industry-benchmarking-layout

[RiesBen]

Hi, I think it would be great if our folder structure follows this here: https://docs.openfree.energy/en/stable/tutorials/rbfe_cli_tutorial.html

in my understanding the final folder structure, after full execution should look like this:

some_benchmark_folder

--network_setup -----ligand_network.graphml -----alchemical_network.json -----transformations -------*jsons

--results ----fun1 ------shared* --------nc -----fun1.json ----fun2 ------shared --------*nc -----fun2.json ---- ...

--final_results.tsv

[IAlibay]

@RiesBen

-----ligand_*json

Sorry for the silly question, but what is this? The alchemical network?

--results

I think the way we wanted to go was:

-- network_setup

• ligand_network.graphml
• alchemical_network.json --transformations --- transformation JSONs -- results_0
  • replica 0 results for each transformation -- results_1
  • replica 1 results for each transformation -- results_2
  • replica 2 results for each transformation

Does that match what you envision?

[hannahbaumann]

I don't think I would put the results under network_setup since that seems confusing to me, but may just be me!

[IAlibay]

I don't think I would put the results under network_setup since that seems confusing to me, but may just be me!

Yes sorry! That should be separate

[RiesBen]

@IAlibay - file name of ligand_*json: ja my bad, I corrected that in the initial post

[IAlibay]

I've opened PR #76 with the aim of fixing this