ThermOptCC

ThermOptCC(model, tol, TICs, Dir)

Identifies thermodynamically feasible flux directions for all the reactions in the input model

USAGE:

[a,TICs,Dir] = ThermOptiCC (model,tol)

INPUTS:

• model – COBRA model structure for which thermodynamic feasibility of the reactions has to be identified

• tol – Tolerance value (User defined non-zero value).

OPTIONAL INPUTS:

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

• Dir – The flux directions for reactions in the corresponding TICs

OUTPUTS:

• a – A cell describing the thermodynamically feasible direction of the reactions in the given input model

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

• Dir – The flux directions for reactions in the corresponding TICs

findConsistentIDS(model, core, TICmat, rev2irrev, tol, runtime)

Identifies the thermodynamically consistent IDs for the given input irreversible reaction model

USAGE:

reacInd = findConsistentIDS (model,core,TICmat,rev2irrev,tol)

INPUTS:

• model – COBRA model structure with irreversible reactions only

• core – Reaction IDs for which thermodynamic consistency has to be verified

• TICmat – Matlab matrix with information on TICs in the model

• rev2irrev – Mapping between the reversible reactions to its corresponding irreversible reactions

• tol – Minimum positive number defined as non-zero

• runtime – Maximum runtime for the MILP problem

OUTPUTS:

reacInd – Indices of reactions that are identified to be thermodynamically consistent