psamm.fluxcoupling – Flux coupling analysis

Flux coupling analysis

Described in [Burgard04].

class psamm.fluxcoupling.CouplingClass

Enumeration of coupling types.

Inconsistent = 0

Reaction is flux inconsistent (v1 is always zero).

Uncoupled = 1

Uncoupled reactions.

DirectionalForward = 2

Directionally coupled from reaction 1 to 2.

DirectionalReverse = 3

Directionally coupled from reaction 2 to 1.

Partial = 4

Partially coupled reactions.

Full = 5

Fully coupled reactions.

class psamm.fluxcoupling.FluxCouplingProblem(model, bounded, solver)

A specific flux coupling analysis applied to a metabolic model.

Parameters:

• model – MetabolicModel to apply the flux coupling problem to
• bounded – Dictionary of reactions with minimum flux values
• solver – LP solver instance to use.

solve(reaction_1, reaction_2)

Return the flux coupling between two reactions

The flux coupling is returned as a tuple indicating the minimum and maximum value of the v1/v2 reaction flux ratio. A value of None as either the minimum or maximum indicates that the interval is unbounded in that direction.

psamm.fluxcoupling.classify_coupling(coupling)

Return a constant indicating the type of coupling.

Depending on the type of coupling, one of the constants from CouplingClass is returned.

Parameters:coupling – Tuple of minimum and maximum flux ratio