Backboner

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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.

View the source code on GitHub (licensed under MIT).

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
3×660 Backbone{Float32, Matrix{Float32}}:
 22.346  22.901  23.227  24.115  24.478  …  21.48   22.041  21.808  22.263  21.085
 17.547  18.031  16.793  16.923  15.779     14.668  14.866  13.861  13.862  14.233
 23.294  21.993  21.163  20.175  19.336      4.974   3.569   2.734   1.355   0.446

julia> is_knotted(backbone)
false

julia> ChainedBonds(backbone)
ChainedBonds{Float32, Vector{Float32}} with 659 bonds, 658 angles, and 657 dihedrals
  • 1In some contexts, the term backbone may be used more loosely, and allow for atoms that do 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.