msmbuilder.tpt.calculate_ensemble_mfpt

msmbuilder.tpt.calculate_ensemble_mfpt(sources, sinks, tprob, lag_time)

Calculates the average ‘Folding Time’ of an MSM defined by T and a LagTime. The Folding Time is the average of the MFPTs (to F) of all the states in U.

Note here ‘Folding Time’ is defined as the avg MFPT of {U}, to {F}. Consider this carefully. This is probably NOT the experimental folding time!

Parameters:

sources : array, int

indices of the source states

sinks : array, int

indices of the sink states

tprob : matrix

transition probability matrix

lag_time : float

the lag time used to create T (dictates units of the answer)

Returns:

avg : float

the average of the MFPTs

std : float

the standard deviation of the MFPTs