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Goal: unify on BioStructures for PDB reading #77
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Hi @timholy! Once Cheers, |
Hi @timholy ! MIToS 3.0 now has BioStructures as a dependency and adds the |
There's a growing ecosystem for handling protein structure in Julia, including two visualization packages https://github.com/MurrellGroup/ProtPlot.jl and https://github.com/BioJulia/BioMakie.jl, neither of which supports the representation used by MIToS.
I started a conversation on the Julia slack (@diegozea was invited) about unifying around a single reader for PDB files, and the conversation has spilled out to public fora like BioJulia/BioStructures.jl#48. I propose that common reader be BioStructures, and that package has undergone several recent changes to make it more palatable as a common foundation. Regardless of what decision we end up making, I think it makes a lot of sense for Julia to have a common PDB reader so that everyone can leverage all the cool tools. In my opinion, MIToS is a bit "heavy" (it does so many things which I love!) for it to serve well as the common reader that everybody depends on. That would mean migrating MIToS to work with the format read by BioStructures. Alternatively, if the community ends up preferring the MIToS representation, one could split out the PDB component of MIToS into a smaller, standalone package.
Feel free to comment here or elsewhere about any obstacles, technical or otherwise, that would stand in the way of converging on a common core.
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