lrs

equivalentSets(model)

Finds the stoichiometrically balanced loops and the equivalent sets

USAGE:

[loops, eqSets, P, P2, cyclicBool] = equivalentSets(model)

INPUT:

model: COBRA Toolbox model with fields:

  • .S - matrix

  • .lb - lower bounds

  • .ub - upper bounds

  • .biomassAbbr - biomass abbreviation

OUTPUTS:

loops: stoichiometrically balanced loops eqSets: equivalent sets P: as P2 but additinally dependent on cyclicBool P2: output of lrsOutputReadRay cyclicBool: boolean variable

extremePathways(model, positivity, inequality)

Calculates the extreme pathways of a stoichiometric model using the vertex/facet enumeration package

USAGE:

[R, V] = extremePathways(model, positivity, inequality)

INPUTS:

model: COBRA Toolbox model with fields:

  • .description - string used to name files

  • .lb - lower bounds and

  • .ub - upper bounds to derive directionality

  • .b - dxdt

OPTIONAL INPUT:

positivity: {0, (1)} if positivity == 1, then positive orthant base inequality: {(0), 1} if inequality == 1, then use two inequalities rather than a single equality

OUTPUTS:

R: nDim by nRay matrix of extreme rays V: nDim by nVertex matrix of vertices

extremePools(model, positivity, inequality)

Calculates the extreme pools of a stoichiometric model using the vertex / facet enumeration package

INPUT:

model: structure with:

  • .S - m x n Stoichiometric matrix with integer coefficients. If no other inputs are specified it is assumed that all reactions are reversible and S.v = 0

  • .SIntRxnBool - n x 1 boolean vector with 1 for internal reactions

  • .description - description

OPTIONAL INPUT:

positivity: {0, (1)} if positivity == 1, then positive orthant base inequality: {(0), 1} if inequality == 1, then use two inequalities rather than a single equaltiy