Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Test more cases of handling GROMACS residue IDs #1024

Merged
merged 2 commits into from
Aug 30, 2024

Conversation

mattwthompson
Copy link
Member

@mattwthompson mattwthompson commented Aug 2, 2024

Description

Does something with #1016

Fixes #1028

Checklist

  • Add tests
    • residue IDs offset from 1
    • residue IDs not specified in input
    • some, but not all, residue IDs specified in input
    • residue IDs > 99,999
    • discontinuous residue IDs
  • Consider offering a way for users to re-index (i.e. to avoid zero or negative residue IDs)
  • Lint
  • Update docstrings
    • Document current behavior and what is currently undefined

Comment on lines -101 to -103
@pytest.mark.slow
@skip_if_missing("openmm")
def test_residue_info(self, sage):
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

FTR: Any removed tests are duplicated; some amount of this file is just leftover from a botched merge some time ago

Copy link

codecov bot commented Aug 2, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.38%. Comparing base (426e3eb) to head (197240d).
Report is 26 commits behind head on main.

Additional details and impacted files

@mattwthompson
Copy link
Member Author

This fixes #1028; running that script produces a file with the IDs incremented on the second molecule:

Generated by Interchange
6
    1MOL0     O    1   0.089   0.885   0.898
    1MOL0     H    2   0.170   0.538   0.836
    1MOL0     H    3   0.586   0.616   0.386
    2MOL0     O    4   0.552   0.965   0.526
    2MOL0     H    5   0.408   0.095   0.491
    2MOL0     H    6   0.879   0.165   0.706
  5.0000000  5.0000000  5.0000000

@j-wags
Copy link
Member

j-wags commented Aug 21, 2024

@Yoshanuikabundi Could you give this a review when you get a chance?

@mattwthompson mattwthompson merged commit 57dd53a into main Aug 30, 2024
22 checks passed
mattwthompson added a commit that referenced this pull request Aug 30, 2024
Test more cases of handling GROMACS residue IDs
@mattwthompson mattwthompson deleted the more-gromacs-residue-id branch October 16, 2024 19:00
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.

GROMACS Residue IDs not incremented when writing multiple copies of a unique molecule
2 participants