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SynKit

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Graph-native reaction informatics and executable electron-flow models

SynKit is a Python toolkit for atom-mapped reactions, chemical graph transformations, Lewis-labelled graphs, and explicitly supplied reaction mechanisms. It connects reaction representation, rule extraction, graph rewriting, stereochemistry, and mechanism verification through a common attributed-graph model.

SynKit verifies mechanisms supplied by the user; it does not claim to predict the kinetically or thermodynamically preferred mechanism.

SynKit graphical abstract

Highlights

  • Convert mapped reaction SMILES into ITS and reaction-centre graphs.
  • Extract and apply attributed graph-transformation rules.
  • Represent lone pairs, radicals, and separate sigma and pi occupancies with Lewis-labelled graphs.
  • Execute curved-arrow and atomically coupled fishhook events.
  • Preserve tetrahedral, axial, and extended stereochemical information.
  • Build and analyse mechanism trajectory graphs and chemical reaction networks.

Installation

SynKit requires Python 3.11 or later.

python -m pip install synkit

Install the optional dependencies with:

python -m pip install "synkit[all]"

Alternatively, use the published container:

docker pull tieulongphan/synkit:latest
docker run --rm tieulongphan/synkit:latest \
  python -c "import synkit; print(synkit.__version__)"

Quick start

This self-contained example converts an atom-mapped substitution into an imaginary transition-state graph and reports its changed bonds:

from synkit.IO import rsmi_to_its

reaction = "[CH3:1][Br:2].[OH-:3]>>[CH3:1][OH:3].[Br-:2]"
its = rsmi_to_its(reaction, core=False, format="tuple")

changed_bonds = [
    (source, target, data["order"])
    for source, target, data in its.edges(data=True)
    if data["order"][0] != data["order"][1]
]
print(changed_bonds)

The output records the broken C-Br bond as (1.0, 0.0) and the formed C-O bond as (0.0, 1.0). Continue with the graph, rule, and synthesis guides.

Supplied-mechanism verification

SynKit can parse typed electron-flow annotations, replay their elementary steps, and return a verification certificate and mechanism trajectory graph. Canonical electron loci distinguish lone pairs, sigma bonds, pi bonds, and radical electrons. Curved arrows carry two electrons; fishhooks carry one; coupled radical events commit atomically from a common pre-state.

See the mechanism documentation for the supported interchange formats, verification policies, and complete examples.

Documentation

Publications

Contributing

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.sh

Questions can be sent to tieu@bioinf.uni-leipzig.de.

Contributors

License

SynKit is distributed under the MIT License. See LICENSE.

Acknowledgments

This project received funding from the European Union's Horizon Europe Doctoral Network programme under Marie Skłodowska-Curie grant agreement No. 101072930 (TACsy).

Project links

Data verified by PyPI on Aug 15, 2026
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  • Released:
Newer release available (1.6.2)

1 maintainer

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Avatar for Tieu from gravatar.com Tieu

Credits

Author: Tieu Long Phan

GitHub Statistics

Data verified by PyPI on Aug 15, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License (MIT)

Requires

Python >=3.11

Provides Extra

all docs

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