feat(mcp): add get_prediction_pdb tool (latest/by name) and simplify to read-only

esm/mcp_output/mcp_plugin/mcp_service.py

@@ -196,6 +196,51 @@ def predict_structure(sequence: str):
             "error": f"Error predicting structure: {str(e)}"
         }
 
+@mcp.tool(name="get_prediction_pdb", description="Fetch saved PDB by filename or latest from predictions directory")
+def get_prediction_pdb(filename: str):
+    """Return PDB content saved under predictions directory.
+
+    Parameters:
+        filename (str): Filename in predictions directory. Use "latest" to fetch the most recent file.
+
+    Returns:
+        dict: success/result/error. result contains { filename, pdb_content, path }
+    """
+    try:
+        import glob
+        predictions_dir = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "predictions")
+        if not os.path.isdir(predictions_dir):
+            return {"success": False, "result": None, "error": f"Predictions dir not found: {predictions_dir}"}
+
+        target_path: str
+        if filename.strip().lower() == "latest":
+            files = sorted(
+                glob.glob(os.path.join(predictions_dir, "*.pdb")),
+                key=lambda p: os.path.getmtime(p),
+                reverse=True,
+            )
+            if not files:
+                return {"success": False, "result": None, "error": "No PDB files found"}
+            target_path = files[0]
+            filename = os.path.basename(target_path)
+        else:
+            # prevent path traversal
+            safe_name = os.path.basename(filename)
+            target_path = os.path.join(predictions_dir, safe_name)
+            if not os.path.isfile(target_path):
+                return {"success": False, "result": None, "error": f"File not found: {safe_name}"}
+
+        with open(target_path, "r") as f:
+            content = f.read()
+
+        return {
+            "success": True,
+            "result": {"filename": filename, "pdb_content": content, "path": target_path},
+            "error": None,
+        }
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
 @mcp.tool(name="analyze_protein_sequence", description="Analyze protein sequence features")
 def analyze_protein_sequence(sequence: str):
     """Analyze basic features of a protein sequence"""