add the script for the paper

scripts/papersuru.jl

@@ -0,0 +1,39 @@
+using ISOKANN
+using ISOKANN.IsoMu
+using Random
+
+using Plots, JLD2
+
+datapath = "/data/numerik/ag_cmd/trajectory_transfers_for_isokann/data/Feb16_data_for_paper_disulfide_sims"
+
+function papersuru(n=30_000)
+  Random.seed!(42)
+
+  links = [DataLink("$datapath/_$i") for i in 1:10]
+
+  mu = isokann(links, learnrate=1e-4, regularization=1e-2)
+
+  train!(mu, n)
+  IsoMu.cpu!(mu)
+
+  ids = save_reactive_path(mu, sigma=0.7, out="out/paper/react.pdb")
+
+  scatter(
+    1:size(mu.iso.data[1], 2),
+    mu.iso.model(mu.iso.data[1]) |> vec,
+    xlabel="frame",
+    ylabel="\\chi",
+    legend=false,
+    markersize=1,
+    xticks=0:1000:10000,
+    markerstrokewidth=0,
+  ) |> display
+  savefig("out/paper/paperplot.pdf")
+
+  chi = mu.iso.model(mu.iso.data[1])
+
+  plot!(ids, chi[ids], linealpha=1, linecolor="Salmon") |> display
+  savefig("out/paper/paperplot2.pdf")
+
+  jldsave("out/paper/results.jld2", mu=mu)
+end

src/IsoMu/datalink.jl

@@ -71,7 +71,7 @@ function isodata(ds::Vector{DataLink})
   mc = mean_and_std(dists, 2)
   ndists = (dists .- mc[1]) ./ mc[2]
 
-  data = mapreduce((x,y)->hcat.(x,y), 1:length(inds1)) do i
+  data = mapreduce(ISOKANN.joindata, 1:length(inds1)) do i
     rng = inds1[i]:inds2[i]
     ISOKANN.data_from_trajectory(@view(ndists[:, rng]); reverse)
   end