add more functions

app.py

@@ -237,7 +237,7 @@ def analyze_single_smiles(smiles):
             #'Peptide Cycles': 'Error',
             #'Aromatic Cycles': 'Error'
         }
-
+"""
 def annotate_cyclic_structure(mol, sequence):
     """Create annotated 2D structure with clear, non-overlapping residue labels"""
     # Generate 2D coordinates
@@ -332,6 +332,36 @@ def annotate_cyclic_structure(mol, sequence):
     
     return img
 
+"""
+def annotate_cyclic_structure(mol, sequence):
+    """Create structure visualization with just the sequence header"""
+    # Generate 2D coordinates
+    AllChem.Compute2DCoords(mol)
+    
+    # Create drawer with larger size for annotations
+    drawer = Draw.rdMolDraw2D.MolDraw2DCairo(2000, 2000)  # Even larger size
+    
+    # Draw molecule first
+    drawer.drawOptions().addAtomIndices = False
+    drawer.DrawMolecule(mol)
+    drawer.FinishDrawing()
+    
+    # Convert to PIL Image
+    img = Image.open(BytesIO(drawer.GetDrawingText()))
+    draw = ImageDraw.Draw(img)
+    small_font = ImageFont.load_default()
+    
+    # Add just the sequence header at the top
+    seq_text = f"Sequence: {sequence}"
+    bbox = draw.textbbox((1000, 100), seq_text, font=small_font)
+    padding = 10
+    draw.rectangle([bbox[0]-padding, bbox[1]-padding, 
+                   bbox[2]+padding, bbox[3]+padding], 
+                  fill='white', outline='white')
+    draw.text((1000, 100), seq_text, 
+             font=small_font, fill='black', anchor="mm")
+    
+    return img
 def create_enhanced_linear_viz(sequence, smiles):
     """
     Create an enhanced linear representation showing segment identification process
@@ -515,9 +545,15 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False):
     # Handle file input
     if file_obj is not None:
         try:
-            content = file_obj.decode('utf-8')
+            # Handle file content based on file object type
+            if hasattr(file_obj, 'name'):  # If it's a file path
+                with open(file_obj.name, 'r') as f:
+                    content = f.read()
+            else:  # If it's file content
+                content = file_obj.decode('utf-8') if isinstance(file_obj, bytes) else str(file_obj)
+            
             output_text = ""
-            for line in StringIO(content):
+            for line in content.splitlines():
                 smiles = line.strip()
                 if smiles:
                     if not is_peptide(smiles):
@@ -528,6 +564,7 @@ def process_input(smiles_input=None, file_obj=None, show_linear=False):
                     output_text += f"Is Cyclic: {result['Is Cyclic']}\n"
                     output_text += "-" * 50 + "\n"
             return output_text, None, None
+            
         except Exception as e:
             return f"Error processing file: {str(e)}", None, None
     
@@ -544,7 +581,8 @@ iface = gr.Interface(
         ),
         gr.File(
             label="Or upload a text file with SMILES",
-            file_types=[".txt"]
+            file_types=[".txt"],
+            type="binary"
         ),
         gr.Checkbox(
             label="Show linear representation"
@@ -573,9 +611,13 @@ iface = gr.Interface(
     
     Input: Either enter a SMILES string directly or upload a text file containing SMILES strings
     
-    Example SMILES strings:
-    1. 'CC(C)C[C@@H]1NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@@H](C)N(C)C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)N(C)C(=O)[C@H]2CCCN2C1=O'
-    2. 'C(C)C[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H](CC(C)C)NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@H](C)NC(=O)[C@H](Cc2ccccc2)NC1=O'
+    Example SMILES strings (copy and paste):
+    ```
+    CC(C)C[C@@H]1NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@@H](C)N(C)C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)N(C)C(=O)[C@H]2CCCN2C1=O
+    ```
+    ```
+    C(C)C[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H](CC(C)C)NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@H](C)NC(=O)[C@H](Cc2ccccc2)NC1=O
+    ```
     """,
     flagging_mode="never"
 )