Remove Backboner extension; stop accounting for inter-chain hydrogen …

…bonds

Project.toml

@@ -1,25 +1,17 @@
 name = "AssigningSecondaryStructure"
 uuid = "8ed43e74-60fb-4e11-99b9-91deed37aef7"
 authors = ["Anton Oresten <[email protected]>"]
-version = "0.4.2"
+version = "0.5.0"
 
 [deps]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
-[weakdeps]
-Backboner = "9ac9c2a2-1cfe-46d3-b3fd-6fa470ea56a7"
-
-[extensions]
-BackbonerExt = "Backboner"
-
 [compat]
-Backboner = "0.11"
 LinearAlgebra = "1"
 julia = "1"
 
 [extras]
-Backboner = "9ac9c2a2-1cfe-46d3-b3fd-6fa470ea56a7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "Backboner"]
+test = ["Test"]

kd.ipynb

@@ -0,0 +1,111 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\u001b[32m\u001b[1m  Activating\u001b[22m\u001b[39m project at `c:\\Users\\anton\\.julia\\dev\\AssigningSecondaryStructure`\n"
+     ]
+    }
+   ],
+   "source": [
+    "using Pkg; Pkg.activate(\".\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 81,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "WARNING: using LinearAlgebra.I in module Main conflicts with an existing identifier.\n"
+     ]
+    }
+   ],
+   "source": [
+    "using AssigningSecondaryStructure\n",
+    "import AssigningSecondaryStructure as ASS\n",
+    "\n",
+    "using Backboner, NearestNeighbors\n",
+    "using LinearAlgebra"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 99,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "10-element Vector{Bool}:\n",
+       " 0\n",
+       " 0\n",
+       " 0\n",
+       " 0\n",
+       " 0\n",
+       " 0\n",
+       " 0\n",
+       " 0\n",
+       " 0\n",
+       " 0"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "coords = reshape(Protein.readpdb(\"test/data/1ASS.pdb\")[1].backbone.coords, 3, 3, :)\n",
+    "L = size(coords, 3)\n",
+    "\n",
+    "Ca_pos = coords[:, 2, :]\n",
+    "\n",
+    "pad_pos = fill(NaN, 3)\n",
+    "C_pos = coords[:, 3, :]\n",
+    "O_pos = [ASS.get_oxygen_positions(coords) pad_pos]\n",
+    "N_pos = coords[:, 1, :]\n",
+    "H_pos = [pad_pos ASS.get_hydrogen_positions(coords)]\n",
+    "\n",
+    "kdtree = KDTree(Ca_pos, Euclidean())\n",
+    "\n",
+    "for i in axes(coords, 3)[[4]]\n",
+    "    js, dists = knn(kdtree, view(Ca_pos, :, 1), 10, true)\n",
+    "    Hbonds = map(js) do j\n",
+    "        i <= j <= i+2 && return false\n",
+    "        r_ON = norm(O_pos[:, i] - N_pos[:, j])\n",
+    "        r_CH = norm(C_pos[:, i] - H_pos[:, j])\n",
+    "        r_OH = norm(O_pos[:, i] - H_pos[:, j])\n",
+    "        r_CN = norm(C_pos[:, i] - N_pos[:, j])\n",
+    "        E = ASS.Q1Q2 * ASS.F * (1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)\n",
+    "        return E < ASS.CUTOFF\n",
+    "    end\n",
+    "    display(Hbonds)\n",
+    "end"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.10.0",
+   "language": "julia",
+   "name": "julia-1.10"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia",
+   "version": "1.10.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

src/AssigningSecondaryStructure.jl

@@ -1,7 +1,8 @@
 module AssigningSecondaryStructure
 
-include("hbonds.jl")
-include("dssp.jl")
+export assign_secondary_structure!, assign_secondary_structure
+
+include("hydrogen_bonds.jl")
 include("assign.jl")
 
 end

src/assign.jl

@@ -1,23 +1,79 @@
-export assign_secondary_structure!, assign_secondary_structure
+using LinearAlgebra: diag
 
