BespokeFit parameters notebook

[jthorton]

This adds my opinionated view on using BespokeFit with an OpenFE protocol in production with TYK2 as an example system.

Running the entire notebook is very slow as you will need to parameterise all of tyk2 ligands, but the main point is how someone would set the bespoke parameters in the protocol. If we want users to be able to run the notebook fully we should probably supply a force field with the parameters already fit.

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👈 Launch a binder notebook on branch OpenFreeEnergy/ExampleNotebooks/bespokefit_guide

[IAlibay]

Thanks @jthorton - however I think we need to discuss this a bit more.

My vision here is that, for our docs, we really should just have a cookbook that starts after Bespokefit has been run. I.e. you could consider it a "how do I get these parameters into my Protocol" rather than "here is a full workflow for how you do this".

We can have this entire notebook as an example, but because we can't take ownership of any tools (or explain how you should use a tool over any other), our user facing docs really need to be "once you have an offxml, what do you do".

So maybe read this as:

1. We need a cookbook that starts from the output of bespokefit.
2. We can keep this as a "tutorial", but we should make it pretty clear that this is an example set of parameters etc.. and point folks to relevant bespokefit tutorials/user docs. Maybe some warning boxes with extra exposition?

[IAlibay]

(resetting the asignee because the PR writer is assigned to the issue and the reviewer is assigned to the PR - or at least that's how we try to do it)

[jthorton]

Thanks @IAlibay I took a go at that by removing all but the last section of the notebook which makes it much simpler and hopefully shows how easy it is to use a custom force field with the protocol. If we want to add a more complicated example I'll keep that for a different PR to keep the review more focused on what we want with this first notebook.

[atravitz]

I think the simplification is good - should this live under "cookbooks" now?

[IAlibay]

I think the simplification is good - should this live under "cookbooks" now?

Yes! Our docs infrastructure is very loosely tied into how we define the directories, so cookbooks kinda have to live in cookbooks (I think you can use any relative path, but it does make life a ton easier).

[IAlibay]

couple of reviewnb comments to address but other lgtm from me!

[jthorton]

@IAlibay how do we want to handle testing the bepokefit cookbook, should I provide an example bespoke force field in the assets?

[IAlibay]

@IAlibay how do we want to handle testing the bepokefit cookbook, should I provide an example bespoke force field in the assets?

Yeah if you have one on hand that would be great.