fix save_trajectory

scripts/multitraj.jl

@@ -20,19 +20,21 @@ molecule = load_trajectory(pdbfile)
 pdist_inds = restricted_localpdistinds(molecule, MAXRADIUS, atom_indices(pdbfile, "not water and name==CA"))
 
 
+
 datas = map(trajfiles) do trajfile
     traj = load_trajectory(trajfile, top=pdbfile, stride=STRIDE)  # for large datasets you may use the memory-mapped LazyTrajectory
-    feats = pdists(traj, pdist_inds)
-    data = data_from_trajectory(feats, reverse=true)
+    xs, ys = data_from_trajectory(traj, reverse=true)
 end
 
-data = reduce(mergedata, datas)
+xs, ys = reduce(mergedata, datas)
+
+data = pdists(xs, pdist_inds), pdists(ys, pdist_inds)
 
-iso = Iso(data)
+iso = Iso(data, opt=NesterovRegularized())
 run!(iso, 1000)
 
 # saving the reactive path for multiple trajectories could work like this
 # note that the above data is probably too big for this to terminate in sufficient time
 
 # coords = ISOKANN.LazyMultiTrajectory(ISOKANN.LazyTrajectory.(trajfiles))
-# save_reactive_path(iso, coords, sigma=.1, source=pdbfile)
+save_reactive_path(iso, xs, sigma=0.1, source=pdbfile)

src/ISOKANN.jl

@@ -72,6 +72,7 @@ export exit_rates
 export load_trajectory, save_trajectory
 export atom_indices
 export localpdistinds, pdists, restricted_localpdistinds
+export data_from_trajectory, mergedata
 
 
 export reactionpath_minimum, reactionpath_ode

src/molutils.jl

@@ -143,9 +143,9 @@ save the trajectory given in `coords` to `filename` with the topology provided b
 """
 function save_trajectory(filename, coords::AbstractMatrix; top::String)
     mdtraj = pyimport_conda("mdtraj", "mdtraj", "conda-forge")
-    traj = mdtraj.load(filename, stride=-1)
+    traj = mdtraj.load(top, stride=-1)
     xyz = reshape(coords, 3, :, size(coords, 2))
-    traj.xyz = PyReverseDims(xyz)
+    traj = mdtraj.Trajectory(PyReverseDims(xyz), traj.topology)
     traj.save(filename)
 end