Change to the UI

[xbello]

This UI was proposed:

https://slack-files.com/T01JPHYBFGF-F01NRMZ06G4-1d48ae0770

It seems a good idea, and it looks good. Images are already downloaded for the network, and the SMILE for each molecule is stored in the DB.

• Do we want a 3D viewer and is it achievable? (careful with the bloatting of the view).
• What to put in "parameters" subwindow? The parameters used to create the network or the form to go to the next view?

[JenkeScheen]

• 3D viewer should be achievable, I think @esguerra had some good ideas on this, there are quite a few open-source ones out there that we can use. Additionally, might be worth being able to load protein structure around the ligand.
• I would suggest tabs for e.g. network parameters, FEP parameters, structure prep parameters, hardware parameters?

Also, do you think it would be possible to allow the user to swap around the three boxes in the UI design? I can imagine that at times the user will want to focus on the network and in that case having it on the left-hand side could enlarge it. Or perhaps it would be easier to implement drag to change size of the boxes?

[JenkeScheen]

notes from meeting:

UI idea looks good for now, this is a standard and clear approach to showing the interface. We discussed a few features, although the majority of these should probably be implemented at a later stage:

• we will need the option to have a focus view/ switch boxes around, so that users can focus on e.g. the network or on the ligands
  • optionally we can include the option to adjust box sizes, although this might be messy to implement
• easy scrolling through ligands, i.e. some way to select which ligand is being viewed
• 'help' button for all blocks explaining how to use them

some thoughts on the ligand viewer box: We want to keep this minimal, i.e. not include structure editing functionality because that is too advanced for the current direction of the software (for now..).

Ligand viewer (NGL) should have toggles to show

• 1) just ligand in 2D
• 2) just ligand in 3D
• 3) ligand with whole protein in 3D
• 4) ligand with protein binding pocket in 2D with interactions, will look further into what we can use for this, but some examples are:
  • https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/ LigPlot by EMBL-EBI -> licensing issue? Also looks a bit outdated
  • https://www.playmolecule.com/PlexView/ -> not open-source?
  • http://www.pegase-biosciences.com/leview-ligand-environment-viewer/ -> java issue?
  • https://core.ac.uk/download/pdf/185526656.pdf
• 5) ligand with protein in sphere (requires protein prep)