Add a SepTop RBFE tutorial

[hannahbaumann]

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

[hannahbaumann]

I'm currently creating the network using an atom mapper which may be confusing. I could instead either do a star map, looping over the ligands[1:] creating transformations using the first ligand as center, not creating a LigandNetwork first. Or load in a file with the names of the edges that we want to run (this is what I've been doing as I wanted to use the same edges in industry benchmarking). Or only show a single transformation between two random ligands?

[IAlibay]

I think doing it with network planning is fine, just have a bolded note that says that the mapping isn't used outside of the score.

Alternatively manually specifying edges is also fine IMHO.

[IAlibay]

We're doing this here for SepTop but not for ABFE. Not sure if intentional but just checking.

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[hannahbaumann]

Ah yes, I had used different templates for the two notebooks. Should I add this to the ABFE notebook?

[IAlibay]

Long term I think the idea would be to replace this with a "our ligands are pre-charged, see this cookbook here for an example of how you can go about charging your ligands".

Probably best to just add this into ABFEs for now and fix both the notebooks later to match whenever we're ready to make the change?

[hannahbaumann]

Sounds good!

[IAlibay]

Is this is the right diagram? (looks different from Fig 1 from your paper)

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[hannahbaumann]

In the paper I'm only showing the complex leg in detail, I thought that might be confusing here, and that it would be better to just show the simple full cycle. But I can also change it to the figure from the paper!

[IAlibay]

That's fair, this works for me if it works for you.