msmbuilder.clustering.Hierarchical¶

class msmbuilder.clustering.Hierarchical(metric, trajectories, method='single', precomputed_values=None)[source]¶

__init__(metric, trajectories, method='single', precomputed_values=None)[source]¶

Initialize a hierarchical clusterer using the supplied distance metric and method.

Method should be one of the fastcluster linkage methods, namely ‘single’, ‘complete’, ‘average’, ‘weighted’, ‘centroid’, ‘median’, or ‘ward’.

Parameters:	metric : msmbuilder.metrics.AbstractDistanceMetric A metric capable of handling ptraj trajectory : Trajectory list of Trajectorys data to cluster method : {‘single’, ‘complete’, ‘average’, ‘weighted’, ‘centroid’, ‘median’, ‘ward’} precomputed_values : : used internally to implement load_from_disk()

Notes

This is implemenred with the fastcluster library, which can be downloaded from CRAN http://cran.r-project.org/web/packages/fastcluster/

Methods

__init__(metric, trajectories[, method, ...])	Initialize a hierarchical clusterer using the supplied distance metric and method.
get_assignments([k, cutoff_distance])	Assign the frames into clusters.
load_from_disk(cls, filename)	Load up a clusterer from disk
save_to_disk(filename)	Save this clusterer to disk.

Attributes

allowable_methods