Add assign_oxygens!, fix typo

MurrellGroup · May 16, 2024 · 8c16a1b · 8c16a1b · AntonOresten · May 16, 2024
1 parent d6eafbb
commit 8c16a1b
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Showing 3 changed files with 10 additions and 2 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Backboner"
 uuid = "9ac9c2a2-1cfe-46d3-b3fd-6fa470ea56a7"
 authors = ["Anton Oresten <anton.oresten42@gmail.com>"]
-version = "0.9.6"
+version = "0.9.7"
 
 [deps]
 BioStructures = "de9282ab-8554-53be-b2d6-f6c222edabfc"

diff --git a/src/backbone.jl b/src/backbone.jl
@@ -1,7 +1,7 @@
 export Backbone
 
 """
-    Backbone{T <: Real} <: AbstractMatrix{T}
+    Backbone{T <: Real, M <: AbstractMatrix{T}} <: AbstractMatrix{T}
 
 The `Backbone` type is designed to efficiently store and manipulate the three-dimensional coordinates of backbone atoms.
 

diff --git a/src/protein/oxygen.jl b/src/protein/oxygen.jl
@@ -92,6 +92,14 @@ function oxygen_coords(chain::Chain)
     return stack(get_oxygen(chain, i) for i in 1:length(chain))
 end
 
+function assign_oxygens!(chain::Chain)
+    for (i, residue) in enumerate(chain)
+        deleteat!(residue.atoms, findfirst(==("O") ∘ (atom -> atom.name), residue.atoms))
+        insert!(residue.atoms, 4, Atom("O", estimate_oxygen_position(chain, i)))
+    end
+    return chain
+end
+
 function assign_missing_oxygens!(chain::Chain)
     for (i, residue) in enumerate(chain)
         !any(==("O") ∘ (atom -> atom.name), residue.atoms) && insert!(residue.atoms, 4, Atom("O", estimate_oxygen_position(chain, i)))