Required `ratar` updates

[dominiquesydow]

Updates needed for this code base:

December 2021

See PR #14 for details.

• [x] Update environment file as suggested by @t-kimber in #12
• [x] Check if CLI is still running > now it is again.
• [x] Update README + installation + usage instructions (update tutorial!!!!)
• [x] Fill follow-up section below

Follow-up

Methodology / encoding

• [ ] So far only full pocket encoding; we probably need subpocket encoding (overlapping patches)
• [ ] Define binding sites and their size #7
• [ ] Include non-standard amino acids #8
• [ ] Check units of 4th to 6th dimensions of reference points
• [ ] Check units and scaling of moments - First three moments of distribution:
  • Same units: 2nd moment - standard deviation; 3rd moment: 3rd root of skewness
  • Scaling: none (should fingerprint/moments be normalised?)
• [ ] We started to look into pdbqt files to be added as "physchem" properties to our fingerprint, take a look at this notebook if still of interest
• [ ] We already started to benchmark the method against similar/dissimilar pocket pairs from FuzCav, ProSPECCTs, and TOUGH-M1 (see README)
• [ ] Encoding workers fine for mol2 files; pdb files may not and need revision
• [ ] Since we probably have to move to NGLview anyways, PyMol functions have not been checked since 2019; probably they do not work anymore.

Testing and CI

• [ ] Add unit tests for similarity module
• [ ] CI: Add back Windows + MacOS support, lint package, format+lint+test docs tutorials

Code

• [ ] Check similarity module - refactoring needed?
• [ ] Address #FIXMEs and #TODOs in code (left-overs of major refactoring in PR #1); to be done after setting up unit tests
• [ ] Remove pymol dependency (not on conda-forge; currently installed from tpeulen)
• [ ] Remove flatten-dict dependency (only pip-installable)
• [ ] Add from_path class method to all ratar.encoding classes: Write class method from_path, analogous to from_molecule. Current problem: files can contain multiple molecules, thus from_path would return a list of molecule objects instead of a molecule object as in the case of from_molecule.
• [ ] We set up a logging.conf file to fine-grain our logging. Include back into the package if of interest.

Packaging

• [ ] Update ratar environment - enable conda packaging

[dominiquesydow]

Hi @AndreaVolkamer, just for visibility, this is a list of todos I put together before I left in Dec 2021. It is probably outdated already but some of the things might be relevant for your new student.