-function assign_secondary_structure! end
+# 3-turn   >>3<<                      
+# 4-turn            >>44<<            
+# 5-turn                      >>555<< 
+# MINIMAL   X        X         X      
+# LONGER    GGG      HHHH      IIIII  
+function get_helices(Hbonds::AbstractMatrix{Bool})
+    turn3 = [diag(Hbonds, 3) .> 0; falses(3)]
+    turn4 = [diag(Hbonds, 4) .> 0; falses(4)]
+    turn5 = [diag(Hbonds, 5) .> 0; falses(5)]
+
+    # "Minimal" helices: the previous and current
+    # residue is bonding to a residue n steps ahead respectively
+    h3 = [get(turn3, i-1, false) & turn3[i] for i in eachindex(turn3)]
+    h4 = [get(turn4, i-1, false) & turn4[i] for i in eachindex(turn4)]
+    h5 = [get(turn5, i-1, false) & turn5[i] for i in eachindex(turn5)]
+
+    # Longer helices: smearing out the minimal helix
+    # residues to the residues they bond to
+    helix4 = reduce(.|, circshift(h4, i) for i in 0:3)
+
+    mask = .!(helix4 .| circshift(helix4, 1))
+    h3 = h3 .& mask
+    h5 = h5 .& mask
+
+    helix3 = reduce(.|, circshift(h3, i) for i in 0:2)
+    helix5 = reduce(.|, circshift(h5, i) for i in 0:4)
+    helix = helix3 .| helix4 .| helix5
+
+    return helix |> collect
+end
+
+function get_bridges(Hbonds::AbstractMatrix{Bool})
+    Parallel_Bridge = falses(size(Hbonds))
+    Antiparallel_Bridge = falses(size(Hbonds))
+    for j in 2:size(Hbonds, 2)-1, i in 2:size(Hbonds, 1)-1
+            Parallel_Bridge[i,j] = (Hbonds[i-1,j] & Hbonds[j,i+1]) |
+                                   (Hbonds[j-1,i] & Hbonds[i,j+1])
+        Antiparallel_Bridge[i,j] = (Hbonds[i,j] & Hbonds[j,i]) |
+                                   (Hbonds[i-1,j+1] & Hbonds[j-1,i+1])
+    end
+    return Parallel_Bridge, Antiparallel_Bridge
+end
+
+function get_strands(Hbonds::AbstractMatrix{Bool})
+    Parallel_Bridge, Antiparallel_Bridge = get_bridges(Hbonds)
+    return mapslices(any, Parallel_Bridge .| Antiparallel_Bridge, dims=1) |> vec |> collect
+end
 
 """
+    assign_secondary_structure(chain_backbone::Array{T,3}}) where T<:Real
     assign_secondary_structure(chain_backbones::Vector{Array{T,3}}) where T<:Real
 
 Given a vector of chain backbones, each represented as a 3-dimensional array of size 3x3xL, this function assigns the secondary structure to each residue.
 
 Returns a vector of vectors of integers, each of which is the secondary structure assignment
-for the corresponding chain and their respective residues. The integers are encoded as follows:
-- `1`: loop; neither helix nor strand.
-- `2`: helix; α, 3_10, or π.
-- `3`: strand; part of a β-sheet.
+for the corresponding chain and their respective residues. The secondary structure  encoded as follows:
+- `1`: loop (neither helix nor strand)
+- `2`: helix; α, 3_10, or π
+- `3`: strand; part of a β-sheet
 """
-function assign_secondary_structure(chain_backbones::Vector{Array{T,3}}) where T<:Real
-    concatenated_backbone = cat(chain_backbones..., dims=3)
-    secondary_structure = dssp(convert(Array{Float64}, concatenated_backbone))
-    lengths = size.(chain_backbones, 3)
-    chain_ends = [0; cumsum(lengths)]
-    secondary_structure_by_chain = [secondary_structure[i+1:j] for (i,j) in zip(chain_ends, chain_ends[2:end])]
-    return secondary_structure_by_chain
+function assign_secondary_structure(coords::Array{T,3}) where T <: Real
+    size(coords)[1:2] == (3, 3) || throw(DimensionMismatch("Expected 3x3xL array, got $(size(coords))"))
+    size(coords, 3) < 5 && return ones(Int, size(coords, 3))
+    Hbonds = get_hbond_map(coords)
+
+    helix = get_helices(Hbonds)
+    strand = get_strands(Hbonds)
+    loop = .!(helix .| strand)
+
+    # 1 for helix, 2 for strand, 3 for loop
+    secondary_structure = vec(mapslices(findfirst, [loop helix strand], dims=2))
+    return secondary_structure
 end
+
+assign_secondary_structure(chain_backbones::Vector{<:Array{<:Real,3}}) = assign_secondary_structure.(chain_backbones)
+
+function assign_secondary_structure! end

src/hbonds.jl → src/hydrogen_bonds.jl

@@ -30,7 +30,7 @@ function get_hydrogen_positions(coords::Array{T,3}) where T<:Real
 end
 
 # i:C=O, j:N-H
-function get_Hbonds(coords::Array{T,3}, cutoff::Real=CUTOFF) where T<:Real
+function get_hbond_map(coords::Array{T,3}, cutoff::Real=CUTOFF) where T<:Real
     C_pos = coords[:, 3, :]
     O_pos = get_oxygen_positions(coords)
     N_pos = coords[:, 1, :]