bug fixing

app.py

@@ -1,7 +1,17 @@
 import os
 import gradio as gr
 import gradio.blocks
-gradio.blocks.Blocks.get_api_info = lambda self: {}
+from gradio.blocks import Blocks
+
+original_get_api_info = Blocks.get_api_info
+
+def safe_get_api_info(self):
+    try:
+        return original_get_api_info(self)
+    except Exception as e:
+        print("⚠️ Failed to generate API schema:", e)
+        return {}
+
 import re
 import pandas as pd
 from io import StringIO
@@ -867,35 +877,74 @@ def process_input(
                 except Exception as e:
                     return f"Error generating 3D structures: {str(e)}", None, None, []
                 
-            # Process the structure
-            result = analyzer.analyze_structure(smiles)
+            segments = analyzer.split_on_bonds(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})"
             
-            # Create the 2D structure visualization
-            img_cyclic = annotate_cyclic_structure(mol, result['three_letter'])
+            img_cyclic = annotate_cyclic_structure(mol, three_letter)
             
             # Create linear representation if requested
             img_linear = None
             if show_linear:
-                fig_linear = create_enhanced_linear_viz(result['three_letter'], smiles)
+                fig_linear = create_enhanced_linear_viz(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: {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"
+            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"
             
             if structure_files:
                 summary += "\n3D Structures Generated:\n"
                 for filepath in structure_files:
                     summary += f"- {os.path.basename(filepath)}\n"
             
-            # Return the results
-            return summary, img_cyclic, img_linear, structure_files if structure_files else []
+            return summary + output_text, img_cyclic, img_linear, structure_files if structure_files else []
             
         except Exception as e:
             return f"Error processing SMILES: {str(e)}", None, None, []
@@ -960,6 +1009,10 @@ iface = gr.Interface(
             label="Show linear representation",
             value=False
         ),
+        gr.Checkbox(
+            label="Show show segmentation details",
+            value=False
+        ),
         gr.Checkbox(
             label="Generate 3D structure (sdf file format)",
             value=False
@@ -1014,4 +1067,5 @@ iface = gr.Interface(
 )
 
 if __name__ == "__main__":
+    Blocks.get_api_info = safe_get_api_info
     iface.launch(share=True)