msmbuilder.tpt.calculate_all_to_all_mfpt¶

msmbuilder.tpt.calculate_all_to_all_mfpt(tprob, populations=None)[source]¶

Calculate the all-states by all-state matrix of mean first passage times.

This uses the fundamental matrix formalism, and should be much faster than GetMFPT for calculating many MFPTs.

Parameters:

tprob : matrix

transition probability matrix

populations : array_like, float

optional argument, the populations of each state. If not supplied, it will be computed from scratch

Returns:

MFPT : array, float

MFPT in time units of LagTime, square array for MFPT from i -> j