Update to Backboner 0.11

Project.toml

@@ -1,7 +1,7 @@
 name = "AssigningSecondaryStructure"
 uuid = "8ed43e74-60fb-4e11-99b9-91deed37aef7"
 authors = ["Anton Oresten <[email protected]>"]
-version = "0.4.1"
+version = "0.4.2"
 
 [deps]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -13,7 +13,7 @@ Backboner = "9ac9c2a2-1cfe-46d3-b3fd-6fa470ea56a7"
 BackbonerExt = "Backboner"
 
 [compat]
-Backboner = "0.9, 0.10"
+Backboner = "0.11"
 LinearAlgebra = "1"
 julia = "1"
 

README.md

@@ -15,10 +15,14 @@ The package is registered in the General registry, and can be installed from the
 
 ## Usage
 
+The `assign_secondary_structure` function takes a vector of atom coordinate arrays of size (3, 3, L). The first axis is for the x, y, and z coordinates, the second axis is for the atom types (N, CA, C), and the third axis is for the residues.
+
+In cases where the coordinates aren't already loaded, one can import Backboner, which adds support for .pdb and .cif files. 
+
 ```julia
-julia> using AssigningSecondaryStructure
+julia> using AssigningSecondaryStructure, Backboner
 
-julia> using Backboner # package with an extension that adds support for PDB files 
+julia> using Backboner
 
 julia> assign_secondary_structure("test/data/1ASS.pdb") # 1 chain
 1-element Vector{Vector{Int64}}:
@@ -30,8 +34,6 @@ julia> assign_secondary_structure("test/data/1ZAK.pdb") # 2 chains
  [1, 1, 1, 1, 3, 3, 3, 3, 3, 3  …  2, 2, 2, 2, 2, 2, 2, 1, 1, 1]
 ```
 
-Without Backboner, `assign_secondary_structure` takes a vector of atom coordinate arrays of size (3, 3, L), in cases where the atom coordinates are already loaded. The first axis is for the x, y, and z coordinates, the second axis is for the atom types (N, CA, C), and the third axis is for the residues.
-
 ## Acknowledgements
 
 This package was originally ported from the [PyDSSP](https://github.com/ShintaroMinami/PyDSSP) package, created by Shintaro Minami. The code has since been rewritten to look more like the 1983 paper (Kabsch W and Sander C), and to be more Julian, understandable, and efficient, at the cost of it no longer being differentiable like the PyDSSP version. The time complexity is still quadratic, so it may be slow for larger proteins. We plan on making a more efficient version with k-d trees.

ext/BackbonerExt.jl

@@ -7,6 +7,7 @@ get_coords(chain::Backboner.Protein.Chain) = reshape(chain.backbone.coords, 3, 3
 
 AssigningSecondaryStructure.assign_secondary_structure(chains::Vector{Backboner.Protein.Chain}) = assign_secondary_structure(get_coords.(chains))
 AssigningSecondaryStructure.assign_secondary_structure(chain::Backboner.Protein.Chain) = assign_secondary_structure([chain])[1]
-AssigningSecondaryStructure.assign_secondary_structure(filename::AbstractString) = assign_secondary_structure(Backboner.Protein.readpdb(filename))
+AssigningSecondaryStructure.assign_secondary_structure(path::AbstractString, format) = assign_secondary_structure(Backboner.Protein.readchains(path, format))
+AssigningSecondaryStructure.assign_secondary_structure(path::AbstractString) = assign_secondary_structure(Backboner.Protein.readchains(path))
 
 end