cycles = analyzer.is_cyclic(smiles)
-                    sequence = f"cyclo({'-'.join(sequence_parts)})" if is_cyclic else '-'.join(sequence_parts)
+                if not smiles:
+                    continue
+                
+                if not analyzer.is_peptide(smiles):
+                    output_text += f"Skipping non-peptide SMILES: {smiles}\n"
+                    continue
+                
+                try:
+                    # Process the structure
+                    result = analyzer.analyze_structure(smiles)
                     
                     output_text += f"\nSummary for SMILES: {smiles}\n"
-                    output_text += f"Sequence: {sequence}\n"
-                    output_text += f"Is Cyclic: {'Yes' if is_cyclic else 'No'}\n"
-                    if is_cyclic:
-                        output_text += f"Peptide Cycles: {', '.join(peptide_cycles)}\n"
+                    output_text += f"Sequence: {result['three_letter']}\n"
+                    output_text += f"One-letter code: {result['one_letter']}\n"
+                    output_text += f"Is Cyclic: {'Yes' if result['is_cyclic'] else 'No'}\n"
+                    output_text += "-" * 50 + "\n"
+                except Exception as e:
+                    output_text += f"Error processing SMILES: {smiles} - {str(e)}\n"
                     output_text += "-" * 50 + "\n"
             
             return output_text, None, None, []
@@ -1008,10 +953,6 @@ iface = gr.Interface(
             label="Show linear representation",
             value=False
         ),
-        gr.Checkbox(
-            label="Show segment details",
-            value=False
-        ),
         gr.Checkbox(
             label="Generate 3D structure (sdf file format)",
             value=False

requirements.txt

@@ -1,4 +1,4 @@
-gradio==4.19.2
+gradio
 pandas==2.2.0
 rdkit==2023.9.1
 Pillow==10.0.0