debug

app.py

@@ -117,8 +117,7 @@ class PeptideAnalyzer:
                 'content': complex_part
             })
             
-            # Debug
-            print(f"Protected {pos['type']}: {complex_part[:20]}... as {placeholder}")
+            #print(f"Protected {pos['type']}: {complex_part[:20]}... as {placeholder}")
         
         return preprocessed_smiles, protected_residues
     def split_on_bonds(self, smiles, protected_residues=None):
@@ -574,16 +573,16 @@ class PeptideAnalyzer:
     
     def analyze_structure(self, smiles):
         """Main analysis function with preprocessing for complex residues"""
-        print("\nAnalyzing structure:", smiles)
+        #print("\nAnalyzing structure:", smiles)
 
         # Pre-process to identify complex residues first
         preprocessed_smiles, protected_residues = self.preprocess_complex_residues(smiles)
-        
+        """
         if protected_residues:
             print(f"Identified {len(protected_residues)} complex residues during pre-processing")
             for i, residue in enumerate(protected_residues):
                 print(f"Complex residue {i+1}: {residue['type']}")
-
+        """
         
         # Check if it's cyclic
         is_cyclic, peptide_cycles, aromatic_cycles = self.is_cyclic(smiles)
@@ -591,22 +590,24 @@ class PeptideAnalyzer:
         # Split into segments, respecting protected residues
         segments = self.split_on_bonds(preprocessed_smiles, protected_residues)
         
-        print("\nSegment Analysis:")
+        #print("\nSegment Analysis:")
         sequence = []
         for i, segment in enumerate(segments):
+            """
             print(f"\nSegment {i}:")
             print(f"Content: {segment.get('content', 'None')}")
             print(f"Bond before: {segment.get('bond_before', 'None')}")
             print(f"Bond after: {segment.get('bond_after', 'None')}")
-            
+            """
             residue, mods = self.identify_residue(segment)
             if residue:
                 if mods:
                     sequence.append(f"{residue}({','.join(mods)})")
                 else:
                     sequence.append(residue)
-                print(f"Identified as: {residue}")
-                print(f"Modifications: {mods}")
+
+                #print(f"Identified as: {residue}")
+                #print(f"Modifications: {mods}")
             else:
                 print(f"Warning: Could not identify residue in segment: {segment.get('content', 'None')}")
         
@@ -619,13 +620,13 @@ class PeptideAnalyzer:
         if is_cyclic:
             three_letter = f"cyclo({three_letter})"
             one_letter = f"cyclo({one_letter})"
-        
+        """
         print(f"\nFinal sequence: {three_letter}")
         print(f"One-letter code: {one_letter}")
         print(f"Is cyclic: {is_cyclic}")
         print(f"Peptide cycles: {peptide_cycles}")
         print(f"Aromatic cycles: {aromatic_cycles}")
-        
+        """
         return {
             'three_letter': three_letter,
             'one_letter': one_letter,
@@ -994,11 +995,12 @@ def process_input(
                 for filepath in structure_files:
                     summary += f"- {os.path.basename(filepath)}\n"
             
-            return summary, img_cyclic, img_linear, structure_files if structure_files else None
-            
+            #return summary, img_cyclic, img_linear, structure_files if structure_files else None
+            return summary, img_cyclic
+
         except Exception as e:
-            return f"Error processing SMILES: {str(e)}", None, None, []
-    
+            #return f"Error processing SMILES: {str(e)}", None, None, []
+            return f"Error processing SMILES: {str(e)}", None
     # Handle file input
     if file_obj is not None:
         try:
@@ -1055,6 +1057,7 @@ iface = gr.Interface(
             label="Or upload a text file with SMILES",
             file_types=[".txt"]
         ),
+        """
         gr.Checkbox(
             label="Show linear representation",
             value=False
@@ -1071,6 +1074,7 @@ iface = gr.Interface(
             label="Use UFF optimization (may take long)",
             value=False
         )
+        """
     ],
     outputs=[
         gr.Textbox(
@@ -1081,6 +1085,7 @@ iface = gr.Interface(
             label="2D Structure with Annotations",
             type="pil"
         ),
+        """
         gr.Image(
             label="Linear Representation",
             type="pil"
@@ -1088,7 +1093,7 @@ iface = gr.Interface(
         gr.File(
             label="3D Structure Files",
             file_count="multiple"
-        )
+        )"""
     ],
     title="Peptide Structure Analyzer and Visualizer",
     description="""