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forwardReversibleFigures2(model, directions)

Figures of different classes of reactions: qualitatively forward -> quantitatively reversible

USAGE:

forwardReversibleFigures2 (model, directions)

INPUTS:

• model – structure with fields:

  • .S - m x n stoichiometric matrix

  • .DrGt0Min - n x 1 lower bound on standard transformed reaction Gibbs energy

  • .DrGt0Max - n x 1 upper bound on standard transformed reaction Gibbs energy

  • .DrGtMin - n x 1 lower bound on transformed reaction Gibbs energy

  • .DrGtMax - n x 1 upper bound on transformed reaction Gibbs energy

  • .DrGtMean - n x 1 mean transformed reaction Gibbs energy

  • .dGt0Min - n x 1 lower bound on standard transformed reaction Gibbs energy

  • .dGt0Max - n x 1 upper bound on standard transformed reaction Gibbs energy

  • .dGtMin - n x 1 lower bound on transformed reaction Gibbs energy

  • .dGtMax - n x 1 upper bound on transformed reaction Gibbs energy

  • .directions - structure of directionality-assignment vectors

• directions – structure of subsets of qualitatively forward -> quantitatively reversible reactions, with fields:

  • .forwardReversible - reactions reassigned from forward to reversible

  • .forwardReversible_bydGt0Mid - reassigned, standard Gibbs energy range spanning zero

  • .forwardReversible_byConc_negative_uncertain_DrG0 - reassigned by concentration, negative uncertain standard Gibbs energy

  • .forwardReversible_byConc_positive_uncertain_DrG0 - reassigned by concentration, positive uncertain standard Gibbs energy

  • .forwardProbability - n x 1 probability that each reaction proceeds forward

forwardReversibleFiguresKeq(model, directions, thorStandard)

Figure of qualitatively forward -> quantitatively reversible (keq)

Make a figure of reactions that have changed from qualitatively forward to quantitatively reversible, where all metabolite dGt0 were back-calculated from Keq. Omits reactions that are transport reactions.

USAGE:

forwardReversibleFiguresKeq (model, directions, thorStandard)

INPUTS:

• model – structure with fields:

  • .S - m x n stoichiometric matrix

  • .dGt0Min - n x 1 lower bound on standard transformed reaction Gibbs energy

  • .dGt0Max - n x 1 upper bound on standard transformed reaction Gibbs energy

  • .dGtMin - n x 1 lower bound on transformed reaction Gibbs energy

  • .dGtMax - n x 1 upper bound on transformed reaction Gibbs energy

• directions – structure with field:

  • .ChangeForwardReversible_dGfKeq - reactions changed from forward to reversible via Keq

• thorStandard – {(0), 1} use new standard reactant concentration half way between upper and lower concentration bounds