Colab has old requirements for AlphaFold

rgn2_prediction.ipynb

@@ -1,21 +1,29 @@
 {
   "cells": [
     {
+      "attachments": {},
       "cell_type": "markdown",
+      "id": "3SDCdyj7XneF",
+      "metadata": {
+        "id": "3SDCdyj7XneF"
+      },
       "source": [
         "# RGN2 Colab\n",
         "## Instructions\n",
         "1. Paste your protein sequence in the input field.\n",
         "2. Run the cells in the Colab individually with the play button on the left or via _Runtime_ > _Run all._\n",
         "3. The predicted protein structure will be downloaded after the final \"Refinement\" cell is executed."
-      ],
-      "metadata": {
-        "id": "3SDCdyj7XneF"
-      },
-      "id": "3SDCdyj7XneF"
+      ]
     },
     {
       "cell_type": "code",
+      "execution_count": null,
+      "id": "_ds-a3EgRUsb",
+      "metadata": {
+        "cellView": "form",
+        "id": "_ds-a3EgRUsb"
+      },
+      "outputs": [],
       "source": [
         "#@title Download RGN2 and Install Dependencies\n",
         "\n",
@@ -52,7 +60,7 @@
         "      https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \\\n",
         "        && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n",
         "        && rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n",
-        "    \n",
+        "\n",
         "    PATH=%env PATH\n",
         "    %env PATH=/opt/conda/bin:{PATH}\n",
         "\n",
@@ -70,12 +78,14 @@
         "    %shell rm -rf alphafold\n",
         "    %shell git clone --branch v2.2.4 {AF2_GIT_REPO} alphafold\n",
         "    %shell {CONDA_INIT} && conda create -y -q --name af2 python=3.7\n",
-        "    %shell {AF2_ENV_INIT} && pip install -r ./alphafold/requirements.txt\n",
+        "    %shell {AF2_ENV_INIT} && pip install ml-collections==0.1.0 numpy==1.21.6 pandas==1.3.4 protobuf==3.20.1 scipy==1.7.0 tensorflow-cpu==2.9.0\n",
         "    %shell {AF2_ENV_INIT} && pip install --no-dependencies ./alphafold\n",
-        "    %shell {AF2_ENV_INIT} && pip install --upgrade jax==0.3.17 \\\n",
-        "      jaxlib==0.3.15+cuda11.cudnn805 \\\n",
+        "    %shell {AF2_ENV_INIT} && pip install --upgrade jax==0.3.25 \\\n",
+        "      jaxlib==0.3.25+cuda11.cudnn82 \\\n",
         "      -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n",
-        "    \n",
+        "    %shell {AF2_ENV_INIT} && pip install biopython==1.81 chex==0.1.5 dm-haiku==0.0.9 dm-tree==0.1.8 docker==6.1.3 immutabledict==2.2.5\n",
+        "    %shell {AF2_ENV_INIT} && pip install --upgrade typing_extensions\n",
+        "\n",
         "    %shell mkdir --parents \"{AF2_PARAMS_DIR}\"\n",
         "    %shell wget -O \"{AF2_PARAMS_PATH}\" \"{AF2_SOURCE_URL}\"\n",
         "    %shell tar --extract --verbose --file=\"{AF2_PARAMS_PATH}\" \\\n",
@@ -95,17 +105,17 @@
         "except subprocess.CalledProcessError:\n",
         "  print(captured)\n",
         "  raise"
-      ],
-      "metadata": {
-        "id": "_ds-a3EgRUsb",
-        "cellView": "form"
-      },
-      "id": "_ds-a3EgRUsb",
-      "execution_count": null,
-      "outputs": []
+      ]
     },
     {
       "cell_type": "code",
+      "execution_count": null,
+      "id": "7GBilHivRmgP",
+      "metadata": {
+        "cellView": "form",
+        "id": "7GBilHivRmgP"
+      },
+      "outputs": [],
       "source": [
         "#@title Import Python Packages\n",
         "\n",
