SynKit#
SynKit is a graph-based Python toolkit for reaction informatics: canonicalization, matching, rule manipulation, and lightweight chemical reaction network (CRN) exploration. It is designed to be modular, extensible, and friendly for both research and production workflows.
Documentation quick links#
Install, quick examples, and basic usage.
CRN building, hypergraph conversions, canonicalization utilities.
Readers/writers and format conversion recipes.
Reaction validation, AAM checks, balance and fingerprinting.
ITS/MTG construction, WL hashing, and cluster/search primitives.
Molecule, reaction, ITS, and diagnostic graph rendering.
Auto-generated API docs and class references.
Citation#
Please cite the SynKit paper when using the software. For exact release provenance, also cite the archived v1.0.0 Zenodo snapshot and record the Git tag or commit used for the analysis.
Paper: SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis, Journal of Chemical Information and Modeling 2025, 65 (24), 13012–13019. DOI: 10.1021/acs.jcim.5c02123.
Archive: SynKit v1.0.0 on Zenodo.
@article{phan2025synkit,
title = {SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis},
author = {Phan, Tieu-Long and González Laffitte, Marcos E. and Fagerberg, Rolf and Gatter, Thomas and Stadler, Peter F.},
journal = {Journal of Chemical Information and Modeling},
volume = {65},
number = {24},
pages = {13012--13019},
year = {2025},
doi = {10.1021/acs.jcim.5c02123}
}
@software{synkit_v1_0_0,
title = {SynKit v1.0.0},
author = {Phan, Tieu-Long and others},
year = {2025},
doi = {10.5281/zenodo.16925060}
}
Contributions & support#
Report issues or feature requests on GitHub: TieuLongPhan/SynKit#issues To contribute: fork, create a topic branch, add tests, and open a PR against main. For API changes update docs and tests. For contribution enquiries or collaborations: tieu@bioinf.uni-leipzig.de
Acknowledgments#
Funded by the European Union Horizon Europe Doctoral Network (Marie-Skłodowska-Curie, grant No. 101072930 — TACsy).