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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Pot Threshold Correction #32

Closed RiesBen closed 3 years ago

RiesBen commented 3 years ago

Description

The code here is not doing what it is supposed to do. I'm adapting the code, such it does what is described in the manuscript and as we discussed. After this no code changes more on the main branch for now.

31

Todos

Notable points that this PR has either accomplished or will accomplish.

[x] potential Threshold from B are used and read in C
[x] potential Threshold from A are used in D and E
[x] reintroduce SSM flag, as not all lab members use this approach.

Status

[x] Ready to go

RiesBen commented 3 years ago

Hi, ok now it escalated a bit but I added now even some more stuff, than I wanted.

For all RE-EDS Modules:

pot_thresh: auto parsing or potion to manually overwrite on global_def level
fract_tresh: added to global level, can be added to global devs
minor eoff text improvements and restructuring as here the pot_tresh was not correct!
update off PEOE jupyter

RiesBen commented 3 years ago

+update of docs

RiesBen commented 3 years ago