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Support residue "ins codes", linear backbone indexing only + other ch…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,84 +1,33 @@ | ||
| export Backbone | ||
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| """ | ||
| Backbone{T <: Real, M <: AbstractMatrix{T}} <: AbstractMatrix{T} | ||
| Backbone{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. | ||
| # Examples | ||
| A `Backbone` can be created from a matrix of coordinates: | ||
| ```jldoctest | ||
| julia> backbone = Backbone(zeros(3, 5)) # 5 atoms with 3 coordinates each | ||
| 3×5 Backbone{Float64, Matrix{Float64}}: | ||
| 0.0 0.0 0.0 0.0 0.0 | ||
| 0.0 0.0 0.0 0.0 0.0 | ||
| 0.0 0.0 0.0 0.0 0.0 | ||
| julia> backbone[1] = [1.0, 2.0, 3.0]; # set the first atom's coordinates | ||
| julia> backbone | ||
| 3×5 Backbone{Float64, Matrix{Float64}}: | ||
| 1.0 0.0 0.0 0.0 0.0 | ||
| 2.0 0.0 0.0 0.0 0.0 | ||
| 3.0 0.0 0.0 0.0 0.0 | ||
| julia> backbone[1:2] # indexing by range returns a new Backbone | ||
| 3×2 Backbone{Float64, Matrix{Float64}}: | ||
| 1.0 0.0 | ||
| 2.0 0.0 | ||
| 3.0 0.0 | ||
| ``` | ||
| Arrays will always be flattened to a 3xN matrix: | ||
| ```jldoctest | ||
| julia> backbone = Backbone(zeros(3, 3, 4)) # e.g. 3 coordinates per atom, 3 atoms per residue, 4 residues | ||
| 3×12 Backbone{Float64, Matrix{Float64}}: | ||
| 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 | ||
| 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 | ||
| 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 | ||
| ``` | ||
| """ | ||
| struct Backbone{T <: Real, M <: AbstractMatrix{T}} <: AbstractMatrix{T} | ||
| struct Backbone{T<:Real,M<:AbstractMatrix{T}} <: AbstractVector{AbstractVector{T}} | ||
| coords::M | ||
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| function Backbone{T, M}(coords::M) where {T <: Real, M <: AbstractMatrix{T}} | ||
| function Backbone{T,M}(coords::M) where {T<:Real,M<:AbstractMatrix{T}} | ||
| size(coords, 1) == 3 || throw(ArgumentError("Expected the first dimension of coords to have a size of 3")) | ||
| return new{T, M}(coords) | ||
| return new(coords) | ||
| end | ||
| end | ||
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| Backbone{T}(coords::M) where {T <: Real, M <: AbstractMatrix{T}} = Backbone{T, M}(coords) | ||
| Backbone{T}(coords::AbstractArray{T}) where T <: Real = Backbone{T}(reshape(coords, size(coords, 1), :)) | ||
| Backbone{T}(coords::AbstractArray{<:Real}) where T <: Real = Backbone{T}(convert.(T, coords)) | ||
| Backbone{T}(backbone::Backbone) where T <: Real = Backbone{T}(backbone.coords) | ||
| Backbone(coords::AbstractArray{T}) where T <: Real = Backbone{T}(coords) | ||
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| Backbone{T, M}(::UndefInitializer, n::Integer) where {T <: Real, M <: AbstractMatrix{T}} = Backbone{T, M}(M(undef, 3, n)) | ||
| Backbone{T}(::UndefInitializer, n::Integer) where T = Backbone{T, Matrix{T}}(undef, n) | ||
| Backbone{T}() where T = Backbone{T}(undef, 0) | ||
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| Base.values(backbone::Backbone) = backbone.coords | ||
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| @inline Base.size(backbone::Backbone) = size(backbone.coords) | ||
| @inline Base.getindex(backbone::Backbone, i, j) = backbone.coords[i, j] | ||
| @inline Base.view(backbone::Backbone, i, j) = view(backbone.coords, i, j) | ||
| @inline Base.setindex!(backbone::Backbone, v, i, j) = (backbone.coords[i, j] .= v) | ||
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| @inline Base.length(backbone::Backbone) = size(backbone, 2) | ||
| @inline Base.size(backbone::Backbone) = Tuple(size(backbone.coords, 2)) | ||
| @inline Base.getindex(backbone::Backbone, i) = Backbone(backbone.coords[:, i]) | ||
| @inline Base.view(backbone::Backbone, i) = Backbone(view(backbone.coords, :, i)) | ||
| @inline Base.setindex!(backbone::Backbone, v, i) = (backbone.coords[:, i] .= v) | ||
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| @inline Base.getindex(backbone::Backbone, i::Integer) = backbone.coords[:, i] | ||
| @inline Base.view(backbone::Backbone, i::Integer) = view(backbone.coords, :, i) | ||
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| Base.copy(backbone::Backbone) = copy(backbone.coords) | ||
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| Base.:(==)(backbone1::Backbone, backbone2::Backbone) = backbone1.coords == backbone2.coords | ||
| Base.:(==)(backbone::Backbone, coords::AbstractMatrix) = backbone.coords == coords | ||
| Base.:(==)(coords::AbstractMatrix, backbone::Backbone) = coords == backbone.coords | ||
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| Base.hash(backbone::Backbone, h::UInt) = hash(backbone.coords, h) |
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@JuliaRegistrator register
Release notes:
Backbone{T}a subtype ofAbstractVector{AbstractVector{T}}, instead ofAbstractMatrix{T}.get_bond_lengths(bond_vectors),get_bond_angles(bond_vectors), andget_dihedrals(bond_vectors)methods, in favor of only having the method for backbones, which calls_get_bond_lengths(bond_vectors),_get_bond_angles(bond_vectors), and_get_dihedrals(bond_vectors).35a27e8There was a problem hiding this comment.
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Registration pull request created: JuliaRegistries/General/108219
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