Added an SSClass type

README.md

@@ -8,15 +8,15 @@ This package provides a quick way to assign secondary structure using the [DSSP]
 This is not a complete implementation of DSSP, as it only assigns '-' for loops, 'H' for alpha helices, and 'E' for beta strands. In spite of that, it matches the original DSSP to a large extent, with the added advantage of being more than 10x faster. For the full DSSP algorithm, check out [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl) or [ProteinSecondaryStructures.jl](https://github.com/m3g/ProteinSecondaryStructures.jl), which both use the [DSSP_jll.jl](https://docs.juliahub.com/General/DSSP_jll/stable/) package that was auto-generated using [BinaryBuilder.jl](https://github.com/JuliaPackaging/BinaryBuilder.jl). 
 
 ```julia
-julia> ss_nums = dssp("test/data/1ASS.pdb") # 1 chain, returns numeric codes
-1-element Vector{Vector{Int64}}:
- [1, 1, 1, 3, 3, 3, 1, 1, 1, 1  …  3, 3, 3, 3, 3, 3, 3, 1, 1, 1]
+julia> dssp("test/data/1ASS.pdb") # 1 chain, returns numeric codes
+1-element Vector{Vector{SSClass}}:
+ [Loop, Loop, Loop, Strand, Strand, Strand  …  Strand, Strand, Strand, Loop, Loop, Loop]
 
-julia> join.(sscodes.(ss_nums)) # 1 chain, converted to chars with sscodes, joined into string
+julia> string.(dssp("test/data/1ASS.pdb")) # 1 chain, Vector{SSClass} converted to string
 1-element Vector{String}:
  "---EEE-----------EEE-EEEEEE---E" ⋯ 90 bytes ⋯ "--------EEE-EEEEEEE--EEEEEEE---"
 
-julia> join.(sscodes.(dssp("test/data/3GOU.pdb"))) # 4 chains
+julia> string.(dssp("test/data/3GOU.pdb")) # 4 chains
 4-element Vector{String}:
  "---HHHHHHHHHHHHHH---HHHHHHHHHHH" ⋯ 79 bytes ⋯ "HH------HHHHHHHHHHHHHHHHHH-----"
  "---HHHHHHHHHHHHHH---HHHHHHHHHHH" ⋯ 84 bytes ⋯ "---HHHHHHHHHHHHHHHHHH---------H"

src/AssigningSecondaryStructure.jl

@@ -1,8 +1,8 @@
 module AssigningSecondaryStructure
 
+include("ssclass.jl")
 include("utils.jl")
 include("dssp.jl")
 include("pdb.jl")
-include("ss.jl")
 
 end

src/dssp.jl

@@ -7,14 +7,14 @@ const Q1Q2_F = 0.084 * 332
 const DEFAULT_CUTOFF = -0.5
 const DEFAULT_MARGIN = 1.0
 
-function _unfold(a::Array, window::Int, axis::Int)
+function _unfold(a::AbstractArray, window::Int, axis::Int)
     axis = axis < 0 ? ndims(a) + axis + 1 : axis
     idx = (0:window-1) .+ (1:size(a, axis) - window + 1)'
     unfolded = selectdim(a, axis, idx)
     return _moveaxis(unfolded, axis, ndims(unfolded))
 end
 
-function get_hydrogen_positions(coord::Array{T, 3}) where T <: Real
+function get_hydrogen_positions(coord::AbstractArray{T, 3}) where T <: Real
     vec_cn = coord[2:end, 1, :] .- coord[1:end-1, 3, :]
     vec_cn ./= mapslices(norm, vec_cn, dims=2)
     vec_can = coord[2:end, 1, :] .- coord[2:end, 2, :]
@@ -25,7 +25,7 @@ function get_hydrogen_positions(coord::Array{T, 3}) where T <: Real
 end
 
 function get_hbond_map(
-    coord::Array{T, 3};
+    coord::AbstractArray{T, 3};
     cutoff::Float64 = DEFAULT_CUTOFF,
     margin::Float64 = DEFAULT_MARGIN,
     return_e::Bool = false,
@@ -75,7 +75,7 @@ function get_hbond_map(
 end
 
 """
-    dssp(coords_chains::Vararg{Array{T, 3}, N})
+    dssp(coords_chains::Vararg{AbstractArray{T, 3}, N})
 
 Takes a variable number of chains, each of which is a 3D array of shape `(residue_count, 4, 3)`.
 Returns a vector of vector of integers denoting the secondary structure of each residue in each chain:
@@ -84,7 +84,7 @@ Returns a vector of vector of integers denoting the secondary structure of each
 - `3` for strands
 Use the `sscodes` function to convert the integers to characters.
 """
-function dssp(coords_chains::Vararg{Array{T, 3}, N}) where {T, N}
+function dssp(coords_chains::Vararg{AbstractArray{T, 3}, N}) where {T, N}
     chain_lengths = size.(coords_chains, 1)
     coords = vcat(coords_chains...)
 
@@ -127,14 +127,14 @@ function dssp(coords_chains::Vararg{Array{T, 3}, N}) where {T, N}
     strand = ladder
     loop = .!helix .& .!strand
 
-    ss_nums = findfirst.(eachrow(cat(loop, helix, strand, dims=2)))
+    classes = SSClass.(findfirst.(eachrow(cat(loop, helix, strand, dims=2))))
 
-    ss_nums_chains = Vector{Int}[]
+    classes_chains = Vector{SSClass}[]
     i = 0
     for l in chain_lengths
-        push!(ss_nums_chains, ss_nums[i+1:i+l])
+        push!(classes_chains, classes[i+1:i+l])
     end
 
-    return ss_nums_chains
+    return classes_chains
 end
 

src/ssclass.jl

@@ -0,0 +1,19 @@
+export SSClass, Loop, Helix, Strand, ss_composition
+
+struct SSClass
+    n::Int
+end
+
+const CHAR_VEC = ['-', 'H', 'E']
+Base.convert(::Type{Char}, cls::SSClass) = CHAR_VEC[cls.n]
+Base.string(ss::Vector{SSClass}) = join(convert(Char, cls) for cls in ss)
+
+const Loop   = SSClass(1)
+const Helix  = SSClass(2)
+const Strand = SSClass(3)
+
+const SSCLASS_NAMES = Dict(Loop => "Loop", Helix => "Helix", Strand => "Strand")
+
+Base.show(io::IO, cls::SSClass) = print(io, get(SSCLASS_NAMES, cls, "SSClass($(cls.n))"))
+
+ss_composition(ss::Vector{SSClass}) = [count(==(cls), ss) for cls in [Loop, Helix, Strand]]

test/runtests.jl

@@ -2,7 +2,7 @@ using AssigningSecondaryStructure
 using Test
 
 @testset "AssigningSecondaryStructure.jl" begin
-    @test ss_composition.(dssp("data/1ASS.pdb")) == [[60 53 39]]
-    @test ss_composition.(dssp("data/1ZAK.pdb")) == [[72 116 32], [72 116 32]]
-    @test ss_composition.(dssp("data/3GOU.pdb")) == [[40 101 0], [44 102 0], [40 101 0], [44 102 0]]
+    @test ss_composition.(dssp("data/1ASS.pdb")) == [[60, 53, 39]]
+    @test ss_composition.(dssp("data/1ZAK.pdb")) == [[72, 116, 32], [72, 116, 32]]
+    @test ss_composition.(dssp("data/3GOU.pdb")) == [[40, 101, 0], [44, 102, 0], [40, 101, 0], [44, 102, 0]]
 end