Metadata-Version: 2.4
Name: syntheseus
Version: 0.7.0
Summary: A package for retrosynthetic planning.
Author: Austin Tripp, Krzysztof Maziarz, Guoqing Liu, Megan Stanley, Marwin Segler
License:     MIT License
        
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Project-URL: Documentation, https://microsoft.github.io/syntheseus
Project-URL: Repository, https://github.com/microsoft/syntheseus
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: more_itertools
Requires-Dist: networkx
Requires-Dist: numpy
Requires-Dist: omegaconf
Requires-Dist: rdkit
Requires-Dist: tqdm
Provides-Extra: viz
Requires-Dist: pillow; extra == "viz"
Requires-Dist: graphviz; extra == "viz"
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: pytest-rerunfailures; extra == "dev"
Requires-Dist: pre-commit; extra == "dev"
Provides-Extra: chemformer
Requires-Dist: syntheseus-chemformer==0.3.0; extra == "chemformer"
Provides-Extra: graph2edits
Requires-Dist: syntheseus-graph2edits==0.2.0; extra == "graph2edits"
Provides-Extra: local-retro
Requires-Dist: syntheseus-local-retro==0.5.0; extra == "local-retro"
Provides-Extra: megan
Requires-Dist: syntheseus-megan==0.2.0; extra == "megan"
Provides-Extra: mhn-react
Requires-Dist: syntheseus-mhnreact==1.0.0; extra == "mhn-react"
Provides-Extra: retro-knn
Requires-Dist: syntheseus[local-retro]; extra == "retro-knn"
Provides-Extra: root-aligned
Requires-Dist: syntheseus-root-aligned==0.2.0; extra == "root-aligned"
Provides-Extra: all-single-step
Requires-Dist: syntheseus[chemformer,graph2edits,local-retro,megan,mhn-react,retro-knn,root-aligned]; extra == "all-single-step"
Provides-Extra: all
Requires-Dist: syntheseus[all-single-step,dev,viz]; extra == "all"
Dynamic: license-file

<div align="center">
    <img src="https://github.com/microsoft/syntheseus/assets/61470923/f01a9939-61fa-4461-a124-c13eddcdd75a" height="50px">
    <h3><i>Navigating the labyrinth of synthesis planning</i></h3>

---

<p align="center">
  <a href="https://microsoft.github.io/syntheseus/stable">Docs</a> •
  <a href="https://microsoft.github.io/syntheseus/stable/cli/eval_single_step/">CLI</a> •
  <a href="https://microsoft.github.io/syntheseus/stable/tutorials/quick_start/">Tutorials</a> •
  <a href="https://arxiv.org/abs/2310.19796">Paper</a>
</p>

[![CI](https://github.com/microsoft/syntheseus/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/microsoft/syntheseus/actions/workflows/ci.yml)
[![Python Version](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
[![pypi](https://img.shields.io/pypi/v/syntheseus.svg)](https://pypi.org/project/syntheseus/)
[![code style](https://img.shields.io/badge/code%20style-black-202020.svg)](https://github.com/ambv/black)
[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/microsoft/syntheseus/blob/main/LICENSE)

</div>

## Overview

Syntheseus is a package for end-to-end retrosynthetic planning.
- ⚒️ 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

## Quick Start

To install `syntheseus` with all the extras, run

```bash
conda env create -f environment_full.yml
conda activate syntheseus-full

pip install "syntheseus[all]"
```

This sample environment pins `torch` to version `2.2.2`. To run the models under `1.x` please downgrade to `syntheseus 0.6.0`.

See [here](https://microsoft.github.io/syntheseus/stable/installation) if you prefer a more lightweight installation that only includes the parts you actually need.

## Citation and usage

Since the release of our package, we've been thrilled to see syntheseus be used in the following projects:

| **Project** | **Usage** | **Reference(s)** |
|:--------------|:-----|:-----------|
|Retro-fallback search|Multi-step search|ICLR [paper](https://arxiv.org/abs/2310.09270), [code](https://github.com/AustinT/retro-fallback-iclr24)|
|RetroGFN|Pre-packaged single-step models|arXiv [paper](https://arxiv.org/abs/2406.18739), [code](https://github.com/gmum/RetroGFN)|
|TANGO|Single-step and multi-step|arXiv [paper](https://arxiv.org/abs/2410.11527)|
|SimpRetro|Multi-step search|JCIM [paper](https://pubs.acs.org/doi/10.1021/acs.jcim.4c00432), [code](https://github.com/catalystforyou/SimpRetro)|

If you use syntheseus in an academic project, please consider citing our
[associated paper from Faraday Discussions](https://pubs.rsc.org/en/content/articlelanding/2024/fd/d4fd00093e)
(bibtex below). You can also message us or submit a PR to have your project added to the table above!

```
@article{maziarz2024re,
  title={Re-evaluating retrosynthesis algorithms with syntheseus},
  author={Maziarz, Krzysztof and Tripp, Austin and Liu, Guoqing and Stanley, Megan and Xie, Shufang and Gainski, Piotr and Seidl, Philipp and Segler, Marwin},
  journal={Faraday Discussions},
  year={2024},
  publisher={Royal Society of Chemistry}
}
```

## Development

Syntheseus is currently under active development.
If you want to help us develop syntheseus please install and run `pre-commit`
checks before committing code.

We use `pytest` for testing. Please make sure tests pass on your branch before
submitting a PR (and try to maintain high test coverage).

```bash
python -m pytest --cov syntheseus/tests
```

## Contributing

This project welcomes contributions and suggestions.  Most contributions require you to agree to a
Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us
the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.

When you submit a pull request, a CLA bot will automatically determine whether you need to provide
a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions
provided by the bot. You will only need to do this once across all repos using our CLA.

This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
For more information see the [Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/) or
contact [opencode@microsoft.com](mailto:opencode@microsoft.com) with any additional questions or comments.

## Trademarks

This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft
trademarks or logos is subject to and must follow
[Microsoft's Trademark & Brand Guidelines](https://www.microsoft.com/en-us/legal/intellectualproperty/trademarks/usage/general).
Use of Microsoft trademarks or logos in modified versions of this project must not cause confusion or imply Microsoft sponsorship.
Any use of third-party trademarks or logos are subject to those third-party's policies.
