Contacts

docs/make.jl

@@ -16,6 +16,7 @@ makedocs(
             "Dihedral angle analysis" => "Dihedrals.md",
             "Secondary structure" => "secondary_structures.md",
             "Structural alignment" => "structural_alignment.md",
+            "Contacts" => "contacts.md",
         ],
         "Simulation statistics" => Any[ 
             " Block averages" => "block_averages.md",

docs/src/contacts.md

@@ -0,0 +1,33 @@
+```@meta
+CollapsedDocStrings = true
+```
+# Contact analysis
+
+Contact analysis routines allow the computation and tracking of contacts along a simulation.
+
+## Distance between two residues
+
+This function computes the minimum distance between the atoms of two residues. It can be 
+used standalone, but it is also the basis for the computation of contact maps. 
+
+```@docs
+residue_residue_distance
+```
+
+## Contact map
+
+The `contact_map` function is used to evaluate contacts within a structure, or among
+two structures.
+
+```@docs
+contact_map
+```
+
+The output of `contact_map` is a `ContactMap` data structure:
+
+```@docs
+ContactMap
+```
+
+
+

ext/Contacts.jl

@@ -0,0 +1,70 @@
+using MolSimToolkit: ContactMap
+import PDBTools
+import Plots: heatmap, cgrad
+
+# the size of the plot should be proportional to the number 
+# of residues in each dimension, with a 100 residues for 
+# a 500px axis, by default
+function _plot_size(map::ContactMap)
+    nres1 = size(map.matrix, 1)
+    nres2 = size(map.matrix, 2)
+    xpixels = min(600, max(300, round(Int,500 * nres1 / 100)))
+    ypixels = min(600, max(300, round(Int,500 * nres2 / 100)))
+    return (xpixels, ypixels)
+end
+
+function heatmap(
+    map::ContactMap{<:Real}; 
+    xstep=max(1, div(size(map.matrix, 1), 20)), 
+    ystep=max(1, div(size(map.matrix, 2), 20)),
+    xticks=PDBTools.residue_ticks(map.residues1; stride=xstep, serial=true),
+    yticks=PDBTools.residue_ticks(map.residues2; stride=ystep, serial=true),
+    xrotation=60,
+    xlabel="residue",
+    ylabel="residue",
+    colorbar_title="distance (Å)",
+    aspect_ratio=1,
+    xlims=(1,size(map.matrix, 1)),
+    ylims=(1,size(map.matrix, 2)),
+    color=:grayC,
+    size=_plot_size(map),
+    framestyle=:box,
+    grid=false,
+    clims=(1,2) .* extrema(skipmissing(map.matrix)),
+    kargs...
+)
+    return heatmap(map.matrix; 
+        xlabel, ylabel, xticks, yticks, xrotation,
+        colorbar_title, color, aspect_ratio, xlims, ylims,
+        size, framestyle, grid, clims,
+        kargs...
+    )
+end
+
+function heatmap(
+    map::ContactMap{<:Bool}; 
+    xstep=max(1, div(size(map.matrix, 1), 20)), 
+    ystep=max(1, div(size(map.matrix, 2), 20)),
+    xticks=PDBTools.residue_ticks(map.residues1; stride=xstep, serial=true),
+    yticks=PDBTools.residue_ticks(map.residues2; stride=ystep, serial=true),
+    xrotation=60,
+    xlabel="residue",
+    ylabel="residue",
+    aspect_ratio=1,
+    xlims=(1,size(map.matrix, 1)),
+    ylims=(1,size(map.matrix, 2)),
+    color=:Greys_9,
+    size=_plot_size(map),
+    framestyle=:box,
+    grid=false,
+    clims=(0,1),
+    colorbar=:none,
+    kargs...
+)
+    return heatmap(map.matrix; 
+        xlabel, ylabel, xticks, yticks, xrotation,
+        color, colorbar, aspect_ratio, xlims, ylims,
+        size, framestyle, grid, clims,
+        kargs...
+    )
+end

ext/MolSimStyle.jl

@@ -8,8 +8,8 @@ const MolSimStyle_parameters = Dict{Symbol,Any}(
     :fontfamily => "Computer Modern",
     :margin => 0.5Plots.Measures.cm,
     :grid => false,
-    :xlabel => "x",
-    :ylabel => "y",
+#    :xlabel => "x",
+#    :ylabel => "y",
     :adjust_latex_font => true,
 )
 

ext/Plotting.jl

@@ -6,4 +6,5 @@ module Plotting
     include("./BlockAverages.jl")
     include("./REMD.jl")
     include("./SecondaryStructure.jl")
+    include("./Contacts.jl")
 end

src/MolSimToolkit.jl

@@ -57,6 +57,7 @@ include("./miscelaneous_functions/distances.jl")
 include("./miscelaneous_functions/dihedrals.jl")
 include("./miscelaneous_functions/center_of_mass.jl")
 include("./miscelaneous_functions/most_representative_structure.jl")
+include("./miscelaneous_functions/contacts.jl")
 include("./secondary_structure/secondary_structure.jl")
 
 # Time-dependent properties