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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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GO IDP bugfix #590

Closed csbrasnett closed 2 months ago

csbrasnett commented 2 months ago

Need to add secstruc to the water bias application, otherwise can't apply across a whole protein (starting resid has to be > 1). this should fix that. And add preprint citation.

csbrasnett commented 2 months ago

I'm not certain, but I think adding again there would be degenerate anyway? VirtualSiteCreator gets called both in the Go model and if args.water_bias is used, so I think just adding it there should be fine.

Happy to write an integration test. It strikes me this might be a good opportunity to deal with #585 at the same time, so I can do that as well?

fgrunewald commented 2 months ago

@csbrasnett I'd rather have 2 separate PRs, so that we can release this bug fix in near time

csbrasnett commented 2 months ago

This should bring things in line with polyply for generating topologies of idps. Maybe this is the right approach, maybe it isn't, but here's some kind of implementation either way. Happy to be advised whatever.

To do:

1) properly check against polyply 2) make some tests 3) maybe propagate secondary structure for automatic id/suggestions of IDRs?