Merge Backboner.Protein module and private ProteinData.jl package, ad…

…d properties

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 anton083 <[email protected]> and contributors
+Copyright (c) 2024 Anton Oresten <[email protected]> and contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Project.toml

@@ -1,10 +1,25 @@
 name = "ProteinChains"
 uuid = "b8e8f2a5-48d3-44f1-ba0d-c71cb7726ff8"
-authors = ["anton083 <[email protected]> and contributors"]
-version = "1.0.0-DEV"
+authors = ["Anton Oresten <[email protected]> and contributors"]
+version = "0.0.1"
+
+[deps]
+AssigningSecondaryStructure = "8ed43e74-60fb-4e11-99b9-91deed37aef7"
+Backboner = "9ac9c2a2-1cfe-46d3-b3fd-6fa470ea56a7"
+BioStructures = "de9282ab-8554-53be-b2d6-f6c222edabfc"
+
+[weakdeps]
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
+
+[extensions]
+ZygoteExt = "Zygote"
 
 [compat]
-julia = "1.6.7"
+AssigningSecondaryStructure = "0.4"
+Backboner = "0.11"
+BioStructures = "4"
+Zygote = "0.6"
+julia = "1"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -4,3 +4,12 @@
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://MurrellGroup.github.io/ProteinChains.jl/dev/)
 [![Build Status](https://github.com/MurrellGroup/ProteinChains.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/MurrellGroup/ProteinChains.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/MurrellGroup/ProteinChains.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/MurrellGroup/ProteinChains.jl)
+
+This Julia package provides implements the `ProteinChain` type: an efficient representation of protein chains with a simple and intuitive interface to assign and implement arbitrary properties such as secondary structure, backbone bond geometry, knots, and more. 
+
+## Installation
+
+```julia
+using Pkg
+Pkg.add("ProteinChains")
+```

ext/ZygoteExt.jl

@@ -0,0 +1,24 @@
+module ZygoteExt
+
+using ProteinChains
+
+import Zygote
+
+function idealize!(chain::ProteinChain; ideal::BackboneGeometry=BackboneGeometry())
+    backbone = Backboner.Backbone(chain.backbone)
+    T = eltype(backbone.coords)
+    ideal_lengths = T[ideal.N_Ca_length, ideal.Ca_C_length, ideal.C_N_length]
+    ideal_angles = T[ideal.N_Ca_C_length, ideal.Ca_C_N_length, ideal.C_N_Ca_length]
+    new_backbone = Backboner.idealize(backbone, ideal_lengths, ideal_angles)
+    chain.backbone = new_backbone
+    return chain
+end
+
+function idealize!(structure::ProteinStructure; kwargs...)
+    for chain in structure
+        idealize!(chain; kwargs...)
+    end
+    return structure
+end
+
+end

src/ProteinChains.jl

@@ -1,5 +1,28 @@
 module ProteinChains
 
-# Write your package code here.
+using Backboner
+
+using BioStructures: BioStructures, PDBFormat, MMCIFFormat
+
+include("properties.jl")
+
+include("chain.jl")
+export ProteinChain
+export countresidues
+
+include("structure.jl")
+export ProteinStructure
+
+include("idealize.jl")
+export BackboneGeometry
+
+include("secondary-structure.jl")
+
+include("chain-properties.jl")
+
+include("io.jl")
+export readrecord
+export readpdb
+export readcif
 
 end

src/chain-properties.jl

@@ -0,0 +1,38 @@
+function assign_bond_lengths!(chain::ProteinChain)
+    chain.bond_lengths = Backboner.get_bond_lengths(Backboner.Backbone(chain.backbone))
+end
+
+function assign_bond_angles!(chain::ProteinChain)
+    chain.bond_angles = Backboner.get_bond_angles(Backboner.Backbone(chain.backbone))
+end
+
+function assign_torsion_angles!(chain::ProteinChain)
+    chain.torsion_angles = Backboner.get_torsional_angles(Backboner.Backbone(chain.backbone))
+end
+
+function assign_secondary_structure!(chain::ProteinChain, dict::Union{Dict{ProteinChain,Any},Nothing}=nothing)
+    number_vector = isnothing(dict) ? ASS.assign_secondary_structure(chain) : dict[chain]
+    chain.secondary_structure = number_vector_to_code_string(number_vector)
+end
+
+function assign_standard_residue!(chain::ProteinChain, standard_residue::Matrix{<:Real}=STANDARD_RESIDUE_ANGSTROM)
+    chain.standard_residue = standard_residue
+end
+
+function assign_residue_rotations!(chain::ProteinChain)
+    frames = Backboner.Frames(Backboner.Backbone(chain.backbone), chain.standard_residue)
+    chain.residue_rotations = frames.rotations
+end
+
+function assign_residue_rotations_quat!(chain::ProteinChain)
+    frames = Backboner.Frames(Backboner.Backbone(chain.backbone), chain.standard_residue)
+    chain.residue_rotations_quat = rotation_matrices_to_quaternions(frames.rotations)
+end
+
+function assign_residue_translations!(chain::ProteinChain)
+    chain.residue_translations = Backboner.centroid(chain.backbone; dims=2)
+end
+
+function assign_is_knotted!(chain::ProteinChain)
+    chain.is_knotted = Backboner.is_knotted(Backboner.Backbone(chain.backbone)[2:3:end])
+end

