lrs¶
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equivalentSets
(model)[source]¶ 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
- model –
COBRA Toolbox model with fields:
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extremePathways
(model, positivity, inequality)[source]¶ Calculates the extreme pathways of a stoichiometric model using the vertex/facet enumeration package
Usage
[R, V] = extremePathways(model, positivity, inequality)Input
- 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 inputs
- 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
- model –
COBRA Toolbox model with fields:
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extremePools
(model, positivity, inequality)[source]¶ 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 inputs
- 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
- model –
structure with: