Add support for short chains

MurrellGroup · Dec 9, 2023 · fec6169 · fec6169
1 parent 08f068c
commit fec6169
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/src/dssp.jl b/src/dssp.jl
@@ -74,6 +74,11 @@ function dssp(coords::AbstractArray{T, 3}) where T
     @assert size(coords, 1) == 3
     @assert size(coords, 2) == 4
 
+    N = size(coords, 3)
+    if N < 6
+        coords = cat(coords, fill(Inf, 3, 4, 6-N), dims=3)
+    end
+
     coords = permutedims(coords, (3, 2, 1))
 
     hbmap = _get_hbond_map(coords)
@@ -114,7 +119,7 @@ function dssp(coords::AbstractArray{T, 3}) where T
     strand = ladder
     loop = .!helix .& .!strand
 
-    num_vector = findfirst.(eachrow(hcat(loop, helix, strand)))
+    num_vector = findfirst.(eachrow(hcat(loop, helix, strand)))[1:N]
 
     return num_vector
 end
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -23,6 +23,13 @@ ss_composition(ss::Vector{Char}) = [count(==(code), ss) for code in ['-', 'H', '
 
     @testset "DSSP" begin
 
+        @testset "dssp" begin
+            coords = load_pdb_backbone_coords("data/1ASS.pdb")[1]
+            @test AssigningSecondaryStructure.dssp(coords[:, :, 35:39]) == [1, 1, 1, 1, 1] # minimum helix length is 4
+            @test AssigningSecondaryStructure.dssp(coords[:, :, 35:40]) == [1, 2, 2, 2, 2, 1] # ends don't count towards helix length :shrug:
+            @test AssigningSecondaryStructure.dssp(coords[:, :, 35:41]) == [1, 2, 2, 2, 2, 2, 1]
+        end
+
         @testset "1ASS" begin
             ss = assign_secondary_structure("data/1ASS.pdb")
             @test length(ss) == 1