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Commit e09dd313 authored by jnwei's avatar jnwei
Browse files

Fixes imports to colab notebook.

parent 099769d2
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notebooks/OpenFold.ipynb
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{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"accelerator": "GPU",
"colab": {
"name": "OpenFold.ipynb",
"provenance": [],
"collapsed_sections": []
},
"kernelspec": {
"display_name": "Python 3",
"name": "python3"
},
"language_info": {
"name": "python"
}
},
"cells": [
{
"cell_type": "markdown",
......@@ -57,10 +40,12 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "rowN0bVYLe9n",
"cellView": "form"
"cellView": "form",
"id": "rowN0bVYLe9n"
},
"outputs": [],
"source": [
"#@markdown ### Enter the amino acid sequence to fold ⬇️\n",
"sequence = 'MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH' #@param {type:\"string\"}\n",
......@@ -78,16 +63,16 @@
"\n",
"#@markdown After making your selections, execute this cell by pressing the\n",
"#@markdown *Play* button on the left."
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "woIxeCPygt7K",
"cellView": "form"
"cellView": "form",
"id": "woIxeCPygt7K"
},
"outputs": [],
"source": [
"#@title Install third-party software\n",
"#@markdown Please execute this cell by pressing the *Play* button on \n",
......@@ -97,75 +82,54 @@
"#@markdown **Note**: This installs the software on the Colab \n",
"#@markdown notebook in the cloud and not on your computer.\n",
"\n",
"import sys\n",
"import os, time\n",
"from IPython.utils import io\n",
"import os\n",
"from sys import version_info\n",
"import subprocess\n",
"import tqdm.notebook\n",
"\n",
"TQDM_BAR_FORMAT = '{l_bar}{bar}| {n_fmt}/{total_fmt} [elapsed: {elapsed} remaining: {remaining}]'\n",
"python_version = f\"{version_info.major}.{version_info.minor}\"\n",
"\n",
"python_version = '.'.join(sys.version.split('.')[:2]) #get string like \"3.9\"\n",
"\n",
"os.system(\"wget -qnc https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh\")\n",
"os.system(\"bash Mambaforge-Linux-x86_64.sh -bfp /usr/local\")\n",
"os.system(\"mamba config --set auto_update_conda false\")\n",
"os.system(f\"mamba install -y -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 openmm=7.7.0 python={python_version} pdbfixer\")\n",
"\n",
"\n",
"os.system(\"pip install -q \\\"torch<2\\\" biopython ml_collections py3Dmol modelcif\")\n",
"\n",
"try:\n",
" with io.capture_output() as captured:\n",
" %shell sudo apt install --quiet --yes hmmer\n",
"\n",
" # Install py3dmol.\n",
" %shell pip install py3dmol\n",
"\n",
" %shell rm -rf /opt/conda\n",
" %shell wget -q -P /tmp \\\n",
" 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",
" PATH=%env PATH\n",
" %env PATH=/opt/conda/bin:{PATH}\n",
"\n",
" # Install the required versions of all dependencies.\n",
" %shell conda install -y -q conda==4.13.0\n",
" %shell conda install -y -q -c conda-forge -c bioconda \\\n",
" kalign2=2.04 \\\n",
" hhsuite=3.3.0 \\\n",
" python={python_version} \\\n",
" openmm=7.7.0 \\\n",
" pdbfixer \\\n",
" 2>&1 1>/dev/null\n",
" %shell pip install -q \\\n",
" ml-collections==0.1.0 \\\n",
" PyYAML==5.4.1 \\\n",
" biopython==1.79 \\\n",
" modelcif==0.7\n",
"\n",
" # Create a ramdisk to store a database chunk to make Jackhmmer run fast.\n",
" %shell sudo apt install --quiet --yes hmmer\n",
" %shell sudo mkdir -m 777 --parents /tmp/ramdisk\n",
" %shell sudo mount -t tmpfs -o size=9G ramdisk /tmp/ramdisk\n",
"\n",
" %shell wget -q -P /content \\\n",
" https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt\n",
"\n",
" # Install AWS CLI\n",
" %shell curl \"https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip\" -o \"awscliv2.zip\"\n",
" %shell unzip -qq awscliv2.zip\n",
" %shell sudo ./aws/install\n",
" %shell rm awscliv2.zip\n",
" %shell rm -rf ./aws\n",
" %shell mkdir -p /content/openfold/openfold/resourcees\n",
" \n",
" commit = \"099769d2ecfd01a8baa8d950030df454a042c910\"\n",
" os.system(f\"pip install -q git+https://github.com/aqlaboratory/openfold.git@{commit}\")\n",
" \n",
" %shell cp -f /content/stereo_chemical_props.txt /usr/local/lib/python3.10/site-packages/openfold/resources/\n",
"\n",
"except subprocess.CalledProcessError as captured:\n",
" print(captured)\n",
" raise"
],
"execution_count": null,
"outputs": []
" print(captured)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "VzJ5iMjTtoZw",
"cellView": "form"
"cellView": "form",
