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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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@@ -1,5 +1,5 @@
default_language_version:
python: python3.11
python: python3.12

repos:
- repo: local
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -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.
2 changes: 1 addition & 1 deletion docs/index.md
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion src/fragmentretro/substructure_matcher.py
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Expand Up @@ -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:
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