psamm.fluxcoupling
– Flux coupling analysis¶
Flux coupling analysis
Described in [Burgard04].
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class
psamm.fluxcoupling.
CouplingClass
¶ Enumeration of coupling types.
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Inconsistent
= 0¶ Reaction is flux inconsistent (v1 is always zero).
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Uncoupled
= 1¶ Uncoupled reactions.
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DirectionalForward
= 2¶ Directionally coupled from reaction 1 to 2.
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DirectionalReverse
= 3¶ Directionally coupled from reaction 2 to 1.
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Partial
= 4¶ Partially coupled reactions.
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Full
= 5¶ Fully coupled reactions.
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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.
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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.
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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