flux - Reactive flux an transition pathways (msmtools.flux)

This module contains functions to compute reactive flux networks and find dominant reaction pathways in such networks.


tpt(T, A, B[, mu, qminus, qplus, rate_matrix]) Computes the A->B reactive flux using transition path theory (TPT)
ReactiveFlux(A, B, flux[, mu, qminus, …]) A->B reactive flux from transition path theory (TPT)

Reactive flux

flux_matrix(T, pi, qminus, qplus[, netflux]) Compute the TPT flux network for the reaction A–>B.
to_netflux(flux) Compute the netflux from the gross flux.
flux_production(F) Returns the net flux production for all states
flux_producers(F[, rtol, atol]) Return indexes of states that are net flux producers.
flux_consumers(F[, rtol, atol]) Return indexes of states that are net flux producers.
coarsegrain(F, sets) Coarse-grains the flux to the given sets.

Reaction rates and fluxes

total_flux(F[, A]) Compute the total flux, or turnover flux, that is produced by the flux sources and consumed by the flux sinks.
rate(totflux, pi, qminus) Transition rate for reaction A to B.
mfpt(totflux, pi, qminus) Mean first passage time for reaction A to B.

Pathway decomposition

pathways(F, A, B[, fraction, maxiter]) Decompose flux network into dominant reaction paths.