This package offers types and functions for working with molecular backbones, defined here as continuous chains of bonded atoms.1
Backbones can be represented with different types:
Backbone: a type containing a 3xN matrix of coordinatesChainedBonds: a type that holds vectors of bond lengths, bond angles, and dihedral anglesFrames: a collection of rotations and translations (e.g. for representing orientations and locations of protein residues)
The Protein submodule contains utilities for working specifically with proteins. A protein can be loaded from a PDB file using the Backboner.Protein.readpdb function, which returns a Vector{Backboner.Protein.Chain}. Conversely, a Vector{Backboner.Protein.Chain} instance can be written to a PDB file using the writepdb function.
Backboner is registered, and can be installed in the Julia REPL. Press ] to enter pkg mode, and then run:
add Backboner
julia> using Backboner, Backboner.Protein
julia> chains = readpdb("test/data/1ZAK.pdb")
2-element Vector{Chain}:
Chain A with 220 residues
Chain B with 220 residues
julia> backbone = chains[1].backbone
660-element Backbone{Float64, Matrix{Float64}}:
[22.346, 17.547, 23.294]
[22.901, 18.031, 21.993]
[23.227, 16.793, 21.163]
[24.115, 16.923, 20.175]
[24.478, 15.779, 19.336]
⋮
[21.480, 14.668, 4.974]
[22.041, 14.866, 3.569]
[21.808, 13.861, 2.734]
[22.263, 13.862, 1.355]
[21.085, 14.233, 0.446]
julia> ChainedBonds(backbone)
ChainedBonds{Float64, Vector{Float64}} with 659 bonds, 658 angles, and 657 dihedrals
julia> is_knotted(backbone)
false
julia> import Zygote # unlock the `idealize` method for backbones
julia> idealize(backbone, Float64[1.46, 1.52, 1.33], Float64[1.94, 2.04, 2.13])
660-element Backbone{Float64, Matrix{Float64}}:
[22.348574, 17.582397, 23.289886]
[22.90583, 17.977451, 21.999538]
[23.216103, 16.762234, 21.140835]
[24.204561, 16.88515, 20.259508]
[24.52946, 15.827013, 19.307465]
⋮
[21.501173, 14.705252, 4.9825864]
[22.007494, 14.864742, 3.5582967]
[21.822643, 13.836198, 2.7356021]
[22.24875, 13.874594, 1.3396943]
[21.091076, 14.233609, 0.42247167]Footnotes
-
In some contexts, the term backbone may be used more loosely, and allow for atoms that are not part of the main continuous chain of atoms. This package does not support storing e.g. oxygen and beta-carbon atoms in the matrix of coordinates, as they are not part of the continuous chain of atoms. ↩