Backboner API
Backboner.Backbone
— TypeBackbone{T<:Real,M<:AbstractMatrix{T}} <: AbstractVector{AbstractVector{T}}
The Backbone
type is designed to efficiently store and manipulate the three-dimensional coordinates of backbone atoms.
Backboner.ChainedBonds
— TypeChainedBonds{T <: Real, V <: AbstractVector{T}}
A lazy way to store a backbone as a series of bond lengths, angles, and dihedrals.
Examples
julia> backbone = Protein.readpdb("test/data/1ZAK.pdb")["A"].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> bonds = ChainedBonds(backbone)
ChainedBonds{Float64, Vector{Float64}} with 659 bonds, 658 angles, and 657 dihedrals
Backboner.append_bonds
— Methodappend_bonds(backbone, lengths, angles, dihedrals)
Backboner.idealize
— FunctionZygote must be imported in order to activate the ZygoteIdealizationExt
extension, which defines the idealize(::Backbone)
method.
Backboner.is_knotted
— Functionis_knotted(backbone::Backbone)
Check if a backbone is knotted.
Backboner.prepend_bonds
— Methodprepend_bonds(backbone, lengths, angles, dihedrals)