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RMSD, RMSF Refactor/Test Coverage #893
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I generally agree to the refactor, Bauhaus-style. (And many thanks for PR #889 which added tests for For enhancements I would open new issues/PRs. I would also like to automate RMSD-calculation between two non-identical structures. PyMOL (and LSQMAN) have algorithms that do RMSD iteratively and throw out atoms that have high RMSD. The |
Some time ago when the It might make more sense to open another issue for an
Note: much of the code in I would be happy to work on this as a separate issue and leave the Bauhaus-style refactoring here. |
For the record, the proposal about on-the-fly coordinate transformation is #786. I've been lacking time lately to work on it, but I can arrange some time if there is interest for the feature. |
@jbarnoud Ah, excellent! Not sure why I missed that. |
Please, go for the refactor. If anything, try to have as much of the logic as possible decoupled from the analyses class so it can be reused elsewhere. |
* fixes MDAnalysis#893 * RMSD refactored with AnalysisBase class and confirms to the new analysis API (see MDAnalysis#719) * Tests added * Documentation and chaining functions * Fixed and updated documentation * Addressed broadcasting and other issues * Updated CHANGELOG
Expected behaviour
RMSD and RMSF are highly used analysis modules. Both should follow the Bauhaus API and both should have full coverage.
Actual behaviour
(EDIT: fixed with PR #889) BothMDAnalysis.analysis.rms.RMSD
has no current test coverage, (which didn't expose the bug fixed by #889).MDAnalysis.analysis.rms.RMSD
andMDAnalysis.analysis.rms.RMSF
are great candidates for a refactor to the Bauhaus API as well.Proposal
Refactor
MDAnalysis.analysis.rms.RMSD
andMDAnalysis.analysis.rms.RMSF
to conform to the Bauhaus API.As a part of this refactor we would add test coverage forAdditional work that could be done, but should probably be its own issue is creating the option for linear programming rmsd similar to that of MDTraj.RMSD
.The text was updated successfully, but these errors were encountered: