diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a62665c..8bdc8dc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ default_language_version: - python: python3.11 + python: python3.12 repos: - repo: local diff --git a/README.md b/README.md index 7919805..aaf4949 100644 --- a/README.md +++ b/README.md @@ -4,14 +4,14 @@ [![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](./LICENSE) -[![arXiv](https://img.shields.io/badge/arXiv-xxx.svg)](https://arxiv.org/abs/xxx) +[![arXiv](https://img.shields.io/badge/arXiv-2509.15409-b31b1b.svg)](https://arxiv.org/abs/2509.15409) ## Overview -FragmentRetro is a fragment-based retrosynthetic method with quadratic complexity, offering a scalable alternative to tree search and [DirectMultiStep](https://github.com/batistagroup/DirectMultiStep/tree/main). The preprint for this work was posted on [arXiv](https://arxiv.org/abs/xxx). +FragmentRetro is a fragment-based retrosynthetic method with quadratic complexity, offering a scalable alternative to tree search and [DirectMultiStep](https://github.com/batistagroup/DirectMultiStep/tree/main). The preprint for this work was posted on [arXiv](https://arxiv.org/abs/2509.15409). See our [documentation](./docs/index.md) for installation, stock preprocessing, and usage examples. ## Licenses -All code is licensed under MIT License. The content of the [pre-print on arXiv](https://arxiv.org/abs/xxx) is licensed under CC-BY 4.0. +All code is licensed under MIT License. The content of the [pre-print on arXiv](https://arxiv.org/abs/2509.15409) is licensed under CC-BY 4.0. diff --git a/docs/index.md b/docs/index.md index 47e29e8..4784142 100644 --- a/docs/index.md +++ b/docs/index.md @@ -89,4 +89,4 @@ uv pip install -e ".[dev]" ## License - Code: MIT License -- Paper content ([arXiv preprint](https://arxiv.org/abs/xxxxx)): CC-BY 4.0 +- Paper content ([arXiv preprint](https://arxiv.org/abs/2509.15409)): CC-BY 4.0 diff --git a/src/fragmentretro/substructure_matcher.py b/src/fragmentretro/substructure_matcher.py index 66040e2..3dc5b6f 100644 --- a/src/fragmentretro/substructure_matcher.py +++ b/src/fragmentretro/substructure_matcher.py @@ -80,7 +80,7 @@ def convert_to_smarts(fragment_smiles: str) -> str: smarts = re.sub(r":\d+\]", "]", smarts) # sub [#0] with *, which is a wildcard for any atom smarts = re.sub(r"\[\d*\#0\]", "*", smarts) - return cast(str, smarts) + return smarts @staticmethod def addH_to_wildcard_neighbors(fragment_smarts: str) -> str: