msmbuilder.MSMLib.get_counts_from_traj

msmbuilder.MSMLib.get_counts_from_traj(states, n_states=None, lag_time=1, sliding_window=True)

Computes the transition count matrix for a sequence of states (single trajectory).

Parameters:

states : array

A one-dimensional array of integers representing the sequence of states. These integers must be in the range [0, n_states]

n_states : int

The total number of states. If not specified, the largest integer in the states array plus one will be used.

lag_time : int, optional

The time delay over which transitions are counted

sliding_window : bool, optional

Use sliding window

Returns:

C : sparse matrix of integers

The computed transition count matrix