""" Trace Plot ========== """ 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)')
{{header}} Meta ---- depends: - meta.pandas.pickl - trajs - top.pdb """ import mdtraj as md from msmbuilder.io import load_meta, itertrajs, save_trajs, preload_top ## Load meta = load_meta() centroids = md.load("centroids.xtc", top=preload_top(meta)) ## Kernel SIGMA = 0.3 # nm from msmbuilder.featurizer import RMSDFeaturizer import numpy as np featurizer = RMSDFeaturizer(centroids) lfeats = {} for i, traj in itertrajs(meta): lfeat = featurizer.partial_transform(traj) lfeat = np.exp(-lfeat**2 / (2 * (SIGMA**2))) lfeats[i] = lfeat save_trajs(lfeats, 'ftrajs', meta)
{{header}} Meta ---- depends: - meta.pandas.pickl - trajs - top.pdb """ import mdtraj as md from msmbuilder.io import load_meta, itertrajs, save_trajs, preload_top ## Load meta = load_meta() centroids = md.load("centroids.xtc", top=preload_top(meta)) ## Kernel SIGMA = 0.3 # nm from msmbuilder.featurizer import RMSDFeaturizer import numpy as np featurizer = RMSDFeaturizer(centroids) lfeats = {} for i, traj in itertrajs(meta): lfeat = featurizer.partial_transform(traj) lfeat = np.exp(-lfeat ** 2 / (2 * (SIGMA ** 2))) lfeats[i] = lfeat save_trajs(lfeats, 'ftrajs', meta)