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rcsb / symmetry

:ferris_wheel: Detect, analyze, and visualize protein symmetry
GNU Lesser General Public License v2.1
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Create FASTA writer for QuatSymm multiple alignment #100

Closed lafita closed 3 years ago

lafita commented 3 years ago

Address issue #99

lafita commented 3 years ago

There is some error related to source.rcsb.org - I will have a look and fix tests using the website.

josemduarte commented 3 years ago

Nice, thanks @lafita

As you noted all access to source.rcsb.org should be discontinued as soon as possible. We are going to be shutting down the service soon. See the related PR in biojava: https://github.com/biojava/biojava/pull/882

lafita commented 3 years ago

Thanks @josemduarte

Would this be fixed by updating to the next BioJava release? SCOP identifiers are still available through the StructureIdentifier interface right?

josemduarte commented 3 years ago

Would this be fixed by updating to the next BioJava release?

That should do it. I hope it doesn't take too long for the next release to come.

SCOP identifiers are still available through the StructureIdentifier interface right?

Yes, the Berkeley provider is available but it is slow to initialise.

lafita commented 3 years ago

Ok, in that case I am going to merge this and we can fix the test issues (unrelated to this PR) when we have a new BioJava version.

josemduarte commented 3 years ago

@lafita regarding new BioJava version and the code I'm removing in https://github.com/biojava/biojava/pull/882, it'd be a good idea to build this project using that biojava branch's snapshot and see if everything is alright. That is to confirm I didn't remove any needed functionality.

josemduarte commented 3 years ago

@lafita I've tried with biojava with the PR branch https://github.com/biojava/biojava/pull/882 and the project built correctly including tests.

lafita commented 3 years ago

Thanks @josemduarte I am merging it then.