ThermOptEnumerator

ThermOptEnumLP(model)

Enumerates all the Thermodynamically infeasible cycles in a given model

USAGE:

[TICs,Direction,TIC_Rxns,modModel] = ThermoOptEnumLP (model)

INPUTS:

model – COBRA model structure for which TICs has be found

OUTPUTS:

  • TICs – List of all the Thermodynamically infeasible cycles in the given input model

  • Direction – Relative flux coefficients for reactions in the corresponding TICs

  • TIC_Rxns – Reaction list that participates in the TICs

  • modModel – Modified model that has no irreversible reactions that carry flux in reverse direction

ThermOptEnumMILP(model, timeLimit)

Enumerates all the Thermodynamically infeasible cycles in a given model

USAGE:

[TICs,Direction,TIC_Rxns,modModel,opt] = ThermoOptEnumMILP (model,timeLimit)

INPUTS:

model – COBRA model structure for which TICs has be found

OPTIONAL INPUTS:

timeLimit – If the algorithm takes more than this time null set will be returned for all the outputs

OUTPUTS:

  • TICs – List of all the Thermodynamically infeasible cycles in the given input model

  • Direction – Relative flux coefficients for reactions in the corresponding TICs

  • TIC_Rxns – Reaction list that participates in the TICs

  • modModel – Modified model that has no irreversible reactions that carry flux in reverse direction. The obtained TICs are for this modModel.

  • opt – Says whether the provided solution is optimal or not

getOrderOfRxns(model)

To get the order of reactions based on the connected components obtained

USAGE:

[order,bins,binsizes] = getOrderOfRxns (model)

INPUTS:

model – COBRA model structure for which the order of reaction has to be obtained

OUTPUTS:

  • order – Reaction IDs

  • bins – Bins defining the IDs of connected components in which the reactions belong

  • binsizes – Size of the connected components obtained

getTICModel(model, core, tol, dir, TICcons)

Obtains the thermodynamically infeasible cycle that has the core reaction in it

USAGE:

[m1,blkdCore,flux,stat] = getTICModel (model,core,tol,dir,TICcons)

INPUTS:

  • model – COBRA model structure

  • core – Reaction ID for which the TIC has to be identified

  • tol – Minimum positive number defined as non-zero

  • dir – 1/-1 to define the flux direction of the core reaction. 1: positive flux -1: negative flux

  • TICcons – Details on the previously identified TICs that involves the core reaction

OUTPUTS:

  • allM1 – A cell of TICs obtained

  • blkdCore – 1/0 to define consistency of the core reaction

  • allFlux – Flux though the reactions in the TICs in allM1

  • stat – Status of the MILP optimization