Remove backbone directory

src/Backboner.jl

@@ -1,9 +1,9 @@
 module Backboner
 
 using LinearAlgebra
-import Rotations
 
-include("backbone/backbone.jl")
+include("backbone.jl")
+include("bonds.jl")
 include("protein/protein.jl")
 
 end

src/backbone/backbone.jl → src/backbone.jl

@@ -27,6 +27,3 @@ end
 @inline Base.size(backbone::Backbone) = Tuple(length(backbone))
 @inline Base.getindex(backbone::Backbone, i::Integer) = view(backbone.coords, :, i)
 @inline Base.getindex(backbone::Backbone, r::AbstractVector{<:Integer}) = Backbone(view(backbone.coords, :, r))
-
-include("rotations.jl")
-include("bonds.jl")

src/backbone/bonds.jl → src/bonds.jl

@@ -1,3 +1,5 @@
+import Rotations
+
 export get_atom_displacements
 export get_atom_distances
 
@@ -49,7 +51,7 @@ end
 
 get_bond_angles(backbone::Backbone) = get_bond_angles(get_bond_vectors(backbone))
 
-# source: en.wikipedia.org/wiki/Dihedral_angle#In_polymer_physics
+# source: https://en.wikipedia.org/w/index.php?title=Dihedral_angle&oldid=1182848974#In_polymer_physics
 function dihedral_angle(u1::V, u2::V, u3::V) where V <: AbstractVector{<:Real}
     c12, c23 = cross(u1, u2), cross(u2, u3)
     return atan(dot(u2, cross(c12, c23)), norm(u2) * dot(c12, c23))

src/protein/protein.jl

@@ -12,5 +12,6 @@ include("chain.jl")
 include("oxygen.jl")
 include("assign.jl")
 include("io.jl")
+include("rotations.jl")
 
 end

src/backbone/rotations.jl → src/protein/rotations.jl

@@ -1,3 +1,5 @@
+import Rotations
+
 export locs_and_rots_to_backbone, backbone_to_locs_and_rots
 
 const STANDARD_TRIANGLE_ANGSTROM = Float32[

test/backbone.jl

@@ -0,0 +1,9 @@
+@testset "backbone.jl" begin
+
+    coords = randn(3, 20)
+    backbone = Backbone(coords)
+    @test length(backbone) == 20
+    @test size(backbone) == (20,)
+    @test backbone[1] == coords[:, 1]
+
+end

test/protein/protein.jl

@@ -4,4 +4,5 @@ include("residue.jl")
 include("chain.jl")
 include("oxygen.jl")
 include("assign.jl")
-include("io.jl")
+include("io.jl")
+include("rotations.jl")

test/runtests.jl

@@ -5,7 +5,8 @@ using LinearAlgebra
 
 @testset "Backboner.jl" begin
 
-    include("backbone/backbone.jl")
+    include("backbone.jl")
+    include("bonds.jl")
     include("protein/protein.jl")
 
 end