minor fix

app.py

@@ -551,7 +551,7 @@ def create_enhanced_linear_viz(sequence, smiles):
     plt.tight_layout()
     return fig
 
-def process_input(smiles_input=None, file_obj=None, show_linear=False):
+def process_input(smiles_input=None, file_obj=None, show_linear=False, show_segment_details=False):
     """Process input and create visualizations using PeptideAnalyzer"""
     analyzer = PeptideAnalyzer()
     
@@ -574,23 +574,37 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False):
             
             # Process segments and build sequence
             sequence_parts = []
-            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)})")
+            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:
-                        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 += f"Warning: Could not identify residue in segment: {segment['content']}\n"
+                output_text += "\n"
+            else:
+                # Just build sequence without detailed analysis in output
+                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)
             
             # Check if cyclic using analyzer's method
             is_cyclic, peptide_cycles, aromatic_cycles = analyzer.is_cyclic(smiles)
@@ -610,14 +624,14 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False):
                 plt.close(fig_linear)
             
             # Add summary to output
-            summary = f"\nSummary:\n"
+            summary = "Summary:\n"
             summary += f"Sequence: {sequence}\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"
             
-            return summary + "\n" + output_text, img_cyclic, img_linear
+            return summary + output_text, img_cyclic, img_linear
             
         except Exception as e:
             return f"Error processing SMILES: {str(e)}", None, None
@@ -644,19 +658,37 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False):
                     # Process this SMILES
                     segments = analyzer.split_on_bonds(smiles)
                     sequence_parts = []
-                    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)
+                    
+                    # Add segment details if requested
+                    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)
                     
                     # Get cyclicity and create sequence
                     is_cyclic, peptide_cycles, aromatic_cycles = analyzer.is_cyclic(smiles)
                     sequence = f"cyclo({'-'.join(sequence_parts)})" if is_cyclic else '-'.join(sequence_parts)
                     
-                    output_text += f"SMILES: {smiles}\n"
+                    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:
@@ -673,32 +705,16 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False):
 
 iface = gr.Interface(
     fn=process_input,
-    inputs=[
-        gr.Textbox(
-            label="Enter SMILES string",
-            placeholder="Enter SMILES notation of peptide...",
-            lines=2
-        ),
-        gr.File(
-            label="Or upload a text file with SMILES",
-            file_types=[".txt"],
-            type="binary"
-        ),
-        gr.Checkbox(
-            label="Show linear representation"
-        )
+    iinputs=[
+        gr.Textbox(label="Enter SMILES string", placeholder="Enter SMILES notation of peptide...", lines=2),
+        gr.File(label="Or upload a text file with SMILES", file_types=[".txt"], type="binary"),
+        gr.Checkbox(label="Show linear representation"),
+        gr.Checkbox(label="Show segment details")  # New checkbox for segment details
     ],
     outputs=[
-        gr.Textbox(
-            label="Analysis Results",
-            lines=10
-        ),
-        gr.Image(
-            label="2D Structure with Annotations"
-        ),
-        gr.Image(
-            label="Linear Representation"
-        )
+        gr.Textbox(label="Analysis Results", lines=10),
+        gr.Image(label="2D Structure with Annotations"),
+        gr.Image(label="Linear Representation")
     ],
     title="Peptide Structure Analyzer and Visualizer",
     description="""