New

componentContribution(model, combinedModel, param)[source]

Perform the component contribution method

Note, we assume DfG0 for ‘[H+]’ is zero

USAGE:

[model, solution] = componentContribution (model, combinedModel, param)

INPUTS:

  • model – COBRA model structure with fields:

    • .S - m x n stoichiometric matrix

    • .SIntRxnBool - n x 1 boolean, true for internal reactions

    • .SConsistentRxnBool - n x 1 boolean, true for stoichiometrically consistent reactions (used if present)

    • .transportRxnBool - n x 1 boolean, true for transport reactions (computed internally if absent)

  • combinedModel – structure of combined training and test data with fields:

    • .S - k x n stoichiometric matrix of the combined data

    • .DrG0 - n x 1 experimental standard reaction Gibbs energy

    • .dG0 - legacy name for the standard reaction Gibbs energy, renamed to .DrG0 if present

    • .G - k x g group incidence matrix

    • .groups - g x 1 cell array of group definitions

    • .test2CombinedModelMap - m x 1 mapping of model metabolites to combinedModel metabolites

OPTIONAL INPUTS:

param – structure with optional fields:

  • .debug - if true (default), populate solution with intermediate quantities

OUTPUTS:

  • model – COBRA model structure with added fields:

    • .DfG0 - m x 1 component contribution standard Gibbs energies of formation

    • .DfG0_Uncertainty - m x 1 uncertainty in .DfG0

    • .unconstrainedDfG0_cc - m x 1 boolean, metabolite estimates partially unconstrained by the group fit

    • .DrG0 - n x 1 standard reaction Gibbs energies

    • .DrG0_Uncertainty - n x 1 uncertainty in .DrG0

    • .unconstrainedDrG0_cc - n x 1 boolean, reaction estimates partially unconstrained by the group fit

    • .DfG0_cc_cov - m x m covariance matrix of metabolite standard Gibbs energies

    • .DrG0_cc_cov - n x n covariance matrix of reaction standard Gibbs energies

    • .DfG0_cov - m x m metabolite covariance matrix, referenced in an internal diagnostic message

    • .V_rc - m x m reactant-contribution covariance component (alternative code path)

    • .V_gc - m x m group-contribution covariance component (alternative code path)

    • .V_inf - m x m unconstrained covariance component (alternative code path)

    • .PR_S - projection matrix onto the range of S (alternative code path)

    • .PN_St - projection matrix onto the null space of S transpose (alternative code path)

    • .PN_StGGt - projection matrix onto the null space of (S transpose times G) transpose (alternative code path)

  • solution – structure of intermediate solution vectors and matrices when param.debug is true, otherwise empty

invertProjection(A, epsilon)[source]

Inverts a general matrix A using the pseudoinverse

USAGE:

[inv_A, r, PR, PL] = invertProjection (A, epsilon)

INPUTS:

  • A – general matrix

  • epsilon – default = 1e-10

OUTPUTS:

  • inv_A – the pseudoinverse of A

  • r – the rank of A

  • PR – the projection matrix onto the range(A)

  • PL – the projection matrix onto the null(A’)