Clustering Code

[kyleabeauchamp]

This should do it:

import msmbuilder.cluster
import mdtraj as md

t = md.load("run1-clone1.h5")

X = [t]  # Need list of trajectories as input data

clusterer = msmbuilder.cluster.KMedoids(n_clusters=5, metric="rmsd")
clusterer.fit(X)

labels = clusterer.predict(X)
clusterer.cluster_centers_.save("./cluster_centers.pdb")