Transition Path Theory : msmbuilder.tpt¶
Functions for performing Transition Path Theory calculations.
Path Finding¶
| find_top_paths(sources, sinks, tprob[, ...]) | Calls the Dijkstra algorithm to find the top ‘NumPaths’. |
| Dijkstra(sources, sinks, net_flux) | A modified Dijkstra algorithm that dynamically computes the cost |
| find_path_bottleneck(path, net_flux) | Simply finds the bottleneck along a path. |
| calculate_fluxes(sources, sinks, tprob[, ...]) | Compute the transition path theory flux matrix. |
| calculate_net_fluxes(sources, sinks, tprob) | Computes the transition path theory net flux matrix. |
MFPT & Committor Finding Functions¶
| calculate_ensemble_mfpt(sources, sinks, ...) | Calculates the average ‘Folding Time’ of an MSM defined by T and a LagTime. |
| calculate_avg_TP_time(sources, sinks, tprob, ...) | Calculates the Average Transition Path Time for MSM with: T, LagTime. |
| calculate_mfpt(sinks, tprob[, lag_time]) | Gets the Mean First Passage Time (MFPT) for all states to a set |
| calculate_all_to_all_mfpt(tprob[, populations]) | Calculate the all-states by all-state matrix of mean first passage times. |
| calculate_committors(sources, sinks, tprob) | Get the forward committors of the reaction sources -> sinks. |