Pocket visualization

[dominiquesydow]

Description

So far, in order to work with a structure in the pocket module, a local copy of its structure file was needed to satisfy the Pocket class method visualize (nglview visualization of structure/pocket).

This was mainly the case because I could not make it work to show a structure from text in the mol2 format - but I figured it out now. Let's look at our options:

import nglview

# Show structure from file
view = nglview.show_file(filepath)

# Show structure from text (pdb format only!)
view = nglview.show_text(pdb_text)

# Show structure from text (any file format allowed by `nglview` - I tested only for pdb and mol2)
structure = nglview.adaptor.TextStructure(text, ext="mol2")
view = nglview.widget.NGLWidget(structure)

In this PR, the pocket module is updated in a way that Pocket class can be initialized from a file but also from text. This is helpful for the KlifsPocket subclass, where we fetch data via KLIFS IDs. Before, the file was downloaded and linked to the object via the _filepath attribute; now, we simply fetch the file text and format (_text and _extension attributes).

Todos

• [x] Remove class attribute _filepath but add _text and _extension (to indicate the text format)
• [x] Change class attribute _data (structural data as DataFrame) into property data
• [x] Split Pocket.from_file class method into
  • Pocket.from_text class method: Set all class attributes (new: _text and _extension)
  • Pocket.from_file class method: Get text from file and pass text to Pocket.from_text
• [x] Update KlifsPocket according to changes in Pocket (fetch text from KLIFS - no need for file download any more, yay!!)
• [x] Rerun pocket tutorial using the updated module
• [x] Minor (admittedly unrelated) logging changes
  • [x] Pocket centroid caluclation: Log info if pocket CA atoms are missing.
  • [x] Anchor residues: Log info is anchor residues are missing

Questions

None

Status

• [x] Ready to go

[dominiquesydow]

@jaimergp - this is a minor update in the pocket module (only in the backend). When you have time, could you please take a look if you approve of these changes?

[jaimergp]

Looks good! The PR description itself is a piece of art and should be framed in the lab :D

Btw, I didn't know about nglview.adaptor.TextStructure! I'll revisit if there're other places where we can apply this nice trick.

The only comment I need to make with this approach is memory usage. I don't think it's going to be a problem in 99% of the cases so we'll leave it like that. But just to make sure we remember this if we hit 1% of the cases, I'll add a note to the class that will store the .text attribute. In massive benchmarks, storing the text will add a liiiittle overhead (nothing compared to other problems). Now that I'm writing this I don't think it's even worth writing it down, so yep, whatever, ignore this :)

Merge!

[dominiquesydow]

Thank you :)