Test more cases of handling GROMACS residue IDs

openforcefield / openff-interchange

A project (and object) for storing, manipulating, and converting molecular mechanics data.

https://docs.openforcefield.org/projects/interchange

MIT License

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Test more cases of handling GROMACS residue IDs #1024

Closed mattwthompson closed 2 months ago

mattwthompson commented 3 months ago

Description

Does something with #1016

Fixes #1028

Checklist

[x] Add tests
- [x] residue IDs offset from 1
- [x] residue IDs not specified in input
- [ ] some, but not all, residue IDs specified in input
- [x] 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)
[x] Lint
[x] Update docstrings
- [x] Document current behavior and what is currently undefined

codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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 commented 3 months ago

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 commented 2 months ago

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