murrellgroup / backboner.jl Goto Github PK

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The Backbone type could probably be improved by not including the oxygen slice in the coordinate matrix, since that's not really part of the main backbone. The heavy lifting could be given to the Chain type. Defining the Backbone type to represent only a contiguous chain of atoms has the advantage that you can easily flatten out the coordinates.
AssigningSecondaryStructure.jl still uses a 3x4xL array of coordinates, so the 3x3xL backbone with have to be concatenated along dimension 3 with the 3xL oxygen atom matrix reshaped to be a 3x1xL array.

Please add a constructor that will work for this input: Frames(::Array{T, 3}, ::Matrix{T})

The package has turned out quite clean with nice abstractions. The ideas from earlier versions have been distilled to an elegant set of types and functions, with some new additions.
The elephant in the room however is the Protein submodule, with plenty of arbitrary design decisions having been made. Having support for proteins in the package natively is convenient, but PDB IO basically requires us to have 2 dependencies: BioStructures for robust PDB reading, and PDBTools for easy writing. BioStructures writing is a pain in the ass, as we'd basically need to construct an entire Structure with models, chains, residues from scratch using a Backbone and some extra vectors like amino acids and residue numbers.
Nevertheless, we could technically support proteins with a BioStructures extension, for example by defining a Backbone(chain::BioStructures.Chain, residue_selectors...) constructor or something, keeping the core package clean.
Alternatively, there could be a whole other package for protein stuff.