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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
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Use MDTraj dssp #547

Closed pckroon closed 7 months ago

pckroon commented 9 months ago

This is a first pass to use the mdtraj dssp implementation by default. I had to remove the savedir/savefile mechanism that was used to save the .ssd files 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

fgrunewald commented 8 months ago

@pckroon this one is good once the test coverage is up to speed

fgrunewald commented 8 months ago

@pckroon I've played around and tested it in different circumstances. For me seems to work pretty well

pckroon commented 7 months ago

Alright, test coverage is as high as it's going to get. Left uncovered are mostly error checks.