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