Trace PlotΒΆ

../_images/plot_trace.png

Python source code: [download source: plot_trace.py]

from msmbuilder.example_datasets import FsPeptide
from msmbuilder.featurizer import RMSDFeaturizer

import msmexplorer as msme

# Load Fs Peptide Data
traj = FsPeptide().get().trajectories[0]

# Calculate RMSD
featurizer = RMSDFeaturizer(reference_traj=traj[0])
rmsd = featurizer.partial_transform(traj).flatten()

# Plot Trace
msme.plot_trace(rmsd, label='traj0', xlabel='Timestep', ylabel='RMSD (nm)')