Use shutil to zip and download colab outputs

PiperOrigin-RevId: 501595938
Change-Id: Ib586090d13279eca1371f0e0b046379b728a3e87

notebooks/AlphaFold.ipynb

@@ -342,6 +342,7 @@
         "from concurrent import futures\n",
         "import json\n",
         "import random\n",
+        "import shutil\n",
         "\n",
         "from urllib import request\n",
         "from google.colab import files\n",
@@ -773,7 +774,7 @@
         "    f.write(pae_data)\n",
         "\n",
         "# --- Download the predictions ---\n",
-        "!zip -q -r {output_dir}.zip {output_dir}\n",
+        "shutil.make_archive(base_name='prediction', format='zip', root_dir=output_dir)\n",
         "files.download(f'{output_dir}.zip')"
       ]
     },