Skip to content

Conversation

AnnaKravchenko
Copy link

@AnnaKravchenko AnnaKravchenko commented Sep 2, 2025

Description:

This PR reintroduces calculation of hydrophobic/hydrophilic features:

  • number of hydrophobic–hydrophobic contacts
  • number of hydrophobic–hydrophilic contacts
  • number of hydrophilic–hydrophilic contacts

These use the original amino acid classification.
This PR also prints out % NIS_Polar, which already had been calculatesd by prodigy v2.3.0 (but not printed out).

While not strong affinity predictors (per the PRODIGY paper), the implementation is now available, and can be put behind an optional flag for users who need these metrics.

todo:

  • Add actual calculations
  • Add flag for the output
  • Update tests
  • Update readme (section "all the possible options”)
  • Fix trailing whitespace flagged by Codacy

Related issue

Closes #56

@AnnaKravchenko AnnaKravchenko marked this pull request as draft September 2, 2025 13:36
@AnnaKravchenko AnnaKravchenko changed the title Add a optional flag for hydrophobic/phobic features Add a optional flag for hydrophobic/philic features Sep 2, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Re-implement hydrophobic/philic features calculation
1 participant