Updated

.ipynb_checkpoints/app-checkpoint.py

@@ -45,8 +45,15 @@ def normalize_scores(scores):
 
 def read_mol(pdb_path):
     """Read PDB file and return its content as a string"""
-    with open(pdb_path, 'r') as f:
-        return f.read()
+    try:
+        with open(pdb_path, 'r') as f:
+            return f.read()
+    except FileNotFoundError:
+        print(f"File not found: {pdb_path}")
+        raise
+    except Exception as e:
+        print(f"Error reading file {pdb_path}: {str(e)}")
+        raise
 
 def fetch_structure(pdb_id: str, output_dir: str = ".") -> Optional[str]:
     """
@@ -277,8 +284,17 @@ def process_pdb(pdb_id_or_file, segment, score_type='normalized'):
 
 
 def molecule(input_pdb, residue_scores=None, segment='A'):
+    # Check if the file exists
+    if not os.path.isfile(input_pdb):
+        return f"<p>Error: PDB file not found at {input_pdb}</p>"
+    
+    try:
+        # Read PDB file content
+        mol = read_mol(input_pdb)
+    except Exception as e:
+        return f"<p>Error reading PDB file: {str(e)}</p>"
     # More granular scoring for visualization
-    mol = read_mol(input_pdb)  # Read PDB file content
+    #mol = read_mol(input_pdb)  # Read PDB file content
 
     # Prepare high-scoring residues script if scores are provided
     high_score_script = ""
@@ -491,9 +507,16 @@ with gr.Blocks(css="""
     
     def process_interface(mode, pdb_id, pdb_file, chain_id, score_type_val):
         selected_score_type = 'normalized' if score_type_val == "Normalized Scores" else 'raw'
+        
+        # First get the actual PDB file path
         if mode == "PDB ID":
-            result, mol_vis, files, raw_scores, norm_scores = process_pdb(pdb_id, chain_id, selected_score_type)
-            return result, mol_vis, files, raw_scores, norm_scores, pdb_id, chain_id
+            pdb_path = fetch_pdb(pdb_id)  # Get the actual file path
+            if not pdb_path:
+                return "Failed to fetch PDB file", None, None, None, None, None, None
+            
+            pymol_cmd, mol_vis, files, raw_scores, norm_scores = process_pdb(pdb_path, chain_id, selected_score_type)
+            # Store the actual file path, not just the PDB ID
+            return pymol_cmd, mol_vis, files, raw_scores, norm_scores, pdb_path, chain_id
         elif mode == "Upload File":
             _, ext = os.path.splitext(pdb_file.name)
             file_path = os.path.join('./', f"{_}{ext}")
@@ -501,15 +524,20 @@ with gr.Blocks(css="""
                 pdb_path = convert_cif_to_pdb(file_path)
             else:
                 pdb_path = file_path
-            result, mol_vis, files, raw_scores, norm_scores = process_pdb(pdb_path, chain_id, selected_score_type)
-            return result, mol_vis, files, raw_scores, norm_scores, pdb_path, chain_id
+            
+            pymol_cmd, mol_vis, files, raw_scores, norm_scores = process_pdb(pdb_path, chain_id, selected_score_type)
+            return pymol_cmd, mol_vis, files, raw_scores, norm_scores, pdb_path, chain_id
         else:
             return "Error: Invalid mode selected", None, None, None, None, None, None
-
+            
     def update_visualization(score_type_val, raw_scores, norm_scores, pdb_path, segment):
         if raw_scores is None or norm_scores is None or pdb_path is None or segment is None:
             return None
         
+        # Verify the file exists
+        if not os.path.exists(pdb_path):
+            return f"Error: File not found at {pdb_path}"
+        
         # Choose scores based on radio button selection
         selected_scores = norm_scores if score_type_val == "Normalized Scores" else raw_scores
         

app.py

@@ -45,8 +45,15 @@ def normalize_scores(scores):
 
 def read_mol(pdb_path):
     """Read PDB file and return its content as a string"""
-    with open(pdb_path, 'r') as f:
-        return f.read()
+    try:
+        with open(pdb_path, 'r') as f:
+            return f.read()
+    except FileNotFoundError:
+        print(f"File not found: {pdb_path}")
+        raise
+    except Exception as e:
+        print(f"Error reading file {pdb_path}: {str(e)}")
+        raise
 
 def fetch_structure(pdb_id: str, output_dir: str = ".") -> Optional[str]:
     """
@@ -277,8 +284,17 @@ def process_pdb(pdb_id_or_file, segment, score_type='normalized'):
 
 
 def molecule(input_pdb, residue_scores=None, segment='A'):
+    # Check if the file exists
+    if not os.path.isfile(input_pdb):
+        return f"<p>Error: PDB file not found at {input_pdb}</p>"
+    
+    try:
+        # Read PDB file content
+        mol = read_mol(input_pdb)
+    except Exception as e:
+        return f"<p>Error reading PDB file: {str(e)}</p>"
     # More granular scoring for visualization
-    mol = read_mol(input_pdb)  # Read PDB file content
+    #mol = read_mol(input_pdb)  # Read PDB file content
 
     # Prepare high-scoring residues script if scores are provided
     high_score_script = ""
@@ -491,9 +507,16 @@ with gr.Blocks(css="""
     
     def process_interface(mode, pdb_id, pdb_file, chain_id, score_type_val):
         selected_score_type = 'normalized' if score_type_val == "Normalized Scores" else 'raw'
+        
+        # First get the actual PDB file path
         if mode == "PDB ID":
-            result, mol_vis, files, raw_scores, norm_scores = process_pdb(pdb_id, chain_id, selected_score_type)
-            return result, mol_vis, files, raw_scores, norm_scores, pdb_id, chain_id
+            pdb_path = fetch_pdb(pdb_id)  # Get the actual file path
+            if not pdb_path:
+                return "Failed to fetch PDB file", None, None, None, None, None, None
+            
+            pymol_cmd, mol_vis, files, raw_scores, norm_scores = process_pdb(pdb_path, chain_id, selected_score_type)
+            # Store the actual file path, not just the PDB ID
+            return pymol_cmd, mol_vis, files, raw_scores, norm_scores, pdb_path, chain_id
         elif mode == "Upload File":
             _, ext = os.path.splitext(pdb_file.name)
             file_path = os.path.join('./', f"{_}{ext}")
@@ -501,15 +524,20 @@ with gr.Blocks(css="""
                 pdb_path = convert_cif_to_pdb(file_path)
             else:
                 pdb_path = file_path
-            result, mol_vis, files, raw_scores, norm_scores = process_pdb(pdb_path, chain_id, selected_score_type)
-            return result, mol_vis, files, raw_scores, norm_scores, pdb_path, chain_id
+            
+            pymol_cmd, mol_vis, files, raw_scores, norm_scores = process_pdb(pdb_path, chain_id, selected_score_type)
+            return pymol_cmd, mol_vis, files, raw_scores, norm_scores, pdb_path, chain_id
         else:
             return "Error: Invalid mode selected", None, None, None, None, None, None
-
+            
     def update_visualization(score_type_val, raw_scores, norm_scores, pdb_path, segment):
         if raw_scores is None or norm_scores is None or pdb_path is None or segment is None:
             return None
         
+        # Verify the file exists
+        if not os.path.exists(pdb_path):
+            return f"Error: File not found at {pdb_path}"
+        
         # Choose scores based on radio button selection
         selected_scores = norm_scores if score_type_val == "Normalized Scores" else raw_scores