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feat(docs): Add initial documentation
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| name: Docs | ||
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| on: | ||
| push: | ||
| branches: [ kmaziarz/docs ] | ||
| workflow_dispatch: | ||
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| permissions: | ||
| contents: write | ||
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| jobs: | ||
| deploy: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - name: Configure Git Credentials | ||
| run: | | ||
| git config user.name github-actions[bot] | ||
| git config user.email 41898282+github-actions[bot]@users.noreply.github.com | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.x | ||
| - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV | ||
| - uses: actions/cache@v3 | ||
| with: | ||
| key: mkdocs-material-${{ env.cache_id }} | ||
| path: .cache | ||
| restore-keys: | | ||
| mkdocs-material- | ||
| - run: pip install mkdocs-material | ||
| - run: mkdocs gh-deploy --force |
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| <figure markdown> | ||
| {width="450"} | ||
| <figcaption><h3>Navigating the labyrinth of synthesis planning</h3></figcaption> | ||
| </figure> | ||
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| --- | ||
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| [](https://github.com/microsoft/syntheseus/actions/workflows/ci.yml) | ||
| [](https://www.python.org/downloads/) | ||
| [](https://github.com/ambv/black) | ||
| [](https://github.com/microsoft/syntheseus/blob/main/LICENSE) | ||
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| Syntheseus is a package for end-to-end retrosynthetic planning. | ||
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| - ⚒️ Combines search algorithms and reaction models in a standardized way | ||
| - 🧭 Includes implementations of common search algorithms | ||
| - 🧪 Includes wrappers for state-of-the-art reaction models | ||
| - ⚙️ Exposes a simple API to plug in custom models and algorithms | ||
| - 📈 Can be used to benchmark components of a retrosynthesis pipeline |
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| We support two installation modes: | ||
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| - *core installation* allows you to build and benchmark your own models or search algorithms | ||
| - *full installation* also allows you to perform end-to-end search using the supported models | ||
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| === "Core installation" | ||
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| ```bash | ||
| conda env create -f environment.yml | ||
| conda activate syntheseus | ||
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| pip install -e . | ||
| ``` | ||
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| === "Full installation" | ||
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| ```bash | ||
| conda env create -f environment_full.yml | ||
| conda activate syntheseus-full | ||
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| pip install -e ".[all]" | ||
| ``` | ||
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| Core installation includes only minimal dependencies (no ML libraries), while full installation includes all supported models and also dependencies for visualization/development. | ||
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| Both sets of instructions above assume you already cloned the repository via | ||
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| ```bash | ||
| git clone https://github.com/microsoft/syntheseus.git | ||
| cd syntheseus | ||
| ``` | ||
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| Note that `environment_full.yml` pins the CUDA version (to 11.3) for reproducibility. | ||
| If you want to use a different one, make sure to edit the environment file accordingly. | ||
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| ??? info "Setting up GLN" | ||
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| We also support GLN, but it requires a specialized environment and is thus not installed via `pip`. | ||
| See [here](https://github.com/microsoft/syntheseus/blob/main/syntheseus/reaction_prediction/environment_gln/Dockerfile) for a Docker environment necessary for running GLN. | ||
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| ## Reducing the number of dependencies | ||
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| To keep the environment smaller, you can replace the `all` option with a comma-separated subset of `{chemformer,local-retro,megan,mhn-react,retro-knn,root-aligned,viz,dev}` (`viz` and `dev` correspond to visualization and development dependencies, respectively). | ||
| For example, `pip install -e ".[local-retro,root-aligned]"` installs only LocalRetro and RootAligned. | ||
| If installing a subset of models, you can also delete the lines in `environment_full.yml` marked with names of models you do not wish to use. | ||
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| If you only want to use a very specific part of `syntheseus`, you could also install it without dependencies: | ||
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| ```bash | ||
| pip install -e . --no-dependencies | ||
| ``` | ||
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| You then would need to manually install a subset of dependencies that are required for a particular functionality you want to access. | ||
| See `pyproject.toml` for a list of dependencies tied to the `search` and `reaction_prediction` subpackages. |
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| Syntheseus currently supports 7 established single-step models. For convenience, for each model we also include a checkpoint trained on USPTO-50K. | ||
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| | Model checkpoint link | Source | | ||
| |----------------------------------------------------------------|--------| | ||
| | [Chemformer](https://figshare.com/ndownloader/files/42009888) | finetuned by us starting from checkpoint released by authors | | ||
| | [GLN](https://figshare.com/ndownloader/files/42012720) | released by authors | | ||
| | [LocalRetro](https://figshare.com/ndownloader/files/42012729) | trained by us | | ||
| | [MEGAN](https://figshare.com/ndownloader/files/42012732) | trained by us | | ||
| | [MHNreact](https://figshare.com/ndownloader/files/42012777) | trained by us | | ||
| | [RetroKNN](https://figshare.com/ndownloader/files/42012786) | trained by us | | ||
| | [RootAligned](https://figshare.com/ndownloader/files/42012792) | released by authors | | ||
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| ??? note "More advanced datasets" | ||
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| The USPTO-50K dataset is well-established but relatively small. Advanced users may prefer to retrain their models of interest on a larger dataset, such as USPTO-FULL or Pistachio. To do that, please follow the instructions in the original model repositories. | ||
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| In `reaction_prediction/cli/eval.py` a forward model can be used for computing back-translation (round-trip) accuracy. | ||
| See [here](https://figshare.com/ndownloader/files/42012708) for a Chemformer checkpoint finetuned for forward prediction on USPTO-50K. As for the backward direction, pretrained weights released by original authors were used as a starting point. | ||
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| ??? info "Licenses" | ||
| All checkpoints were produced in a way that involved external model repositories, hence may be affected by the exact license each model was released with. | ||
| For more details about a particular model see the top of the corresponding model wrapper file in `reaction_prediction/inference/`. |
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| site_name: Syntheseus | ||
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| repo_name: microsoft/syntheseus | ||
| repo_url: https://github.com/microsoft/syntheseus | ||
| edit_uri: edit/main/docs/ | ||
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| theme: | ||
| name: material | ||
| palette: | ||
| - media: "(prefers-color-scheme: light)" | ||
| scheme: default | ||
| primary: black | ||
| accent: red | ||
| toggle: | ||
| icon: material/toggle-switch | ||
| name: "Switch to dark mode" | ||
| - media: "(prefers-color-scheme: dark)" | ||
| scheme: slate | ||
| primary: black | ||
| accent: red | ||
| toggle: | ||
| icon: material/toggle-switch-off-outline | ||
| name: "Switch to light mode" | ||
| features: | ||
| - content.code.copy | ||
| - navigation.tabs | ||
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| nav: | ||
| - Get Started: | ||
| - Overview: index.md | ||
| - Installation: installation.md | ||
| - Single-Step Models: single_step.md | ||
| - CLI: | ||
| - Single-Step Evaluation: cli/eval_single_step.md | ||
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| markdown_extensions: | ||
| - admonition | ||
| - attr_list | ||
| - md_in_html | ||
| - pymdownx.details | ||
| - pymdownx.superfences | ||
| - pymdownx.tabbed: | ||
| alternate_style: true |