markovmodel / msmtools

Tools for estimating and analyzing Markov state models
GNU Lesser General Public License v3.0
40 stars 26 forks source link

estimation.effective_count_matrix is slow #34

Closed franknoe closed 8 years ago

franknoe commented 9 years ago

estimation.effective_count_matrix is slow for large data sets, especially with the setting truncate_acf=False. This can probably be sped up by a lot. Essentially a lot of damped autocorrelation functions are computed which itself could be sped up. In addition the looping through the acf's from different trajectories is probably unnecessarily slow.