metric : msmbuilder.metrics.AbstractDistanceMetric
A distance metric used to define “closest”
project : msmbuilder.Project
Used to load the trajectories
generators : msmbuilder.Trajectory
A trajectory containing the structures of all of the cluster centers
assignments_path : str
Path to a file that contains/will contain the assignments, as a 2D array
of integers in hdf5 format
distances_path : str
Path to a file that contains/will contain the assignments, as a 2D array
of integers in hdf5 format
chunk_size : int
The number of frames to load and process per step. The optimal number
here depends on your system memory – it should probably be roughly
the number of frames you can fit in memory at any one time. Note, this
is only important if your trajectories are long, as the effective chunk_size
is really min(traj_length, chunk_size)
atom_indices_to_load : {None, list}
The indices of the atoms to load for each trajectory chunk. Note that
this method is responsible for loading up atoms from the project, but
does NOT load up the generators. Those are passed in as a trajectory
object (above). So if the generators are already subsampled to a restricted
set of atom indices, but the trajectories on disk are NOT, you’ll
need to pass in a set of indices here to resolve the difference.
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