Published June 8, 2026 | Version 0.6.0
Software Open

OpenFreeEnergy/cinnabar: v0.6.0

Authors/Creators

  • 1. Chodera Lab // MSKCC
  • 2. @OpenFreeEnergy
  • 3. @choderalab & @OpenFreeEnergy
  • 4. The Open Molecular Software Foundation
  • 5. Memorial Sloan Kettering Cancer Center
  • 6. @openforcefield
  • 7. Datryllic LLC

Description

Changelog for humans

https://cinnabar.openfree.energy/en/latest/CHANGELOG.html#v0-6-0

All PRs included in this release:

  • Update project to use pyproject.toml by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/154
  • Add basic landing page by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/156
  • Duecredit for the MLE method by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/155
  • add rever for the changelog by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/159
  • add pre-commit for formatting and lint by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/157
  • remove old arsenic code by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/158
  • Core concepts by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/162
  • Fraction of best ligands by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/164
  • Fix DG and DDG spacing in plots by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/167
  • Update the readme by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/166
  • add api tutorials by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/160
  • Fix and expand tests by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/170
  • Raise an error when we have repeated edge results by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/178
  • Add ECDF plots based on industry benchmarks by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/172
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/OpenFreeEnergy/cinnabar/pull/169
  • Remove unused example notebooks by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/184
  • Test MLE order dependence by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/191
  • Add affinity unit conversion function by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/182
  • Update errors by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/185
  • Expose stats by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/186
  • Raise an error for zero uncertainties in the MLE solver by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/177
  • Align all dataframes by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/192
  • Add predictive index metric by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/194
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/OpenFreeEnergy/cinnabar/pull/199
  • bump github action versions by @atravitz in https://github.com/OpenFreeEnergy/cinnabar/pull/200
  • Drop pydantic use by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/190
  • Add support for other estimators by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/193
  • Add pairwise all-to-all analysis by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/187
  • test python 3.13 in CI by @atravitz in https://github.com/OpenFreeEnergy/cinnabar/pull/197
  • Add CI to ecdf plots using bootstrapping by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/201
  • add mypy to CI by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/209
  • Support pIC50 units on dataframes by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/208
  • Add ECDF plotting tutorial by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/206
  • Update plot functions to work with FEMap by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/212
  • Add ability to highlight edges in the draw_graph function by @hannahbaumann in https://github.com/OpenFreeEnergy/cinnabar/pull/203
  • expose _master_plot as pair_plot, add guideline customization by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/204
  • Support pic50 units in all plot types by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/213
  • Add graph edge highlights to docs by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/216
  • Add functions to calculate cycle closure by @hannahbaumann in https://github.com/OpenFreeEnergy/cinnabar/pull/107
  • Add docs for manual stats calculations outside of plots by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/215
  • Prep v0.6.0 by @jthorton in https://github.com/OpenFreeEnergy/cinnabar/pull/222

New Contributors

  • @jthorton made their first contribution in https://github.com/OpenFreeEnergy/cinnabar/pull/154
  • @pre-commit-ci[bot] made their first contribution in https://github.com/OpenFreeEnergy/cinnabar/pull/169

Full Changelog: https://github.com/OpenFreeEnergy/cinnabar/compare/0.5.0...0.6.0

Files

OpenFreeEnergy/cinnabar-0.6.0.zip

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Additional details

Related works

Is supplement to
Software: https://github.com/OpenFreeEnergy/cinnabar/tree/0.6.0 (URL)

Software

Repository URL
https://github.com/OpenFreeEnergy/cinnabar