"id": "VzJ5iMjTtoZw"
},
"outputs": [],
"source": [
"#@title Install OpenFold\n",
"#@title Download model weights \n",
"#@markdown Please execute this cell by pressing the *Play* button on \n",
"#@markdown the left.\n",
"\n",
......@@ -180,13 +144,6 @@
"\n",
"try:\n",
" with io.capture_output() as captured:\n",
" # Run setup.py to install only Openfold.\n",
" %shell rm -rf openfold\n",
" %shell git clone \"{GIT_REPO}\" openfold 2>&1 1> /dev/null\n",
" %shell mkdir -p /content/openfold/openfold/resources\n",
" %shell cp -f /content/stereo_chemical_props.txt /content/openfold/openfold/resources\n",
" %shell /usr/bin/python3 -m pip install -q ./openfold\n",
"\n",
" if(weight_set == 'AlphaFold'):\n",
" %shell mkdir --parents \"{ALPHAFOLD_PARAMS_DIR}\"\n",
" %shell wget -O {ALPHAFOLD_PARAMS_PATH} {ALPHAFOLD_PARAM_SOURCE_URL}\n",
......@@ -194,7 +151,14 @@
" --directory=\"{ALPHAFOLD_PARAMS_DIR}\" --preserve-permissions\n",
" %shell rm \"{ALPHAFOLD_PARAMS_PATH}\"\n",
" elif(weight_set == 'OpenFold'):\n",
" # Install AWS CLI\n",
" %shell curl \"https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip\" -o \"awscliv2.zip\"\n",
" %shell unzip -qq awscliv2.zip\n",
" %shell sudo ./aws/install\n",
" %shell rm awscliv2.zip\n",
" %shell rm -rf ./aws\n",
" %shell mkdir --parents \"{OPENFOLD_PARAMS_DIR}\"\n",
"\n",
" %shell aws s3 cp \\\n",
" --no-sign-request \\\n",
" --region us-east-1 \\\n",
......@@ -203,14 +167,17 @@
" else:\n",
" raise ValueError(\"Invalid weight set\")\n",
"except subprocess.CalledProcessError as captured:\n",
" print(captured)\n",
" raise"
],
"execution_count": null,
"outputs": []
" print(captured)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"cellView": "form",
"id": "_FpxxMo-mvcP"
},
"outputs": [],
"source": [
"#@title Import Python packages\n",
"#@markdown Please execute this cell by pressing the *Play* button on \n",
......@@ -219,8 +186,8 @@
"import unittest.mock\n",
"import sys\n",
"\n",
"sys.path.insert(0, f'/usr/local/lib/python{python_version}/dist-packages/')\n",
"sys.path.insert(0, f'/usr/local/lib/python{python_version}/site-packages/')\n",
"sys.path.append(f'/opt/conda/lib/python{python_version}/site-packages')\n",
"\n",
"# Allows us to skip installing these packages\n",
"unnecessary_modules = [\n",
......@@ -245,6 +212,10 @@
"import py3Dmol\n",
"import torch\n",
"import shutil\n",
"import tqdm\n",
"import tqdm.notebook\n",
"\n",
"TQDM_BAR_FORMAT = '{l_bar}{bar}| {n_fmt}/{total_fmt} [elapsed: {elapsed} remaining: {remaining}]'\n",
"\n",
"# Prevent shell magic being broken by openmm, prevent this cryptic error:\n",
"# \"NotImplementedError: A UTF-8 locale is required. Got ANSI_X3.4-1968\"\n",
......@@ -280,13 +251,7 @@
"from IPython import display\n",
"from ipywidgets import GridspecLayout\n",
"from ipywidgets import Output"
],
"metadata": {
"id": "_FpxxMo-mvcP",
"cellView": "form"
},
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "markdown",
......@@ -301,10 +266,12 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "2tTeTTsLKPjB",
"cellView": "form"
"cellView": "form",
"id": "2tTeTTsLKPjB"
},
"outputs": [],
"source": [
"#@title Search against genetic databases\n",
"\n",
......@@ -420,16 +387,16 @@
"plt.ylabel('Non-Gap Count')\n",
"plt.yticks(range(0, num_alignments + 1, max(1, int(num_alignments / 3))))\n",
"plt.show()"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "XUo6foMQxwS2",
"cellView": "form"
"cellView": "form",
"id": "XUo6foMQxwS2"
},
"outputs": [],
"source": [
"#@title Run OpenFold and download prediction\n",
"\n",
......@@ -693,9 +660,7 @@
"# --- Download the predictions ---\n",
"shutil.make_archive(base_name='prediction', format='zip', root_dir=output_dir)\n",
"files.download(f'{output_dir}.zip')"
],
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "markdown",
......@@ -789,5 +754,22 @@
"* BFD: (modified), by Steinegger M. and Söding J., modified by DeepMind, available under a [Creative Commons Attribution-ShareAlike 4.0 International License](https://creativecommons.org/licenses/by/4.0/). See the Methods section of the [AlphaFold proteome paper](https://www.nature.com/articles/s41586-021-03828-1) for details."
]
}
]
],
"metadata": {
"accelerator": "GPU",
"colab": {
"collapsed_sections": [],
"name": "OpenFold.ipynb",
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
"name": "python3"
},
"language_info": {
"name": "python"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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