OpenFreeEnergy/cinnabar

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Package for consistent reporting of relative free energy results

Stars: 43
Forks: 16
Open beginner issues: 0
Indexed issues: 37

Dominant language: Python
License: MIT
Last GitHub push: Jul 23, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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37 open issues indexed

Cycle closure dataframe hangs on large networks Open

OpenFreeEnergy/cinnabar#238 · 1 assignee · Opened Sep 8, 2026
CLD Labels change depending on the sources provided Open

OpenFreeEnergy/cinnabar#237 · 1 assignee · Opened Sep 4, 2026
Make all plotting functions return subplots Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/cinnabar#235 · Opened Aug 21, 2026
Support multiple sources on plots? Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

OpenFreeEnergy/cinnabar#226 · Opened Jun 17, 2026
`get_cycle_closure_dataframe` does not consider self loop edges Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

OpenFreeEnergy/cinnabar#219 · Opened Jun 3, 2026
Cycle enumeration strategy in `get_cycle_closure_dataframe` Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/cinnabar#218 · Opened Jun 3, 2026
Rework `bootstrap_statistic` to align with metric functions Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

OpenFreeEnergy/cinnabar#217 · Opened Jun 3, 2026
Rework pair_plot mega function Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

OpenFreeEnergy/cinnabar#214 · Opened Jun 1, 2026
Support multiple experimental measures Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

OpenFreeEnergy/cinnabar#196 · Opened Mar 26, 2026
Adding documentation on how to go from `openfe` gather results to cinnabar Open

Difficulty 3/5 Half a day Newbie friendliness 45/100

OpenFreeEnergy/cinnabar#195 · Opened Mar 12, 2026
Update defaults on everything Open

OpenFreeEnergy/cinnabar#179 · 1 comment · 1 assignee · Opened Jan 26, 2026
Add function to draw network with calculated values Open

OpenFreeEnergy/cinnabar#176 · 1 assignee · Opened Jan 19, 2026
Old readme file Open

OpenFreeEnergy/cinnabar#165 · 1 assignee · Opened Oct 21, 2025
Documentation: CLI examples Open

documentation usability

OpenFreeEnergy/cinnabar#142 · 1 comment · 1 assignee · Opened Aug 26, 2025
Linear regression (R2) fails when boostrapping on very few data points Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

OpenFreeEnergy/cinnabar#124 · 3 comments · Opened Aug 22, 2024
wrong estimates with FEMap with single experimental value Open

OpenFreeEnergy/cinnabar#123 · 6 comments · 2 assignees · Opened Jul 10, 2024
add option for get_absolute_dataframe to shift values Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

OpenFreeEnergy/cinnabar#111 · 2 comments · Opened Nov 15, 2023
make FEMap a gufe tokenizable Open

OpenFreeEnergy/cinnabar#108 · 4 comments · 1 assignee · Opened Nov 6, 2023
Seaborn calls in WhyNotToUseR2ForDDG notebook fail Open

Difficulty 2/5 1-3 hours Newbie friendliness 42/100

OpenFreeEnergy/cinnabar#104 · Opened Oct 23, 2023
Add plot_bar to plotly example notebook Open

OpenFreeEnergy/cinnabar#103 · 1 assignee · Opened Oct 23, 2023
not catching node name mismatch Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 38/100

OpenFreeEnergy/cinnabar#101 · 3 comments · Opened Oct 18, 2023
the value of the x/y axis from plot_DGs function does not reflect the true DGs Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

OpenFreeEnergy/cinnabar#93 · 6 comments · Opened Jul 18, 2023
Refactor stats into base and derived class so we can drop in different MLE solvers? Open

OpenFreeEnergy/cinnabar#89 · 1 comment · 1 reaction · 1 assignee · Opened Jun 29, 2023
[Question] Allow arbitrary xy tick frequency when plotting Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

OpenFreeEnergy/cinnabar#88 · Opened Jun 6, 2023
Compare different systems/targets in a single plot Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/cinnabar#87 · Opened Jun 5, 2023
Effect of centralizing Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/cinnabar#75 · Opened Jan 20, 2023
Catch the exception for the R2 computation Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

OpenFreeEnergy/cinnabar#62 · 2 comments · Opened Aug 10, 2022
[proposal] Clear up Python support - NEP29? Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

OpenFreeEnergy/cinnabar#57 · 2 comments · Opened May 17, 2022
Rework FEMap API Open

enhancement

OpenFreeEnergy/cinnabar#55 · 14 comments · 1 reaction · 1 assignee · Opened May 17, 2022
Add module level docstring or general info about what each module does Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/cinnabar#52 · Opened May 17, 2022
Standardize plotly and matplotlib plotting interfaces Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/cinnabar#46 · 1 comment · Opened May 8, 2022
Fix uncertainty factor naming in stats.mle Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

OpenFreeEnergy/cinnabar#45 · Opened May 8, 2022
Add experimental mean ΔG back to calculated and experimental ΔGs when plotting Open

enhancement

OpenFreeEnergy/cinnabar#42 · 1 comment · 1 assignee · Opened Feb 25, 2022
Incorrect solutions obtained when a single node has absolute free energy defined Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

OpenFreeEnergy/cinnabar#28 · 2 comments · Opened Nov 12, 2020
Add health checker for dataset analysis before calculation Open

OpenFreeEnergy/cinnabar#23 · 1 assignee · Opened Sep 29, 2020
Fix node ordering issue Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/cinnabar#21 · Opened Sep 26, 2020
Add option for different colour map in _master_plot Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

OpenFreeEnergy/cinnabar#20 · Opened Sep 21, 2020

OpenFreeEnergy/cinnabar

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