Rework of initialization options

[eruijsena]

Description

This branch contains a rework of the imd manipulation / adaptation for steps a-c as well as some minor tweaks.

Changes to the imd:

• Removed redundant implementations of imd creation in function_libs/pipeline/module_functions.py and created an initialize_imd function intended to be used at the beginning of the pipeline. This function will setup the fields in the imd that should (usually) not change during the pipeline, and will create a template.imd which can be further adapted by the user or program for the following steps.
• Included functionality for initializing distance and/or position restraints, and better number of states determination
• This function is expected to be included in the future "global_parameters" rework as part of the streamlining of the REEDS options
• A script "0_initialize_imd.py" has been added to the template_REEDS_project directory to enable keep the pipeline functional as a temporary measure

Other changes:

• Replaced all 75 instances of "pertubation" with "perturbation"
• removed obsolete code for manual selection of s_values in step c
• reeds_analysis now defaults to copying cnfs from previous run if no ssm folder can be found
• minor changes on PyGromos as well

Todos

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

• [ ] Test the code

[lgtm-com[bot]]

This pull request introduces 7 alerts and fixes 1 when merging ee497357b388a9d4b344fa050f1c871abf8908bb into 84ac08d1b857c371106056110e8562274a7b9828 - view on LGTM.com

new alerts:

• 4 for Unused import
• 3 for Unused local variable

fixed alerts:

• 1 for Unused import

[lgtm-com[bot]]

This pull request introduces 5 alerts and fixes 1 when merging f5aae72cfe0b61501f88f2ec1230ea9f16d51581 into 84ac08d1b857c371106056110e8562274a7b9828 - view on LGTM.com

new alerts:

• 3 for Unused local variable
• 2 for Unused import

fixed alerts:

• 1 for Unused import

[candidechamp]

I just found a small bug in the import statements of reeds/function_libs/pipeline/module_functions.py

the line from pygromos.utils import amino acids as bash should read from pygromos.utils import bash

Apart form that everything else looks very good.

[eruijsena]

Voilà!

[lgtm-com[bot]]

This pull request introduces 5 alerts and fixes 1 when merging d2d5838b781f483bd0294737e9c94b7f4d4b4ea6 into 84ac08d1b857c371106056110e8562274a7b9828 - view on LGTM.com

new alerts:

• 3 for Unused local variable
• 2 for Unused import

fixed alerts:

• 1 for Unused import