Coupling¶
- addCouplingConstraint(model, rxnList, c, d, ineqSense)¶
Constrains one (weighted) sum of fluxes to be above a lower bound. Appends to existing inequality constraints if they are present
USAGE:
modelConstrained = constrainRxnListAboveBound(model, rxnList, c, d, ineqSense)
- INPUTS:
model: model structure rxnList: cell array of reaction names
- OPTIONAL INPUTS:
c: k x 1 vector \(c*v \geq d\) d: n x 1 vector \(c*v \geq d\) ineqSense: k x 1 inequality sense {‘L’,’G’}
- OUTPUT:
modelConstrained: constrained model:
S - Stoichiometric matrix
b - Right hand side = dx/dt
C - Inequality constraint matrix
d - Inequality constraint right hand side \([S; C] * v {=, \leq, \geq } [dxdt, d]\)
- addRatioReaction(model, listOfRxns, ratioCoeff)¶
Adds ratio reaction.
USAGE:
modelNew = addRatioReaction(model, listOfRxns, ratioCoeff)
- INPUTS:
model: COBRA model structure listOfRxns: List of 2 Reactions ratioCoeff: Array of ratio coefficient between the 2 reactions
- OUTPUT:
modelNew: COBRA model structure containing the ratio
Example
%1 v_EX_ac(e) = 2 v_EX_for(e): modelNew = addRatioReaction(model, {‘EX_ac(e)’ ‘EX_for(e)’}, [1 2])
- constrainRxnListAboveBound(model, rxnList, c, d, ineqSense)¶
Constrains one (weighted) sum of fluxes to be above a lower bound. Appends to existing inequality constraints if they are present
USAGE:
modelConstrained = constrainRxnListAboveBound(model, rxnList, c, d, ineqSense)
- INPUTS:
model: model structure rxnList: cell array of reaction names
- OPTIONAL INPUTS:
c: k x 1 vector \(c*v \geq d\) d: n x 1 vector \(c*v \geq d\) ineqSense: k x 1 inequality sense {‘L’,’G’}
- OUTPUT:
modelConstrained: constrained model:
S - Stoichiometric matrix
b - Right hand side = dx/dt
C - Inequality constraint matrix
d - Inequality constraint right hand side \([S; C] * v {=, \leq, \geq } [dxdt, d]\)
- coupleRxnList2Rxn(model, rxnList, rxnC, c, u)¶
This function adds coupling constraints to the fluxes vi of a given list of reactions (RxnList).The constraints are proportional to the flux v of a specified reaction rxnC, so that for all reactions in RxnList vi ~ vrxnC. For all reactions, a threshold u on flux is set (default value: 0.01).
To add a coupling constraint to a reaction, a coupling vector c is determined (default value 1000). c is multiplied by vrxnC, so that for all irreversible reactions in RxnList vi - c * vrxnC <= u.
For all reversible reactions, the following equation holds true for the reverse direction: vi + c * vrxnC >= u.
The output is a coupled model (modelCoupled), in which for every new entry in modelCoupled.b a “slack” variable has been added to modelCoupled.mets.
USAGE:
[modelCoupled] = coupleRxnList2Rxn(model, rxnList, rxnC, c, u)
- INPUTS:
model: model structure rxnList: array of reaction names rxnC: reaction that should be coupled with each reaction in the
reaction list
c: vector of coupling factors for each rxn in rxnList (default c = 1000) u: vector of lower bounds one reaction couples (default u = 0.01)
- OUTPUT:
modelCoupled: coupled model