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rinikerlab / reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
https://rinikerlab.github.io/reeds/
MIT License
30 stars 8 forks source link

minor fixing #2

Closed RiesBen closed 3 years ago

RiesBen commented 3 years ago

Should be done.

Features:

Minors features:

This merge fixes minor things, that I recognized on euler.

candidechamp commented 3 years ago

@SchroederB I already messaged you about this, but I'll just write the info here so its easier to access:

The s-opt final analysis errors with the following:

File "/cluster/work/igc/cchampion/zzz_old/reeds_tutorial/template_dir/d_sopt/job_final_analysis.py", line 15, in do(sopt_root_dir=sopt_root_dir, pot_tresh=pot_tresh, title=title, out_dir=out_dir, ) File "/cluster/home/cchampion/programs/new_reeds/reeds/function_libs/pipeline/worker_scripts/analysis_workers/RE_EDS_soptimization_final.py", line 197, in do visualization_s_optimization_summary(s_opt_data=sopt_data, out_path=out_dir + "/" + title + "_sopt_analysis.png") File "/cluster/home/cchampion/programs/new_reeds/reeds/function_libs/visualization/parameter_optimization_plots.py", line 168, in visualization_s_optimization_summary bar_heights.append([opti["state_sampling"][state] for state in opti["state_sampling"]])

Note the line number in the code might be slightly different as I added a line of code to try to debug, but it seemed more complicated, than the other commit I did, because the dictionary contains a lot of information.

SalomeRonja commented 3 years ago

@candidechamp I think the error you get for the final s-optimization should be fixed by #19

candidechamp commented 3 years ago

@SalomeRonja Oh thats great! Could you push that change to origin/minorfix and I'll test it.

Then if everything is good we can accept this pull request!

SalomeRonja commented 3 years ago

If you quickly want to check it, you just have to change state_sampling to state_domination_sampling in the offending line:

bar_heights.append([opti["state_domination_sampling"][state] for state in opti["state_domination_sampling"]])
candidechamp commented 3 years ago

@SalomeRonja Ok perfect I'll take care of it! Thanks!

candidechamp commented 3 years ago

There was another of the same issues, here is the traceback:

Traceback (most recent call last): File "/cluster/work/igc/cchampion/zzz_old/reeds_tutorial/template_dir/d_sopt/job_final_analysis.py", line 15, in do(sopt_root_dir=sopt_root_dir, pot_tresh=pot_tresh, title=title, out_dir=out_dir, ) File "/cluster/home/cchampion/programs/new_reeds/reeds/function_libs/pipeline/worker_scripts/analysis_workers/RE_EDS_soptimization_final.py", line 201, in do visualize_s_optimisation_sampling_optimization(s_opt_data=sopt_data, out_path=out_dir + "/" + title + "_sopt_sampling_optimumDev.png") File "/cluster/home/cchampion/programs/new_reeds/reeds/function_libs/visualization/parameter_optimization_plots.py", line 322, in visualize_s_optimisation_sampling_optimization mae_mean.append(data['MAE_optimal_sampling']) KeyError: 'MAE_optimal_sampling'

@SchroederB I didn't push the change that Salome describes, but I'll let you figure this one out. Because the bug is for the final plot, you don't have to remake the .npy files (although it might be safer to?) Its probably just version inconsistencies with naming of keys in dictionaries.

RiesBen commented 3 years ago

Hey Candide, Thanks for checking it out! I will have a look at it next week.