Updates for protein/ligand RE-EDS + plot/bug fixes

[candidechamp]

Description

This branch contains a few tweaks and additions to the code which should work for everyone using RE-EDS and pygromos v1.
(code should be used with the PygromosTools_V1.2 branch)

Notable things which changed in this branch:

• Input preparation between steps b (lower bound search) and c (energy offset estimation) now places automatically s-values in the gap region such that a total of 32 s-values make up the initial distribution (this may then be optimized using GRTO).

-Input preparation of ssm configurations now uses the lowest energy conformer of the second half of the 1ns simulation in the optimized state (step a). This is the step which requires the updated pygromos code.

-Modified the plot summarizing the (s)-optimization and energy offset rebalancing steps (added error bars, and changed the s-distribution plot).

-Modified the plots found in analysis/state_sampling folders such that the correct data is shown for the occurrence state sampling, and to make plots slightly clearer.
(an option is now available to display/hide the raw data which was previously always written on the plot).

-Various print statements have been removed as well as a duplicate function.

Todos

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

• Test the code (submission + analysis of all steps) (to do so, checkout the branch candide_2022 from my fork https://github.com/candidechamp/reeds)

Questions

• Question1

Status

• Ready to go

Do not merge before we agree that all the code works for everyone.

[lgtm-com]

This pull request introduces 3 alerts and fixes 3 when merging 8a60649 into 64f4a4a - view on LGTM.com

new alerts:

• 1 for Wrong name for an argument in a call
• 1 for Unused import
• 1 for Unreachable code

fixed alerts:

• 2 for Variable defined multiple times
• 1 for Unused import

[lgtm-com]

This pull request introduces 3 alerts and fixes 3 when merging b52e69f into 64f4a4a - view on LGTM.com

new alerts:

• 1 for Wrong name for an argument in a call
• 1 for Unused import
• 1 for Unreachable code

fixed alerts:

• 2 for Variable defined multiple times
• 1 for Unused import

[lgtm-com]

This pull request introduces 3 alerts and fixes 3 when merging f68df71 into 64f4a4a - view on LGTM.com

new alerts:

• 1 for Wrong name for an argument in a call
• 1 for Unused import
• 1 for Unreachable code

fixed alerts:

• 2 for Variable defined multiple times
• 1 for Unused import

[lgtm-com]

This pull request introduces 3 alerts and fixes 3 when merging a82f320 into 64f4a4a - view on LGTM.com

new alerts:

• 1 for Wrong name for an argument in a call
• 1 for Unused import
• 1 for Unreachable code

fixed alerts:

• 2 for Variable defined multiple times
• 1 for Unused import

[lgtm-com]

This pull request introduces 2 alerts and fixes 3 when merging 3446609 into 64f4a4a - view on LGTM.com

new alerts:

• 1 for Wrong name for an argument in a call
• 1 for Unused import

fixed alerts:

• 2 for Variable defined multiple times
• 1 for Unused import

[lgtm-com]

This pull request fixes 3 alerts when merging 7e9f3b8 into 64f4a4a - view on LGTM.com

fixed alerts:

• 2 for Variable defined multiple times
• 1 for Unused import

[lgtm-com]

This pull request fixes 3 alerts when merging 3fc2ebf into 64f4a4a - view on LGTM.com

fixed alerts:

• 2 for Variable defined multiple times
• 1 for Unused import