Visuals

[glass-w]

Description

This PR adds a new function to write PDB files per interaction type obtained by plipify as well as writing a "total interactions" PDB. This also adds a new class to make PyMol images.

Todos

• [x] Create new function to write PDB files
• [x] Add option to retain bound ligand from plipify.core.Structure
• [x] Update examples in notebook
• [x] ~Create example PyMol scripts~ Add PyMol image making class
  • [x] Add initial class
  • [x] Generalise class for different views

Questions

• [ ] Currently we access the original PDB file path via Structure._path, should we have a separate attribute here, something like Structure.get_file instead?
• [ ] It could be an idea to write out interactions in the current nglview style (i.e. with "bonds" between interaction partners with different colours etc). This could either be done in a PyMol script after structure generation or within the PDB file itself with MDAnalysis.

Status

• [ ] Ready to go

[AndreaVolkamer]

@jaimergp:

• @glass-w is working on pymol scripts to make publication worthy figures in this branch.
• I added a trial visualization in the nb itself to visualize the interaction frequency by color, it is still very rudimentary (and just summing the individual interactions up). Maybe we could add a widget, so one can check the individual contributions, or color the types differently ...

[glass-w]

I've now added a new VisPymol class that handles rendering images of PDB files returned from fingerprint_writepdb. This is cleaner than having example PyMol scripts floating around.

[AndreaVolkamer]

@glass-w the missing residue 163 is now present, added the protonation fix as described in this plip issue.

[glass-w]

I've adapted plipify.visualization.fingerprint_tableto take an optional plipify.core.Structure object to add one letter residue names. This produces a table that looks like this:

I've also added colour blind friendly colours and to only plot necessary legend names / colours.

[glass-w]

@jaimergp I'm unsure why this isn't passing the CI lint checks, when I run Black locally I don't see any errors in plipify.visualization

[jaimergp]

Are you using the same version as CI? This is what is being installed now:

Collecting black
  Downloading black-21.7b0-py3-none-any.whl (141 kB)

The table looks awesome btw :) Thanks!

[glass-w]

Yes, this is what I'm using in my environment:

# Name                    Version                   Build  Channel
black                     21.7b0             pyhd8ed1ab_0    conda-forge

[jaimergp]

Mm, are you using the same options? e.g. black -l 99 plipify --exclude plipify/_version.py?

[AndreaVolkamer]

@glass-w the new fingerprint table is AWESOME!

[AndreaVolkamer]

@glass-w could you check one tiny thing for me. In this cell:

Using the methoxy ligand as an example

TODO need to adapt view to use the wH structure

from plipify.core import Structure

methoxy = Structure.from_pdbfile(path="./data/Mpro/aligned/Mpro-P0157_0A/Mpro-P0157_0A_bound_chainA.pdb") # methoxy = selected_structure

We are still using the unprotonated structure, could you run it with the preprocessed structure (you can simply uncomment the methoxy= selected_structure comment), but the pymol view needs to be updated then and I'm not fully aware how you selected the coordinates.

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[jaimergp]

Superseded by #14