ProteinChains

This Julia package provides implements the ProteinChain type: a chain-level structure-of-arrays type representation of proteins, with support for indexing by residue index.

Installation

using Pkg
Pkg.add("ProteinChains")

Quickstart

The ProteinChain type is meant to only store a basic set of fields, from which some other properties might be derived.

julia> using ProteinChains

julia> structure = pdb"1EYE" # string macro to fetch proteins from the PDB
[ Info: File exists: 1EYE
1-element ProteinStructure "1EYE.cif":
 256-residue ProteinChain{Float64} (A)

julia> chain = structure["A"]
256-residue ProteinChain{Float64} (A)

julia> propertynames(chain)
(:id, :atoms, :sequence, :numbering, :ins_codes)

To store additional properties, simply set them like you would set a field of a mutable struct:

julia> chain.taxid = 83332
83332

For chain-wise properties, the values can be wrapped with Indexable to index the last dimension of the array when the chain gets indexed:

julia> chain.rand3 = Indexable(rand(3,256)) # last dimension matches chain length
Indexable wrapping a Matrix{Float64} (get value with `unwrap(x)`)

julia> chain[1:100].rand3 |> unwrap
3×100 view(::Matrix{Float64}, :, 1:100) with eltype Float64:
 0.273545  0.639173  0.92708   …  0.459441  0.196407  0.880034       
 0.981498  0.70263   0.279264     0.552049  0.89274   0.0328866      
 0.169268  0.117848  0.732741     0.301921  0.187094  0.281187

julia> propertynames(chain)
(:id, :atoms, :sequence, :numbering, :ins_codes, :taxid, :rand3)

See also

• BioStructures.jl
• Backboner.jl
• PDBTools.jl