Update app.py

app.py

@@ -281,15 +281,32 @@ def load_structure_data(uploaded_files, temp_dir):
     return structure_data
 
 
+
 def extract_window_coords(residues, window_indices):
-    """Extract coordinates for a window of residues - using Backbone + Sugar by default"""
-    coords_list = []
+    """
+    Extract coordinates for a specific window of residues.
+    
+    Args:
+        residues: List of all residues
+        window_indices: List of indices to extract
+    
+    Returns:
+        numpy array of coordinates
+    """
+    from rmsd_utils import get_backbone_sugar_coords_from_residue, get_base_coords_from_residue
+    
+    all_coords = []
     for idx in window_indices:
-        res = residues[idx]
-        backbone_coords = get_backbone_sugar_coords_from_residue(res)
-        coords_list.extend(backbone_coords)
-    return np.array(coords_list)
-
+        if idx < len(residues):
+            residue = residues[idx]
+            # Get backbone and sugar coordinates
+            backbone_coords = get_backbone_sugar_coords_from_residue(residue)
+            all_coords.extend(backbone_coords)
+            # Get base coordinates
+            base_coords = get_base_coords_from_residue(residue)
+            all_coords.extend(base_coords)
+    
+    return np.asarray(all_coords)
 
 
 def generate_windows_from_selection(selected_indices, window_size, window_type):