msmbuilder.tpt.calculate_avg_TP_time

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

Calculates the Average Transition Path Time for MSM with: T, LagTime. The TPTime is the average of the MFPTs (to F) of all the states immediately adjacent to U, with the U states effectively deleted.

Note here ‘TP Time’ is defined as the avg MFPT of all adjacent states to {U}, to {F}, ignoring {U}.

Consider this carefully.

Parameters:

sources : array, int

indices of the unfolded states

sinks : array, int

indices of the folded 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