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Merge pull request #102 from churnikov/101-fix-colab-notebook
Made jupyter notebook always pull latest version of AiZynthFinder
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,66 +1,96 @@ | ||
| { | ||
| "nbformat": 4, | ||
| "nbformat_minor": 0, | ||
| "metadata": { | ||
| "colab": { | ||
| "name": "AiZynthFinder.ipynb", | ||
| "private_outputs": true, | ||
| "provenance": [], | ||
| "collapsed_sections": [], | ||
| "toc_visible": true | ||
| }, | ||
| "kernelspec": { | ||
| "name": "python3", | ||
| "display_name": "Python 3" | ||
| }, | ||
| "accelerator": "GPU" | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": { | ||
| "id": "ObD2YL7nM2_X" | ||
| }, | ||
| "source": [ | ||
| "# AiZynthFinder\n", | ||
| "\n", | ||
| "Click the ▶ play button at the left of the **Installation** text below to install the application. The initial installation process may take a few minutes. After installation is done, jupyter notebooks kernel will automatically restart. Then run **Start application cell**. \n", | ||
| "\n", | ||
| "1. Enter the target compound [SMILES][1] code.\n", | ||
| "3. Click the **Run Search** button to start the algorithm.\n", | ||
| "4. Once it stops serching, click the **Show Reactions** button.\n", | ||
| "\n", | ||
| "[1]: https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system" | ||
| ] | ||
| }, | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": { | ||
| "id": "ObD2YL7nM2_X" | ||
| }, | ||
| "source": [ | ||
| "# AiZynthFinder\n", | ||
| "\n", | ||
| "Click the ▶ play button at the left of the **Start** text below to run the application. The initial installation process may take a few minutes.\n", | ||
| "\n", | ||
| "1. Enter the target compound [SMILES][1] code.\n", | ||
| "3. Click the **Run Search** button to start the algorithm.\n", | ||
| "4. Once it stops serching, click the **Show Reactions** button.\n", | ||
| "\n", | ||
| "[1]: https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "metadata": { | ||
| "id": "beDP-CSNM429" | ||
| }, | ||
| "source": [ | ||
| "#@title Start {display-mode: \"form\"}\n", | ||
| "!curl --location --silent bit.ly/rdkit-colab | tar xz -C /\n", | ||
| "!pip install --quiet graphviz\n", | ||
| "!pip install --quiet https://github.com/MolecularAI/aizynthfinder/archive/v2.2.1.tar.gz\n", | ||
| "!mkdir --parents data && download_public_data data\n", | ||
| "from rdkit.Chem.Draw import IPythonConsole\n", | ||
| "from aizynthfinder.interfaces import AiZynthApp\n", | ||
| "application = AiZynthApp(\"./data/config.yml\")\n" | ||
| ], | ||
| "execution_count": null, | ||
| "outputs": [] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": { | ||
| "id": "bwxusoogwlI9" | ||
| }, | ||
| "source": [ | ||
| "# Bibliography\n", | ||
| "\n", | ||
| "_Genheden S, Thakkar A, Chadimova V, et al (2020) AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. J. Cheminf. https://doi.org/10.1186/s13321-020-00472-1 ([GitHub](https://github.com/MolecularAI/aizynthfinder) & [Documentation](https://molecularai.github.io/aizynthfinder/html/index.html))_" | ||
| ] | ||
| } | ||
| ] | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "#@title Installation -- Run this cell to install AiZynthFinder\n", | ||
| "\n", | ||
| "!pip install --quiet graphviz rdkit-pypi\n", | ||
| "!(AIZ_LATEST_TAG=$(git -c 'versionsort.suffix=-' \\\n", | ||
| " ls-remote --exit-code --refs --sort='version:refname' --tags https://github.com/MolecularAI/aizynthfinder '*.*.*' \\\n", | ||
| " | tail --lines=1 \\\n", | ||
| " | cut -f 3 -d /) \\\n", | ||
| " && pip install --quiet https://github.com/MolecularAI/aizynthfinder/archive/${AIZ_LATEST_TAG}.tar.gz)\n", | ||
| "print(\"Restarting kernel\")\n", | ||
| "import os\n", | ||
| "os._exit(00)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "id": "beDP-CSNM429" | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "#@title Start application. Run this cell after kernel restart {display-mode: \"form\"}\n", | ||
| "\n", | ||
| "!mkdir --parents data && download_public_data data\n", | ||
| "from rdkit.Chem.Draw import IPythonConsole\n", | ||
| "from aizynthfinder.interfaces import AiZynthApp\n", | ||
| "application = AiZynthApp(\"./data/config.yml\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": { | ||
| "id": "bwxusoogwlI9" | ||
| }, | ||
| "source": [ | ||
| "# Bibliography\n", | ||
| "\n", | ||
| "_Genheden S, Thakkar A, Chadimova V, et al (2020) AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. J. Cheminf. https://doi.org/10.1186/s13321-020-00472-1 ([GitHub](https://github.com/MolecularAI/aizynthfinder) & [Documentation](https://molecularai.github.io/aizynthfinder/html/index.html))_" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "accelerator": "GPU", | ||
| "colab": { | ||
| "collapsed_sections": [], | ||
| "name": "AiZynthFinder.ipynb", | ||
| "private_outputs": true, | ||
| "provenance": [], | ||
| "toc_visible": true | ||
| }, | ||
| "kernelspec": { | ||
| "display_name": "Python 3 (ipykernel)", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.10.9" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 1 | ||
| } |