src/chain.jl

@@ -0,0 +1,44 @@
+mutable struct ProteinChain
+    id::String
+    aminoacids::String
+    backbone::Array{Float64,3}
+    numbers::Vector{Int}
+    properties::Dict{Symbol,Any}
+
+    function ProteinChain(id::String, aminoacids::String, backbone::Array{Float64,3}, numbers::Vector{Int}, properties::Dict{Symbol,Any})
+        chain = new(id, aminoacids, backbone, numbers, properties)
+        countresidues(chain)
+        @assert all(!in(fieldnames(ProteinChain)), keys(properties))
+        return chain
+    end
+end
+
+Base.getproperty(chain::ProteinChain, property::Symbol) = _getproperty(chain, property)
+Base.setproperty!(chain::ProteinChain, property::Symbol, value) = _setproperty!(chain, property, value)
+
+function countresidues(chain::ProteinChain)
+    @assert length(chain.aminoacids) == size(chain.backbone, 3) == length(chain.numbers)
+    return length(chain.aminoacids)
+end
+
+function ProteinChain(id::String, aminoacids::String, backbone::Array{Float64,3}, numbers::Vector{Int}; kwargs...)
+    chain = ProteinChain(id, aminoacids, backbone, numbers, Dict{Symbol,Any}())
+    !isempty(kwargs) && push!(chain.properties, kwargs...)
+    return chain
+end
+
+Base.summary(chain::ProteinChain) = "$(countresidues(chain))-residue ProteinChain \"$(chain.id)\" with $(length(chain.properties)) properties"
+
+function Base.show(io::IO, ::MIME"text/plain", chain::ProteinChain)
+    print(io, summary(chain), ":")
+    printstyled(io, "\n  fields:", color=:yellow)
+    context = IOContext(io, :compact => true, :limit => true)
+    for fieldname in fieldnames(ProteinChain)[1:end-1]
+        printfield(context, chain, fieldname)
+    end
+    printstyled(io, "\n  properties:", color=:yellow)
+    isempty(chain.properties) && print(io, " (none)")
+    for property in keys(chain.properties)
+        printfield(context, chain, property)
+    end
+end

src/idealize.jl

@@ -0,0 +1,34 @@
+Base.@kwdef struct BackboneGeometry
+    N_Ca_length = 1.46 
+    Ca_C_length = 1.52
+    C_N_length = 1.33
+
+    N_Ca_C_angle = 1.94
+    Ca_C_N_angle = 2.03
+    C_N_Ca_angle = 2.13
+end
+
+# TODO: make this align with default BackboneGeometry
+const STANDARD_RESIDUE_ANGSTROM = [
+    -1.066  -0.200   1.266;
+     0.645  -0.527  -0.118;
+     0.000   0.000   0.000;
+] #  N       Ca      Cs
+
+function append_residue(backbone::Backbone, dihedrals::Vector{<:Real}; ideal::BackboneGeometry=BackboneGeometry())
+    length(dihedrals) == 3 || throw(ArgumentError("length of `dihedrals` must be 3, as only 3 backbone atoms are introduced."))
+    lengths = [ideal.C_N_length, ideal.N_Ca_length, ideal.Ca_C_length]
+    angles = [ideal.Ca_C_N_angle, ideal.C_N_Ca_angle, ideal.N_Ca_C_angle]
+    append_bonds(backbone, Float64.(lengths), Float64.(angles), Float64.(dihedrals))
+end
+
+function prepend_residue(backbone::Backbone, dihedrals::Vector{<:Real}; ideal::BackboneGeometry=BackboneGeometry())
+    length(dihedrals) == 3 || throw(ArgumentError("length of `dihedrals` must be 3, as only 3 backbone atoms are introduced."))
+    lengths = [ideal.N_Ca_length, ideal.Ca_C_length, ideal.C_N_length]
+    angles = [ideal.N_Ca_C_angle, ideal.Ca_C_N_angle, ideal.C_N_Ca_angle]
+    return prepend_bonds(backbone, Float64.(lengths), Float64.(angles), Float64.(dihedrals))
+end
+
+# TODO: use cooldown (and Float64?) to increase precision and accuracy
+# See ext/ZygoteExt.jl
+function idealize! end