add more functions

app.py

@@ -241,16 +241,18 @@ def analyze_single_smiles(smiles):
 def annotate_cyclic_structure(mol, sequence):
     """Create annotated 2D structure with clear, non-overlapping residue labels"""
     # Generate 2D coordinates
+    # Generate 2D coordinates
     AllChem.Compute2DCoords(mol)
     
     # Create drawer with larger size for annotations
     drawer = Draw.rdMolDraw2D.MolDraw2DCairo(2000, 2000)  # Even larger size
     
-    # Get residue list
+    # Get residue list and reverse it to match structural representation
     if sequence.startswith('cyclo('):
         residues = sequence[6:-1].split('-')
     else:
         residues = sequence.split('-')
+    residues = list(reversed(residues))  # Reverse the sequence
     
     # Draw molecule first to get its bounds
     drawer.drawOptions().addAtomIndices = False
@@ -260,6 +262,7 @@ def annotate_cyclic_structure(mol, sequence):
     # Convert to PIL Image
     img = Image.open(BytesIO(drawer.GetDrawingText()))
     draw = ImageDraw.Draw(img)
+    
     try:
         # Try to use DejaVuSans as it's commonly available on Linux systems
         font = ImageFont.truetype("/usr/share/fonts/truetype/dejavu/DejaVuSans.ttf", 60)
@@ -274,7 +277,6 @@ def annotate_cyclic_structure(mol, sequence):
             print("Warning: TrueType fonts not available, using default font")
             font = ImageFont.load_default()
             small_font = ImageFont.load_default()
-
     # Get molecule bounds
     conf = mol.GetConformer()
     positions = []
@@ -296,16 +298,19 @@ def annotate_cyclic_structure(mol, sequence):
     n_residues = len(residues)
     radius = 700  # Distance of labels from center
     
+    # Start from the rightmost point (3 o'clock position) and go counterclockwise
+    # Offset by -3 positions to align with structure
+    offset = 0  # Adjust this value to match the structure alignment
     for i, residue in enumerate(residues):
         # Calculate position in a circle around the structure
-        angle = (2 * np.pi * i / n_residues) - np.pi/2  # Start from top
+        # Start from 0 (3 o'clock) and go counterclockwise
+        angle = -(2 * np.pi * ((i + offset) % n_residues) / n_residues)
         
         # Calculate label position
         label_x = center_x + radius * np.cos(angle)
         label_y = center_y + radius * np.sin(angle)
         
         # Draw residue label
-        # Add white background for better visibility
         text = f"{i+1}. {residue}"
         bbox = draw.textbbox((label_x, label_y), text, font=font)
         padding = 10
@@ -569,8 +574,8 @@ 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]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
-    2. CC(C)C[C@@H]1OC(=O)[C@H](C)NC(=O)[C@H](C(C)C)OC(=O)[C@H](C)N(C)C(=O)[C@@H](C)NC(=O)[C@@H](Cc2ccccc2)N(C)C1=O
+    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
     """,
     flagging_mode="never"
 )