Merge pull request #17 from MurrellGroup/tweaked-defaults

Minor adjustments to defaults, and adding some options.

src/animate.jl

@@ -12,29 +12,42 @@ using ColorSchemes
 """
 function animate_attention(
     chain::Backboner.Protein.Chain, attention::AbstractArray{<:Real, 3};
-    azimuth_start = 1, azimuth_end = 0, output_file::String = "attention.mp4",
-    ribbon_colorscheme = ColorSchemes.jet,
-    attention_colorscheme = ColorSchemes.hawaii,
-    end_padding = 3,
+    azimuth_start = 1, azimuth_end = -6, output_file::String = "attention.mp4",
+    ribbon_colorscheme = ColorSchemes.glasgow,
+    attention_colorscheme = ColorSchemes.hsv,
+    end_padding = 3, grow_limits = false, from_centroid = true, frames_per_residue::Int = 10, framerate::Int = 30
 )
-    points = Backboner.Protein.alphacarbon_coords(chain)
+
+    if from_centroid
+        points = Backboner.Frames(chain.backbone,Backboner.Protein.STANDARD_TRIANGLE_ANGSTROM).locations
+    else
+        points = Backboner.Protein.carbonyl_coords(chain)
+    end
+
     attention = PointAttention(points, attention)
 
     fig = Figure();
     ax = Axis3(fig[1, 1], protrusions=(20, 20, 10, 10), perspectiveness=0.2, aspect=:data);
     hidespines!(ax)
-    #hidedecorations!(ax)
+    hidedecorations!(ax)
+
+    if !grow_limits
+        plot_limits = extrema(points, dims=2)
+        xlims!(ax, plot_limits[1]) 
+        ylims!(ax, plot_limits[2]) 
+        zlims!(ax, plot_limits[3]) 
+    end
 
     ax.azimuth[] = azimuth_start
 
     # Aggregate all the plots from each frame, such that they can be deleted.
     # Ribbon plots are actually made up of multiple plots, so each subplot gets added to the list.
-    # A possible optimization is only deleting the last segment of the ribbon plot.
+    # A possible optimization is only deleting changed segments of the ribbon plot (e.g. last segment, and coils with emerging beta sheets)
     plots = Vector{AbstractPlot}()
 
     n = length(chain)
-    k = 5 # 5 frames per residue
-    framerate = 30
+    k = frames_per_residue # 5 frames per residue
+
     frame_indices = 2:1/k:n+end_padding*framerate/k
     azimuth(t) = (t / (last(frame_indices) - first(frame_indices))) * (azimuth_end - azimuth_start) + azimuth_start
     record(fig, output_file, frame_indices, framerate=framerate) do i

src/attention/attention.jl

@@ -28,11 +28,11 @@ end
 
 function draw_lines_from_point!(container,
     point::P, other_points::AbstractVector{P}, linewidths::AbstractVector{<:Real};
-    color = RGB(1, 1, 1), linewidth_factor = 10.0, plots = nothing, kwargs...
+    color = RGB(1, 1, 1), linewidth_factor = 3.0, plots = nothing, kwargs...
 ) where P
     length(other_points) == length(linewidths) || throw(ArgumentError("The number of linewidths must match the number of other points.")) 
     xs, ys, zs = [reduce(vcat, ([point[i], other_point[i]] for other_point in other_points)) for i in 1:3]
-    p = linesegments!(container, xs, ys, zs; linewidth=linewidths .* linewidth_factor, color, transparency=true)
+    p = linesegments!(container, xs, ys, zs; linewidth=linewidths .* linewidth_factor, color, transparency=true, kwargs...)
     !isnothing(plots) && push!(plots, p)
 end
 
@@ -41,12 +41,12 @@ Take H points, and an LxH attention intensity matrix.
 For each column slice of the attention matrix, draw lines to the corresponding points with the intensities in the vector that exceed a certain threshold. 
 The thickness of the lines should be proportional to the value in the attention matrix.
 """
-function draw_attention_slice!(container,
+function draw_attention!(container,
     point::P, other_points::AbstractVector{P}, intensity_matrix::AbstractMatrix{<:Real};
     threshold::Real=1.0, colors=fill(RGB(1, 1, 1), size(intensity_matrix, 1)), kwargs...
 ) where P
     h, l = size(intensity_matrix)
-    println(h, " ", l, " ", length(other_points))
+    #println(h, " ", l, " ", length(other_points))
     l == length(other_points) || throw(ArgumentError("The number of points must match the number of rows in the attention matrix."))
     for i in 1:h
         intensity_vector = @view intensity_matrix[i, :]
@@ -57,7 +57,7 @@ function draw_attention_slice!(container,
 end
 
 function draw_attention_slice!(container, i::Int, attention::PointAttention; kwargs...)
-    draw_attention_slice!(container, eachcol(attention.points)[i], eachcol(attention.points)[1:i], @view(attention.intensities[:, i, 1:i]); kwargs...)
+    draw_attention!(container, eachcol(attention.points)[i], eachcol(attention.points)[1:i], @view(attention.intensities[:, i, 1:i]); kwargs...)
     return nothing
 end