Optcardthermo

checkThermoFeasibility(model, solution, thermoConsistencyMethod, param)[source]

Check which internal reactions of a flux vector are thermodynamically feasible

USAGE:

[thermoConsistentFluxBool, solutionConsistency] = checkThermoFeasibility (model, solution, thermoConsistencyMethod, param)

INPUTS:

  • model – COBRA model structure with fields:

    • .S - m x n stoichiometric matrix

    • .c - n x 1 linear objective coefficients

    • .SConsistentRxnBool - n x 1 boolean of stoichiometrically consistent reactions

  • solution – flux solution structure with fields:

    • .stat - solver status (the function returns early unless .stat is 1)

    • .v - n x nlt flux vectors

    • .g - n x 1 reaction gradients (used by the ‘signProduct’ method)

    • .thermoConsistentFluxBool - optional precomputed consistency boolean (skips the check)

OPTIONAL INPUTS:

  • thermoConsistencyMethod – consistency test method: ‘cycleFreeFlux’ (default), ‘signProduct’, ‘cardOpt’ or ‘v2QNty’

  • param – structure of parameters with fields:

    • .eta - minimum flux value considered nonzero (default feasTol)

    • .epsilon - minimum flux value considered nonzero for the cardinality method (default feasTol)

    • .thermoConsistency - ‘biochemically’ (default) or ‘chemically’

    • .relaxBounds - boolean, relax bounds (default 0)

    • .debug - boolean, print or save debugging information (default 0)

    • .parallelize - boolean, parallelise cycleFreeFlux (set to 0)

    • .printLevel - verbosity level (default 0)

    • .theta - Capped-L1 approximation parameter (default 0.5)

    • .warmStartMethod - warm start method for optimizeCardinality (default ‘random’)

    • .condenseW - boolean, condense the W block (default 0)

    • .condenseT - boolean, condense the T block (default 0)

OUTPUTS:

  • thermoConsistentFluxBool – n x 1 boolean, true for thermodynamically consistent internal fluxes

  • solutionConsistency – solution structure returned by the thermodynamic consistency check, with fields including:

    • .vThermo: ‘n x 1’ repaired thermodynamically consistent flux

optCardThermo(model, param)[source]

Finds a thermodynamically feasible net flux biased toward presence/absence of metabolites and activity/inactivity of certain reactions by solving the following optimisation problem

min beta*g1.*(p + q) + g0.*|z|_0 + h0(-ve).*|s|_0 + h0(+ve).*|s|_0 + c*[z;w]

s.t. N*z + B*w = b
C*z + D*w <= d (optionally)

z - p + q = 0

A(p + q) - s = 0 Az - r = 0 lb <= [z;w] <= ub 0 <= p 0 <= q

where [N, B] := model.S;

A := F + R, F := -min(N,0) R : = max(N,0)

USAGE:

solution = optCardThermo (model, param)

INPUT:

model – COBRA model structure. Required fields:

  • .S - m x n stoichiometric matrix

  • .c - n x 1 linear objective coefficients

  • .lb - n x 1 lower bounds on reaction rate

  • .ub - n x 1 upper bounds on reaction rate

OPTIONAL INPUTS:

model – (optional fields) * .SConsistentRxnBool - ‘m x 1’ boolean vector indicating stoichiometrically consistent reactions * .b - m x 1 change in concentration with time * .csense - m x 1 character array with entries in {L,E,G} * .osenseStr - Maximize (‘max’)/minimize (‘min’)

(opt, default = ‘max’) only affects the interpretation of linear part of the objective (from model.c).

  • .C - k x n Left hand side of C*v <= d

  • .d - k x n Right hand side of C*v <= d

  • .dsense - k x 1 character array with entries in {L,E,G}

  • .h0 - m x 1, local weight on zero norm of rate of production of each metabolite by internal reactions.

  • .g0 - n x 1 , local weight on zero norm of the net flux of each reaction

  • .g1 - n x 1 , local weight on one norm of the net flux of each reaction

  • .presentMet - m x 1 boolean vector indicating metabolites

    that must be produced by internal reactions in the submodel

  • .absentMet - m x 1 boolean vector indicating metabolites

    that must be produced by internal reactions in the submodel

  • .activeRxn - n x 1 boolean vector indicating reactions that must be active in the submodel

  • .inactiveRxn - n x 1 boolean vector indicating reactions that must be active in the submodel

  • .lambda0 - trade-off parameter on minimise ||x||_0

  • .lambda1 - trade-off parameter on minimise ||x||_1

  • .delta0 - trade-off parameter on maximise ||y||_0

  • .delta1 - trade-off parameter on minimise `||y||_1’

  • .beta - trade-off parameter on minimise `||p||_1’ + `||q||_1’, increase to incentivise thermodynamic feasibility

  • .alpha1 - global weight on the one-norm of the cardinality-free variables

  • .lbr - m x 1 lower bounds on the rate of production by internal reactions

  • .SConsistentMetBool - m x 1 boolean of stoichiometrically consistent metabolites

  • .SIntMetBool - m x 1 boolean of internal metabolites (from findSExRxnInd)

  • .SIntRxnBool - n x 1 boolean of internal reactions (from findSExRxnInd)

  • .fluxConsistentMetBool - m x 1 boolean of flux consistent metabolites (computed if absent)

  • .fluxConsistentRxnBool - n x 1 boolean of flux consistent reactions (computed if absent)

  • .thermoFluxConsistentRxnBool - n x 1 boolean of thermodynamically flux consistent reactions

  • .dummyMetBool - m x 1 boolean of dummy metabolites