Feat: analysis radical migration tool

[ehhartmann]

this tool will create a json file of migrations which can be visualized in pymol using an external script

[ehhartmann]

ToDo:

• write code for all three analysis types
• add option to combine runs
• (try this on the dopa sims)

[ehhartmann]

ready for review!

[jmbuhr]

json, not csv, right?

[ehhartmann]

I don't want to write the tutorial now but the rest has been addressed

[jmbuhr]

How do you want users to run the script? Right now it would be something like python -m kimmdy.assets.scripts.analyse_kimmdy_migration.py, in which case you would want to add the classic if __name__ == "__main__" thing. Though from the # %% comments it looks more like something you expect people to run interactively in their own environment, so I'm wondering if some place in the guide docs folder would be a better solution, to separate it from the regular kimmdy modules. Also, do you want to add pymol to https://github.com/hits-mbm-dev/kimmdy/blob/0bc5a68b7adbd026a7a7cd78176a2d47b602dc68/setup.cfg#L60-L72 ?

[ehhartmann]

I would say installing pymol is a bit messy, so I would leave it to the user.
The script runs with pymol <script_name>. For debugging and adding new features I run it interactively. To me, it is just a nice script to share with people who have kimmdy output. We could put it in guide and just have it as asset for some future tutorial