clean up scripts folder

axsk · Aug 22, 2024 · 75118db · 75118db
1 parent 7cf78d6
commit 75118db
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Showing 12 changed files with 10 additions and 32 deletions.
diff --git a/scripts/0 - trajectories.ipynb → scripts/archive/0 - trajectories.ipynb b/scripts/0 - trajectories.ipynb → scripts/archive/0 - trajectories.ipynb
diff --git a/scripts/adaptivesampling.jl → scripts/archive/adaptivesampling.jl b/scripts/adaptivesampling.jl → scripts/archive/adaptivesampling.jl
diff --git a/scripts/cmp_openmm_molly.jl → scripts/archive/cmp_openmm_molly.jl b/scripts/cmp_openmm_molly.jl → scripts/archive/cmp_openmm_molly.jl
diff --git a/scripts/dataconvergence.jl → scripts/archive/dataconvergence.jl b/scripts/dataconvergence.jl → scripts/archive/dataconvergence.jl
diff --git a/scripts/dataconvergence.png → scripts/archive/dataconvergence.png b/scripts/dataconvergence.png → scripts/archive/dataconvergence.png
diff --git a/scripts/eigenvalues.ipynb → scripts/archive/eigenvalues.ipynb b/scripts/eigenvalues.ipynb → scripts/archive/eigenvalues.ipynb
diff --git a/scripts/macro.jl → scripts/archive/macro.jl b/scripts/macro.jl → scripts/archive/macro.jl
diff --git a/scripts/runs.jl → scripts/archive/runs.jl b/scripts/runs.jl → scripts/archive/runs.jl
diff --git a/scripts/openmmtrajectory.jl b/scripts/openmmtrajectory.jl
@@ -13,14 +13,15 @@ sim = OpenMMSimulation(; pdb, minimize=true, gpu=true)
 x0 = getcoords(sim)
 cainds = atom_indices(pdb, "name==CA")
 featinds = restricted_localpdistinds(x0, radius, cainds)
+featurizer(x) = pdists(x, featinds)
 
 traj = laggedtrajectory(sim, samples)
-data = SimulationData(sim, traj, nk, featurizer=coords -> pdists(coords, featinds))
+data = SimulationData(sim, traj, nk; featurizer)
 
 iso = Iso2(data, opt=NesterovRegularized(), gpu=true)
 
 run!(iso, trainsteps)
 
 iso.data = addcoords(iso.data, laggedtrajectory(sim, samples, x0=iso.data.coords[1][:, end]))
 
-run!(iso, trainsteps)
+run!(iso, trainsteps)
diff --git a/scripts/thesis.jl b/scripts/thesis.jl
diff --git a/scripts/trpcage.jl b/scripts/trpcage.jl
@@ -0,0 +1,7 @@
+sim = OpenMMSimulation(pdb="data/2jof-processed.pdb", forcefields=ISOKANN.OpenMM.FORCE_AMBER_IMPLICIT, features=ISOKANN.OpenMM.noHatoms("data/2jof-processed.pdb"), steps=100, temp=360)
+
+data = SimulationData(sim, nx=100, nk=8)
+
+iso = Iso2(data, model=pairnet(data, activation=Flux.swish, layers=4), gpu=true, opt=AdamRegularized(1e-4, 1e-5), minibatch=100, loggers=[ISOKANN.autoplot(10)])
+
+runadaptive!(iso, generations=1000, nx=3, cutoff=2000, iter=500, keepedges=true)
diff --git a/scripts/vgvadapt.jl → scripts/vgvapg.jl b/scripts/vgvadapt.jl → scripts/vgvapg.jl