@@ -127,17 +137,17 @@
         "\n",
         "sys.path.append('/content/alphafold')\n",
         "from ter2pdb import ter2pdb"
-      ],
-      "metadata": {
-        "id": "7GBilHivRmgP",
-        "cellView": "form"
-      },
-      "id": "7GBilHivRmgP",
-      "execution_count": null,
-      "outputs": []
+      ]
     },
     {
       "cell_type": "code",
+      "execution_count": null,
+      "id": "_5YeBefARz0D",
+      "metadata": {
+        "cellView": "form",
+        "id": "_5YeBefARz0D"
+      },
+      "outputs": [],
       "source": [
         "#@title ### Enter the amino acid sequence to fold ⬇️\n",
         "sequence = 'DEEEIQKAIEELLRKGVSEEEAAIIIVQRFNVAVVVVVQDERQGKHISEYIRRYIPEADVILFANLVVIKVETHELSTRVWEAAQKAY'  #@param {type:\"string\"}\n",
@@ -171,22 +181,15 @@
         "REFINE_DIR = 'output/refine_model1'\n",
         "SEQ_PATH = os.path.join(DATA_DIR, f'{seq_id}.fa')\n",
         "TER_PATH = os.path.join(RUN_DIR, '1', 'outputsTesting', f'{seq_id}.tertiary')"
-      ],
-      "metadata": {
-        "id": "_5YeBefARz0D",
-        "cellView": "form"
-      },
-      "id": "_5YeBefARz0D",
-      "execution_count": null,
-      "outputs": []
+      ]
     },
     {
       "cell_type": "code",
       "execution_count": null,
       "id": "d93c3e44",
       "metadata": {
-        "id": "d93c3e44",
-        "cellView": "form"
+        "cellView": "form",
+        "id": "d93c3e44"
       },
       "outputs": [],
       "source": [
@@ -227,6 +230,13 @@
     },
     {
       "cell_type": "code",
+      "execution_count": null,
+      "id": "IJkrRgF3R63Q",
+      "metadata": {
+        "cellView": "form",
+        "id": "IJkrRgF3R63Q"
+      },
+      "outputs": [],
       "source": [
         "#@title Run RGN2\n",
         "#@markdown This step generates the raw RGN2-predicted C-alpha trace.\n",
@@ -242,17 +252,17 @@
         "  raise\n",
         "\n",
         "print('Prediction completed!')"
-      ],
-      "metadata": {
-        "id": "IJkrRgF3R63Q",
-        "cellView": "form"
-      },
-      "id": "IJkrRgF3R63Q",
-      "execution_count": null,
-      "outputs": []
+      ]
     },
     {
       "cell_type": "code",
+      "execution_count": null,
+      "id": "I0A_TUORSukb",
+      "metadata": {
+        "cellView": "form",
+        "id": "I0A_TUORSukb"
+      },
+      "outputs": [],
       "source": [
         "#@title Refinement and Structure Download\n",
         "#@markdown Once this cell has been executed, a PDB file with the refined\n",
@@ -283,17 +293,16 @@
         "print('Refinement completed!')\n",
         "\n",
         "files.download(os.path.join(REFINE_DIR, f'{seq_id}{out_suffix}.pdb'))"
-      ],
-      "metadata": {
-        "id": "I0A_TUORSukb",
-        "cellView": "form"
-      },
-      "id": "I0A_TUORSukb",
-      "execution_count": null,
-      "outputs": []
+      ]
     }
   ],
   "metadata": {
+    "accelerator": "GPU",
+    "colab": {
+      "collapsed_sections": [],
+      "provenance": []
+    },
+    "gpuClass": "standard",
     "kernelspec": {
       "display_name": "Python 3",
       "language": "python",
@@ -310,14 +319,8 @@
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
       "version": "3.6.8"
-    },
-    "colab": {
-      "provenance": [],
-      "collapsed_sections": []
-    },
-    "accelerator": "GPU",
-    "gpuClass": "standard"
+    }
   },
   "nbformat": 4,
   "nbformat_minor": 5
-}
+}