Use MDTraj dssp #547
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Use MDTraj dssp #547
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The complication is/was caused because AnnotateDSSP has a `run_molecule` method (like it should), `annotate_dssp` accepts said molecule, *and `run_dssp` runs on a system*. This all makes sense and is logical, but it makes the flow rather awkward.
fgrunewald
reviewed
Oct 4, 2023
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Some first comments: I need more time to review the tests and also run this branch.
About the citations: I think we could simply dump the dssp citation in the force-field bibs and then add it to the molecule in the processor. I don't think we should overthink this feature considering most people don't care anyways.
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@pckroon this one is good once the test coverage is up to speed |
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@pckroon I've played around and tested it in different circumstances. For me seems to work pretty well |
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Alright, test coverage is as high as it's going to get. Left uncovered are mostly error checks. |
fgrunewald
approved these changes
Dec 5, 2023
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This is a first pass to use the mdtraj dssp implementation by default. I had to remove the
savedir/savefilemechanism that was used to save the.ssdfiles since I can't quite find a way to cleanly propagate it and it makes no sense for the mdtraj side.I still have to add the mdtraj citation to all molecules touched, but citations are currently bound to force fields, which doesn't make a lot of sense here.
Maybe citation lookup should be changed to use a https://docs.python.org/3/library/collections.html#collections.ChainMap built up of a general set of citations (for e.g. code) and FF specific citations?
At least I can run the integration tests on my machine again now...
Fixes #522