Minor changes

README.md

@@ -5,12 +5,23 @@
 
 This package provides a to calculate the secondary structure using the [DSSP](https://swift.cmbi.umcn.nl/gv/dssp/) algorithm. The package was ported from the [PyDSSP](https://github.com/ShintaroMinami/PyDSSP) package.
 
-It is not a complete implementation of DSSP, as it only assigns '-' for loops, 'H' for alpha helices, and 'E' for beta strands. In spite of that, it matches the original DSSP to a large extent, with the added advantage of being more than 10x faster. For the full DSSP algorithm, check out [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl) or [ProteinSecondaryStructures.jl](https://github.com/m3g/ProteinSecondaryStructures.jl), which both use the [DSSP_jll.jl](https://docs.juliahub.com/General/DSSP_jll/stable/) package, auto-generated using [BinaryBuilder.jl](https://github.com/JuliaPackaging/BinaryBuilder.jl). 
+This is not a complete implementation of DSSP, as it only assigns '-' for loops, 'H' for alpha helices, and 'E' for beta strands. In spite of that, it matches the original DSSP to a large extent, with the added advantage of being more than 10x faster. For the full DSSP algorithm, check out [BioStructures.jl](https://github.com/BioJulia/BioStructures.jl) or [ProteinSecondaryStructures.jl](https://github.com/m3g/ProteinSecondaryStructures.jl), which both use the [DSSP_jll.jl](https://docs.juliahub.com/General/DSSP_jll/stable/) package that auto-generated using [BinaryBuilder.jl](https://github.com/JuliaPackaging/BinaryBuilder.jl). 
 
 ```julia
-julia> join(sscodes(dssp("1ASS.pdb")))
+julia> ss_nums = dssp("test/data/1ASS.pdb") # 1 chain, returns numeric codes
+1-element Vector{Vector{Int64}}:
+ [1, 1, 1, 3, 3, 3, 1, 1, 1, 1  …  3, 3, 3, 3, 3, 3, 3, 1, 1, 1]
+
+julia> join.(sscodes.(ss_nums)) # 1 chain, converted to chars with sscodes, joined into string
 1-element Vector{String}:
  "---EEE-----------EEE-EEEEEE---E" ⋯ 90 bytes ⋯ "--------EEE-EEEEEEE--EEEEEEE---"
+
+julia> join.(sscodes.(dssp("test/data/3GOU.pdb"))) # 4 chains
+4-element Vector{String}:
+ "---HHHHHHHHHHHHHH---HHHHHHHHHHH" ⋯ 79 bytes ⋯ "HH------HHHHHHHHHHHHHHHHHH-----"
+ "---HHHHHHHHHHHHHH---HHHHHHHHHHH" ⋯ 84 bytes ⋯ "---HHHHHHHHHHHHHHHHHH---------H"
+ "---HHHHHHHHHHHHHH---HHHHHHHHHHH" ⋯ 79 bytes ⋯ "HH------HHHHHHHHHHHHHHHHHH-----"
+ "---HHHHHHHHHHHHHH---HHHHHHHHHHH" ⋯ 84 bytes ⋯ "---HHHHHHHHHHHHHHHHHH---------H"
 ```
 
 ## References

src/AssigningSecondaryStructure.jl

@@ -1,7 +1,5 @@
 module AssigningSecondaryStructure
 
-export dssp
-
 include("utils.jl")
 include("dssp.jl")
 include("pdb.jl")

src/dssp.jl

@@ -1,6 +1,8 @@
 using LinearAlgebra
 using PaddedViews
 
+export dssp
+
 const Q1Q2_F = 0.084 * 332
 const DEFAULT_CUTOFF = -0.5
 const DEFAULT_MARGIN = 1.0

src/pdb.jl

@@ -5,14 +5,14 @@ export load_atom_coords, load_pdb_coords
 _coords(atom::Atom) = [atom.x, atom.y, atom.z]
 
 function collect_residues(atoms)
-    quadruplets = Vector{Atom}[]
+    residues = Vector{Atom}[]
     residue_atoms = Atom[]
     current_residue_number = resnum(atoms[1])  # Assuming residue_number function exists
 
     for atom in atoms
         if resnum(atom) != current_residue_number  # New residue started
             if length(residue_atoms) == 4
-                push!(quadruplets, copy(residue_atoms))
+                push!(residues, copy(residue_atoms))
             end
             empty!(residue_atoms)
             current_residue_number = resnum(atom)
@@ -25,14 +25,12 @@ function collect_residues(atoms)
 
     # Handling the last residue
     if length(residue_atoms) == 4
-        push!(quadruplets, copy(residue_atoms))
+        push!(residues, copy(residue_atoms))
     end
 
-    return quadruplets
+    return residues
 end
 
-
-
 function load_atom_coords(atoms::AbstractVector{<:Atom})
     residues = collect_residues(atoms)
     coords = zeros(Float32, (length(residues), 4, 3))