Fixes

src/backbone.jl

@@ -80,5 +80,5 @@ end
 @inline Base.getindex(backbone::Backbone, r::AbstractVector{<:Integer}) = Backbone(backbone.coords[:, r])
 @inline Base.view(backbone::Backbone, I...) = Backbone(view(backbone.coords, :, I...))
 
-@inline Base.setindex!(backbone::Backbone, coords::AbstractVector, i::Integer) = (backbone[i] .= coords)
-@inline Base.setindex!(backbone::Backbone, coords::AbstractMatrix, r::AbstractVector{<:Integer}) = (backbone[r].coords .= coords)
+@inline Base.setindex!(backbone::Backbone, coords::AbstractVector, i::Integer) = (backbone.coords[:, i] .= coords)
+@inline Base.setindex!(backbone::Backbone, coords::AbstractMatrix, r::AbstractVector{<:Integer}) = (backbone.coords[:, r] .= coords)

src/protein/io.jl

@@ -90,32 +90,4 @@ function writepdb(protein::Vector{Chain}, filename, header=:auto, footer=:auto)
     PDBTools.writePDB(atoms, filename, header=header, footer=footer)
 end
 
-pdb_to_protein, protein_to_pdb = readpdb, writepdb
-
-
-function oxygen_coord_matrix(chain_id::AbstractString, oxygens::Vector{PDBTools.Atom})
-    chain_oxygens = filter(a -> PDBTools.chain(a) == chain_id, oxygens)
-    coords = Matrix{Float32}(undef, 3, length(chain_oxygens))
-    for (i, atom) in enumerate(chain_oxygens)
-        coords[:, i] = [atom.x, atom.y, atom.z]
-    end
-    return coords
-end
-
-# Alternative to oxygen_coords function in src/protein/oxygen.jl to get exact coordinates of oxygen atoms
-function pdb_oxygen_coords(filename::String)
-    atoms = PDBTools.readPDB(filename)
-    chain_ids = unique(PDBTools.chain.(atoms))
-    oxygens = PDBTools.Atom[]
-    i = 1
-    while i <= length(atoms) - 3
-        if atoms[i].name == "N" && atoms[i+1].name == "CA" && atoms[i+2].name == "C" && atoms[i+3].name == "O"
-            push!(oxygens, atoms[i+3])
-            i += 4
-        else
-            i += 1
-        end
-    end
-    oxygen_coord_matrices = [oxygen_coord_matrix(chain_id, oxygens) for chain_id in chain_ids]
-    return oxygen_coord_matrices
-end
+pdb_to_protein, protein_to_pdb = readpdb, writepdb

test/backbone.jl

@@ -5,5 +5,14 @@
     @test length(backbone) == 20
     @test size(backbone) == (20,)
     @test backbone[1] == coords[:, 1]
+    @test backbone[1:2] == Backbone(coords[:, 1:2])
+
+    backbone[1] = [0.0, 0.0, 0.0]
+    backbone[1:2] = [0.0 0.0; 0.0 0.0; 0.0 0.0]
+    @test backbone[1] == [0.0, 0.0, 0.0]
+    @test backbone[1:2] == Backbone([0.0 0.0; 0.0 0.0; 0.0 0.0])
+
+    @test length(Backbone{Float32}(undef, 20)) == 20
+    @test length(Backbone(randn(3, 3, 5))) == 15
 
 end