Resolve #1096 with an optional argument for <_generate_unique_atom_names()>

openforcefield / openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

http://openforcefield.org

MIT License

301 stars 88 forks source link

Resolve #1096 with an optional argument for <_generate_unique_atom_names()> #1856

Closed PEFrankel closed 1 month ago

PEFrankel commented 2 months ago

[ ] Resolves: Make atom names more unique #1096, with an optional suffix parameter. Avoids possible conflict with analyses that create atom dictionaries without referencing the resname. Also improves readability of simulation files.
[ ] Add tests
[ ] Update docstrings/documentation, if applicable
[ ] Lint codebase
[ ] Update changelog

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 80.00000% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 82.27%. Comparing base (d6c4113) to head (62d9f7f). Report is 19 commits behind head on main.

:exclamation: Current head 62d9f7f differs from pull request most recent head bb43925

Please upload reports for the commit bb43925 to get more accurate results.

Additional details and impacted files

mattwthompson commented 2 months ago

P.S. don't worry about

failing tests on OpenEye=true runs - these will always fail since we don't expose the OpenEye license on forks, and since these changes probably don't hit RDKit/OpenEye behavior they shouldn't be necessary
the bot reformatting code - it's only for style consistency. You can run it yourself or let it auto-fix stuff (you might need to git pull origin HEAD to avoid merge conflicts, where origin is the remote name of your fork)

j-wags commented 1 month ago

Apologies for the big delay on this. This morning I'm going to:

incorporate Matt's suggestions
move this PR on to a branch so CI will fully run
add @PEFrankel to the developers group so he can modify the branch.