Merge branch 'aqlaboratory:main' into main

notebooks/OpenFold.ipynb

@@ -4,7 +4,7 @@
   "metadata": {
     "accelerator": "GPU",
     "colab": {
-      "name": "Copy of OpenFold.ipynb",
+      "name": "OpenFold.ipynb",
       "provenance": [],
       "collapsed_sections": []
     },
@@ -111,6 +111,11 @@
         "      %shell wget -q -P /content \\\n",
         "        https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt\n",
         "      pbar.update(1)\n",
+        "\n",
+        "      # Install git-lfs\n",
+        "      %shell sudo apt-get install git-lfs\n",
+        "      %shell git lfs install\n",
+        "\n",
         "except subprocess.CalledProcessError as captured:\n",
         "  print(captured)\n",
         "  raise"

scripts/install_third_party_dependencies.sh

@@ -32,7 +32,7 @@ mkdir -p tests/test_data/alphafold/common
 ln -rs openfold/resources/stereo_chemical_props.txt tests/test_data/alphafold/common
 
 echo "Downloading OpenFold parameters..."
-bash scripts/download_openfold_params.sh openfold/resources
+bash scripts/download_openfold_params_huggingface.sh openfold/resources
 
 echo "Downloading AlphaFold parameters..."
 bash scripts/download_alphafold_params.sh openfold/resources