feat(esm mcp): get_prediction_pdb supports optional save_to_path on server

esm/mcp_output/mcp_plugin/mcp_service.py

@@ -253,8 +253,8 @@ def validate_protein_sequence(sequence: str):
         }
 
 
-@mcp.tool(name="get_prediction_pdb", description="Download saved PDB by filename or latest")
-def get_prediction_pdb(filename: str):
+@mcp.tool(name="get_prediction_pdb", description="Download saved PDB by filename or latest; optionally re-save on server")
+def get_prediction_pdb(filename: str, save_to_path: str | None = None):
     """Return PDB content saved under predictions directory.
 
     Parameters:
@@ -290,9 +290,22 @@ def get_prediction_pdb(filename: str):
         with open(target_path, "r") as f:
             content = f.read()
 
+        # Optionally save a copy to a given path (inside container)
+        saved_to: str | None = None
+        if save_to_path:
+            try:
+                save_dir = os.path.dirname(save_to_path)
+                if save_dir and not os.path.isdir(save_dir):
+                    os.makedirs(save_dir, exist_ok=True)
+                with open(save_to_path, "w") as out_f:
+                    out_f.write(content)
+                saved_to = save_to_path
+            except Exception as save_err:
+                return {"success": False, "result": None, "error": f"Save failed: {save_err}"}
+
         return {
             "success": True,
-            "result": {"filename": filename, "pdb_content": content, "path": target_path},
+            "result": {"filename": filename, "pdb_content": content, "path": target_path, "saved_copy_path": saved_to},
             "error": None,
         }
     except Exception as e: