Regarding interaction diagrams

[Kamecs]

Dear ProLIF developers.

Thank you for your maintenance of ProLIF code, and rapid response to my precious report (#331).
I have a suggestion (not issue).

In commercial software, the interaction frequency is often written above the arrow, whether the interaction occurs with the protein's main chain or side chain is clearly indicated, and the hydrogen bond donor and acceptor are often represented by the direction of the arrow.
(e.g. Fig.2 in https://pubs.acs.org/doi/10.1021/acsomega.8b01524)

Would you consider making updates like this in the future?
If such an update were made, it would be extremely useful for discussions in the field of drug discovery.

Best regards.

[cbouy]

Hi @Kamecs and sorry I forgot to reply to your question!

So you can already display the frequency by passing show_interaction_data=True to plot_lignetwork.

Regarding arrows rather than "Donor/Acceptor" it's a good suggestion and I think it might be more appropriate for making more "publication-ready" figures than the current interactive element.
It's not something that I'm going to work on soon I think, but I'd like to find the time to improve the plotting capabilities for sure. We had a Google Summer of Code student work on improving the automatic layout of the LigNetwork plot which is already a big step in the "publication-ready" direction but it still needs a little bit more work.

For the backbone/sidechain annotation, you're not the first one to mention that and I'd like to make ProLIF a bit more flexible on the metadata it gathers on interactions (some other people have requested extracting the PDB atom name for example). This would be part of larger changes that require ProLIF to be a lot more modular than it currently is though, and I doubt I'll have a lot of time to work on that in the near future.

I'll convert this issue to a discussion, but thanks a lot for the feedback !