Rename atom coords functions

MurrellGroup · Dec 28, 2023 · 2fac583 · 2fac583
1 parent ab24913
commit 2fac583
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Showing 2 changed files with 11 additions and 13 deletions.
diff --git a/src/protein/chain.jl b/src/protein/chain.jl
@@ -44,15 +44,15 @@ Base.show(io::IO, chain::Chain) = print(io, summary(chain))
 @inline Base.getindex(protein::AbstractVector{Chain}, id::AbstractString) = protein[findfirst(chain -> chain.id == id, protein)]
 @inline Base.getindex(protein::AbstractVector{Chain}, id::Symbol) = protein[String(id)]
 
-export nitrogens, alphacarbons, carbonyls
+export nitrogen_coords, alphacarbon_coords, carbonyl_coords
 
-nitrogens(backbone::Backbone) = backbone[1:3:end]
-alphacarbons(backbone::Backbone) = backbone[2:3:end]
-carbonyls(backbone::Backbone) = backbone[3:3:end]
+nitrogen_coords(backbone::Backbone) = (@view backbone[1:3:end]).coords
+alphacarbon_coords(backbone::Backbone) = (@view backbone[2:3:end]).coords
+carbonyl_coords(backbone::Backbone) = (@view backbone[3:3:end]).coords
 
-nitrogens(chain::Chain) = nitrogens(chain.backbone)
-alphacarbons(chain::Chain) = alphacarbons(chain.backbone)
-carbonyls(chain::Chain) = carbonyls(chain.backbone)
+nitrogen_coords(chain::Chain) = nitrogen_coords(chain.backbone)
+alphacarbon_coords(chain::Chain) = alphacarbon_coords(chain.backbone)
+carbonyl_coords(chain::Chain) = carbonyl_coords(chain.backbone)
 # oxygen_coords function in src/protein/oxygen.jl
 
 export nitrogen_alphacarbon_distances, alphacarbon_carbonyl_distances, carbonyl_nitrogen_distances

diff --git a/src/protein/oxygen.jl b/src/protein/oxygen.jl
@@ -39,15 +39,13 @@ function get_last_oxygen(
     return O_pos
 end
 
-function oxygen_coords(
-    backbone::Backbone,
-)
+function oxygen_coords(backbone::Backbone)
     T = eltype(eltype(backbone))
     L = length(backbone) ÷ 3
 
-    CAs = alphacarbons(backbone)
-    Cs = carbonyls(backbone)
-    next_Ns = @view nitrogens(backbone)[2:end]
+    CAs = eachcol(alphacarbon_coords(backbone))
+    Cs = eachcol(carbonyl_coords(backbone))
+    next_Ns = eachcol(@view nitrogen_coords(backbone)[:, 2:end])
     oxygen_coords = zeros(T, 3, L)
     for (i, (CA, C, next_N)) in enumerate(zip(CAs, Cs, next_Ns))
         oxygen_coords[:, i] = estimate_oxygen_position(CA, C, next_N)