Welcome to the cinnabar documentation!

cinnabar (formerly arsenic) is an open-source framework within the Open Free Energy (OpenFE) eco-system which enables consistent and reliable plotting of results from free energy calculations. Use of the package ensures a fair comparison of computational methods via robust and reproducible metrics implemented in the analysis functions following standardized best practices [1]. cinnabar is designed with generality in mind, and can be used to analyse results from any free energy calculation software package.

Additionally cinnabar provides methods to estimate absolute binding afinities from calculated relative measurments and powers the OpenFE CLI.

If you are looking to perform free energy calculations, see openfe.

Resources

• github repository: OpenFreeEnergy/cinnabar

• issue tracker: OpenFreeEnergy/cinnabar#issues

• OpenFE discussions board: OpenFreeEnergy/openfe#discussions

Contents

• Installation
• Core Concepts
• Tutorials

Reference

• API Documentation
• Release history

References

[1]

Hahn, D.F., Bayly, C.I., Boby, M.L., Macdonald, H.E.B., Chodera, J.D., Gapsys, V., Mey, A.S., Mobley, D.L., Benito, L.P., Schindler, C.E. and Tresadern, G., 2022. Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [article v1. 0]. Living journal of computational molecular science, 4(1), p.1497.

Index