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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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old functions (ported from gitlab) #14

Closed SalomeRonja closed 3 years ago

SalomeRonja commented 3 years ago

by @SalomeRonja :

I'm currently working on the documentation for the analysis. In reeds/reeds/function_libs/analysis/analysis.py there is a function called fetch_lig_atom which is not called from anywhere in the reeds or pygromos code. I'm also not sure what the original purpose of the function was. Do we still need this function @SchroederB ?

SalomeRonja commented 3 years ago

In order to not start a new issue for every function that's potentially not needed anymore, I'll just add the other functions in this thread, if I find any further cases.

There is also a function called analyse_V_t, which is also not called from anywhere as far as I can tell.

SalomeRonja commented 3 years ago

The function energyOffset_time_convergence from analysis.py is also not used

SalomeRonja commented 3 years ago

comment by @SchroederB : This one might be useful.

SalomeRonja commented 3 years ago

comment by @SchroederB : ^^ probably we don't need them anymore :)

RiesBen commented 3 years ago

hm did we agree here on something? I don't know what to decide on. Somehow, maybe the implelmentations are useful. Maybe not, if a lot in the code changes.

SalomeRonja commented 3 years ago

I just checked the newest main branch. After the latest refactorings, fetch_lig_atoms and analyse_V_t were removed. energyOffset_time_convergence is still there, but it might indeed still be useful, so I'll go ahead and close the issue :)