Coupling¶

addCouplingConstraint(model, rxnList, c, d, ineqSense)[source]

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

• ck x 1 vector $$c*v \geq d$$
• dn x 1 vector $$c*v \geq d$$
• ineqSensek 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 $$[S; C] * v {=, \leq, \geq } [dxdt, d]$$

Example

rxnList = {'PCHOLP_hs_f', 'PLA2_2_f', 'SMS_f','PCHOLP_hs_b', 'PLA2_2_b', 'SMS_b'};
c = [1, 1, 1, 1, 1, 1];
d = 10;
ineqSense = 'G';
modelConstrained = constrainRxnListAboveBound(modelIrrev, rxnList, C, d, ineqSense);

addRatioReaction(model, listOfRxns, ratioCoeff)[source]

Usage

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)[source]

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

• ck x 1 vector $$c*v \geq d$$
• dn x 1 vector $$c*v \geq d$$
• ineqSensek 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 $$[S; C] * v {=, \leq, \geq } [dxdt, d]$$

Example

rxnList = {'PCHOLP_hs_f', 'PLA2_2_f', 'SMS_f','PCHOLP_hs_b', 'PLA2_2_b', 'SMS_b'};
c = [1, 1, 1, 1, 1, 1];
d = 10;
ineqSense = 'G';
modelConstrained = constrainRxnListAboveBound(modelIrrev, rxnList, C, d, ineqSense);

coupleRxnList2Rxn(model, rxnList, rxnC, c, u)[source]

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