fluxConsistency

findFluxConsistentSubset(model, param, printLevel)

Finds the subset of S that is flux consistent using various algorithms, but fastcc from fastcore by default

USAGE:

[fluxConsistentMetBool, fluxConsistentRxnBool, fluxInConsistentMetBool, fluxInConsistentRxnBool, model] = findFluxConsistentSubset(model, param, printLevel)

INPUTS:

model: structure with field:

  • .S - m x n stoichiometric matrix

OPTIONAL INPUTS:
param: can contain:

  • param.LPsolver - the LP solver to be used

  • param.epsilon - minimum nonzero flux, default feasTol*10

    Note that fastcc is very sensitive to the value of parm.epsilon

  • param.modeFlag - {(0),1} 1 = return flux modes

  • param.method - {‘swiftcc’, (‘fastcc’), ‘dc’,’fastB’}

  • param.reduce - {(0),1} 1 = return fluxConsistModel

printLevel: verbose level

model.rev - the 0-1 vector with 1’s corresponding to the reversible reactions (if using swiftcc)

OUTPUTS:

fluxConsistentMetBool: m x 1 boolean vector indicating flux consistent mets fluxConsistentRxnBool: n x 1 boolean vector indicating flux consistent rxns fluxInConsistentMetBool: m x 1 boolean vector indicating flux inconsistent mets fluxInConsistentRxnBool: n x 1 boolean vector indicating flux inconsistent rxns model: structure with fields duplicating the single output arguments:

  • .fluxConsistentMetBool

  • .fluxConsistentRxnBool

  • .fluxInConsistentMetBool

  • .fluxInConsistentRxnBool