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BranniganLab / safep

Tools for Analyzing and Debugging (SA)FEP calculations. See also the SAFEP Tutorial: https://github.com/jhenin/SAFEP_tutorial/tree/main Documentation: https://safep-alchemy.readthedocs.io/en/latest/
GNU Lesser General Public License v2.1
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Put plotting commands in notebooks #23

Open jhenin opened 1 year ago

jhenin commented 1 year ago

Ideally, all numerical processing would be handled by safep functions, and the plot command itself would be in the notebook. That way, users can customize the appearance of plots, and possible further process or combine the data without plotting. Use case: I am adapting the Basic notebook to process a series of replica simulations (the batch case, but I have a specific idea of what I want to do, and others will too). To the number of samples of all replicas on the same graph, I have to 1) replicate the contents of plot_samples to modify it, and 2) call the get_n_samples function, which is hidden. This would be very easy to do if the plotting commands were in the notebook and functions such as get_n_samples were exposed.

jhenin commented 1 year ago

Consensus: make the Basic notebook minimal, and the Advanced notebook customizable.