Created Ribbon module

src/ProtPlot.jl

@@ -1,13 +1,10 @@
 module ProtPlot
 
-using Backboner
+import Backboner
 export Backboner
 
-using GLMakie
-using Colors, ColorSchemes
-using LinearAlgebra
-
-include("utils/utils.jl")
 include("ribbon/ribbon.jl")
 
+export Ribbon
+
 end

src/ribbon/ribbon.jl

@@ -1,3 +1,14 @@
+module Ribbon
+
+using Backboner
+using GLMakie
+using Colors
+using ColorSchemes
+using LinearAlgebra
+
+include("utils/utils.jl")
 include("segment.jl")
 include("shapes.jl")
-include("render.jl")
+include("render.jl")
+
+end

src/ribbon/segment.jl

@@ -85,6 +85,8 @@ function segments(chain::Chain)
 end
 
 
+# utilities
+
 function segment_startpoint(segment::Segment, A=1) # nitrogen
     return segment.backbone.coords[:,A,1] # first residue
 end
@@ -96,4 +98,13 @@ function segment_endpoint(segment::Segment, A=1) # nitrogen
     else
         return segment.chain.backbone[:,A,segment_stop+1] # next residue
     end
+end
+
+function remove_singleton_strands!(chain::Chain)
+    ssvector = chain.ssvector
+    for i in 2:length(ssvector)-1
+        if ssvector[i-1] != Strand && ssvector[i] == Strand && ssvector[i+1] != Strand
+            ssvector[i] = Loop
+        end
+    end
 end

src/ribbon/shapes.jl

@@ -22,26 +22,26 @@ function tube_surface(
     surface_vertices = zeros(T, 3, N, length(tube_angles))
 
     # Precompute tangents and initialize normals
-    tangents = [path_tangent(path[:, max(1, i-1)], path[:, i], path[:, min(N, i+1)]) for i in 1:N]
+    tangents = stack(path_tangent(path[:, max(1, i-1)], path[:, i], path[:, min(N, i+1)]) for i in 1:N)
     normals = zeros(T, 3, N)
 
     # Initial normal vector (arbitrary, but not aligned with the first tangent)
-    normals[:, 1] = abs(tangents[1][1]) < 0.9 ? [1, 0, 0] : [0, 1, 0]
+    normals[:, 1] = abs(tangents[1, 1]) < 0.9 ? [1, 0, 0] : [0, 1, 0]
 
     # Propagate the normal vector along the path
     for idx in 2:N
         prev_normal = normals[:, idx-1]
-        t = tangents[idx]
+        t = tangents[:, idx]
         projected_normal = prev_normal - dot(t, prev_normal) * t
         if norm(projected_normal) < 1e-5
-            projected_normal = cross(tangents[idx - 1], t)
+            projected_normal = cross(tangents[:, idx - 1], t)
         end
         normals[:, idx] = normalize!(projected_normal)
     end
 
     # Generate surface vertices
     for idx in 1:N
-        t = tangents[idx]
+        t = tangents[:, idx]
         n = normals[:, idx]
         b = cross(n, t)
 
@@ -108,6 +108,8 @@ end
 # the shape is normalized such that length of the entire arrow is 1
 arrow_function(l=0.5, w=0.5, W=1.0) = t -> t > l ? W*(t-1)/(l-1) : w
 
+# TODO: just use oxygen atoms for calculating paths
+
 function arrow_surface(
     points1::AbstractMatrix{T},
     points2::AbstractMatrix{T};
@@ -135,7 +137,7 @@ function arrow_surface(
     arrow_head_length = 3.0
     arrow_body_length = length_of_path - arrow_head_length
     l = findfirst(>(arrow_body_length), cumulative_length_of_path) / N
-    arrow = arrow_function(l, width, width*1.8)
+    arrow = arrow_function(l, width, width*2.0)
 
     surface_vertices = zeros(T, 3, N, 5)
     for idx in 1:N

src/utils/utils.jl → src/ribbon/utils/colors.jl

@@ -1,14 +1,3 @@
-include("splines.jl")
-
-function remove_singleton_strands!(chain::Chain)
-    ssvector = chain.ssvector
-    for i in 2:length(ssvector)-1
-        if ssvector[i-1] != Strand && ssvector[i] == Strand && ssvector[i+1] != Strand
-            ssvector[i] = Loop
-        end
-    end
-end
-
 # expand vector to have length N while keeping the same discrete color gradient 
 function expand_colors(colors::Vector, N::Integer)
     L = length(colors)

src/ribbon/utils/utils.jl

@@ -0,0 +1,2 @@
+include("splines.jl")
+include("colors.jl")