Backboner

Backboner is a Julia package that offers a set of types and functions for working with molecular backbones: defined here as continuous chains of bonded atoms.¹ The package provides a few different types for representing backbones:

• Backbone: a type containing a 3xN matrix of coordinates
• ChainedBonds: a type that holds vectors of bond lengths, bond angles, and dihedral angles
• Frames: a collection of rotations and translations (e.g. for representing orientations and locations of protein residues)

The Protein submodule contains functions and types 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.

Installation

Backboner is registered, and can be installed in the Julia REPL. Press ] to enter pkg mode, and then run:

add Backboner

Example usage

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{Float32, Matrix{Float32}}:
 [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]
 ⋮
 [21.48, 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{Float32, Vector{Float32}} 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, Float32[1.46, 1.52, 1.33], Float32[1.94, 2.04, 2.13])
660-element Backbone{Float32, Matrix{Float32}}:
 [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

1. 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. ↩