Convert "Quantity" to raw value for kinetic_energy and potential_energy in OpenMM reader #4548
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…gy in OpenMMSimulationReader.
Linter Bot Results:Hi @orionarcher! Thanks for making this PR. We linted your code and found the following: Some issues were found with the formatting of your code.
Please have a look at the Please note: The |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #4548 +/- ##
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- Coverage 93.66% 93.64% -0.03%
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Files 168 180 +12
Lines 21248 22327 +1079
Branches 3917 3917
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+ Hits 19902 20908 +1006
- Misses 888 961 +73
Partials 458 458 ☔ View full report in Codecov by Sentry. |
| @@ -125,10 +125,10 @@ def _mda_timestep_from_omm_context(self): | |||
| ts.frame = 0 | |||
| ts.data["time"] = state.getTime()._value | |||
| ts.data["potential_energy"] = ( | |||
| state.getPotentialEnergy().in_units_of(u.kilojoule/u.mole) | |||
| state.getPotentialEnergy().in_units_of(u.kilojoule/u.mole)._value | |||
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Would it be possible to add a quick test for these?
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Hello @orionarcher! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found: There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻 Comment last updated at 2024-03-31 02:35:28 UTC |
Changes made in this Pull Request:
.valueto kinetic_energy and potential_energyThis is breaking the ability of a downstream MDAkit to write H5MD files. Issue here. I suspect it is more generally breaking the ability to take in OpenMM and output H5MD, but it is only in
openmm-reporterthat I came across it.PR Checklist
Developers certificate of origin
📚 Documentation preview 📚: https://mdanalysis--4548.org.readthedocs.build/en/4548/