Graph-native reaction informatics and executable electron-flow models
SynKit is a Python toolkit for atom mapping, chemical graph transformations, reaction rules, stereochemistry, and chemical reaction networks. It also represents Lewis-labelled graphs and verifies user-supplied electron-flow mechanisms. It does not predict the kinetically or thermodynamically preferred mechanism.
Requires Python 3.11 or later.
python -m pip install synkitSee Getting Started for examples, optional dependencies, and Docker installation.
- Lewis-labeled graphs: curly arrows and fishhooks as executable electron transfers, submitted (2026).
- SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis, Journal of Chemical Information and Modeling (2025).
Contributions and bug reports are welcome. Create a branch from the current mainline, make a focused change, and run the repository checks before opening a pull request:
git switch -c feature/short-description
bash scripts/lint.sh
bash scripts/pytest.shQuestions can be sent to tieu@bioinf.uni-leipzig.de.
SynKit is distributed under the MIT License. See LICENSE.
This project received funding from the European Union’s Horizon Europe Doctoral Network programme under Marie Skłodowska-Curie grant agreement No. 101072930 (TACsy).