msmbuilder.tpt.top_path¶
-
msmbuilder.tpt.
top_path
(sources, sinks, net_flux)¶ Use the Dijkstra algorithm for finding the shortest path connecting a set of source states from a set of sink states.
Parameters: - sources : array_like, int
One-dimensional list of nodes to define the source states.
- sinks : array_like, int
One-dimensional list of nodes to define the sink states.
- net_flux : np.ndarray, shape = [n_states, n_states]
Net flux of the MSM
Returns: - top_path : np.ndarray
Array corresponding to the top path between sources and sinks. It is an array of states visited along the path.
- flux : float
Flux traveling through this path – this is equal to the minimum flux over edges in the path.
See also
msmbuilder.tpt.paths
- function for calculating many high flux paths through a network.
References
[1] Weinan, E. and Vanden-Eijnden, E. Towards a theory of transition paths. J. Stat. Phys. 123, 503-523 (2006). [2] Metzner, P., Schutte, C. & Vanden-Eijnden, E. Transition path theory for Markov jump processes. Multiscale Model. Simul. 7, 1192-1219 (2009). [3] Berezhkovskii, A., Hummer, G. & Szabo, A. Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J. Chem. Phys. 130, 205102 (2009). [4] Dijkstra, E. W. A Note on Two Problems in Connexion with Graphs. Numeriche Mathematik 1, 269-271 (1959). [5] Noe, Frank, et al. “Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.” PNAS 106.45 (2009): 19011-19016.