From 1e737fd1058d3d6fb413952a8ff9a2f3ef772908 Mon Sep 17 00:00:00 2001 From: AntonOresten Date: Sun, 24 Nov 2024 22:46:51 +0100 Subject: [PATCH] Update compat --- Project.toml | 2 +- src/Ribbon/Ribbon.jl | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/Project.toml b/Project.toml index c777037..fc091d0 100644 --- a/Project.toml +++ b/Project.toml @@ -21,7 +21,7 @@ ColorTypes = "0.8, 0.9, 0.10, 0.11, 0.12" Dierckx = "0.5" LinearAlgebra = "1" Makie = "0.21" -ProteinChains = "0.2" +ProteinChains = "0.3, 0.4, 0.5" julia = "1" [extras] diff --git a/src/Ribbon/Ribbon.jl b/src/Ribbon/Ribbon.jl index 6e9bab9..5ab4e79 100644 --- a/src/Ribbon/Ribbon.jl +++ b/src/Ribbon/Ribbon.jl @@ -28,7 +28,7 @@ include("render.jl") # TODO: observe chains and re-render when they change function Makie.plot!(ribbon::Ribbon{<:Tuple{<:AbstractVector{<:AbstractArray{T,3}}}}) where T<:Real chain_backbones = convert.(Array{T,3}, collect(ribbon[1][])) - isnothing(ribbon.secondary_structures[]) && (ribbon.secondary_structures[] = assign_secondary_structure(chain_backbones)) + isnothing(ribbon.secondary_structures[]) && (ribbon.secondary_structures[] = ASS.assign_secondary_structure(chain_backbones)) isnothing(ribbon.colors[]) && (ribbon.colors[] = [range(0, !isone(L), L) for L in size.(chain_backbones, 3)]) render!(ribbon, chain_backbones) return ribbon @@ -37,13 +37,13 @@ end Makie.convert_arguments(::Type{<:Ribbon}, chain_backbone::AbstractArray{T,3}) where T<:Real = ([coords],) Makie.convert_arguments(R::Type{<:Ribbon}) = Makie.convert_arguments(R, Array{Float64,3}(undef, 3, 3, 0)) -Makie.convert_arguments(R::Type{<:Ribbon}, chains::AbstractVector{<:AbstractProteinChain}) = Makie.convert_arguments(R, map(chain -> chain.backbone, chains)) -Makie.convert_arguments(R::Type{<:Ribbon}, chain::AbstractProteinChain) = Makie.convert_arguments(R, [chain]) +Makie.convert_arguments(R::Type{<:Ribbon}, chains::AbstractVector{<:ProteinChain}) = Makie.convert_arguments(R, map(chain -> get_backbone(chain), chains)) +Makie.convert_arguments(R::Type{<:Ribbon}, chain::ProteinChain) = Makie.convert_arguments(R, [chain]) Makie.convert_arguments(R::Type{<:Ribbon}, path::AbstractString, args...) = Makie.convert_arguments(R, read(path, ProteinStructure, args...)) """ - ribbon_scene(chains::AbstractVector{<:ProteinChains.AbstractProteinChain}; backgroundcolor=:black, camcontrols=(;), kwargs...) + ribbon_scene(chains::AbstractVector{<:ProteinChains.ProteinChain}; backgroundcolor=:black, camcontrols=(;), kwargs...) Render a protein as a ribbon diagram. The display will be automatically centered on the rendered ribbon, unless the user supplies `camcontrols` (see Makie's camera documentation for details). @@ -64,5 +64,5 @@ end import BioStructures -Makie.convert_arguments(R::Type{<:Ribbon}, structure::BioStructures.MolecularStructure) = Makie.convert_arguments(R, ProteinStructure(structure)) -Makie.convert_arguments(R::Type{<:Ribbon}, chain::BioStructures.Chain) = Makie.convert_arguments(R, ProteinChain(chain)) +Makie.convert_arguments(R::Type{<:Ribbon}, structure::BioStructures.MolecularStructure) = Makie.convert_arguments(R, ProteinStructure{Float64}(structure)) +Makie.convert_arguments(R::Type{<:Ribbon}, chain::BioStructures.Chain) = Makie.convert_arguments(R, ProteinChain{Float64}(chain))