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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
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Simplify input for optimization (rebalancing/mixed optimization) #92

Closed candidechamp closed 1 year ago

candidechamp commented 1 year ago

Description

Simply removed (reduce) the number of user available input parameters so only the intensity factor is given to the module starting either type of optimization which involves rebalancing of the energy offsets.

The pseudo-count is calculated automatically inside the code to avoid confusing the user as to which parameter should be changed, and the number of states is simply read from the imd file.

Status

codecov-commenter commented 1 year ago

Codecov Report

Merging #92 (3576105) into main (ac886de) will decrease coverage by 0.02%. The diff coverage is 0.00%.

@@            Coverage Diff             @@
##             main      #92      +/-   ##
==========================================
- Coverage   15.74%   15.72%   -0.02%     
==========================================
  Files          51       51              
  Lines        5526     5533       +7     
==========================================
  Hits          870      870              
- Misses       4656     4663       +7
Flag Coverage Δ
unittests 15.72% <0.00%> (-0.02%) :arrow_down:

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Impacted Files Coverage Δ
reeds/modules/do_RE_EDS_eoffRebalancing.py 0.00% <0.00%> (ø)
reeds/modules/do_RE_EDS_mixedOptimisation.py 0.00% <0.00%> (ø)