Componentcontribution

addThermoToModel(model, params, printLevel)[source]

Given a standard COBRA model, add thermodynamic data to it using the Component Contribution method

USAGE:

model = addThermoToModel (model, params, printLevel)

INPUTS:

model – COBRA model structure

OPTIONAL INPUTS:

  • params – structure with optional fields:

    • .use_cached_kegg_inchis - if true, use cached KEGG InChIs (default true)

    • .use_model_pKas_by_default - if true, use the model pKa values by default (default true)

    • .maxuf - maximum uncertainty threshold used when reporting

  • printLevel – verbosity level (default 0)

OUTPUTS:

model – COBRA model structure with added fields:

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

  • .covf - m x m estimated covariance matrix for standard Gibbs energies of formation.

  • .DfG0_Uncertainty - m x 1 array of uncertainty in estimated standard Gibbs energies of formation. Will be large for metabolites that are not covered by component contributions.

reaction2sparse(s)[source]

Convert a KEGG-style reaction formula string into a sparse stoichiometric vector

Parses a reaction string of the form a C00001 + C00002 = C00003, where each Cddddd is a KEGG compound identifier with an optional integer coefficient, and returns the net stoichiometric coefficients indexed by compound id (negative for substrates on the left, positive for products on the right).

USAGE:

res = reaction2sparse (s)

INPUT:

s – char, KEGG-style reaction formula (e.g. 2 C00001 + C00002 = C00003)

OUTPUT:

res – sparse row vector of net stoichiometric coefficients indexed by KEGG compound id (CID)

setupComponentContribution(model, molFileDir, cid, printLevel)[source]

Estimates standard transformed reaction Gibbs energy and directionality at in vivo conditions in multicompartmental metabolic reconstructions. Has external dependencies on the COBRA toolbox, the component contribution method, Python (with numpy and Open Babel bindings), ChemAxon’s Calculator Plugins, and Open Babel.

USAGE:

model = setupComponentContribution (model, molFileDir, cid, printLevel)

INPUTS:

model – Model structure with the following fields:

  • .mets - m x 1 array of metabolite identifiers

  • .metFormulas - m x 1 cell array of metabolite formulas; formulas for protons should be H, and for water H2O

  • .metCharges - m x 1 numerical array of metabolite charges

OPTIONAL INPUTS:

  • molFileDir – path to a directory containing molfiles for the major tautomer of the major microspecies of each metabolite at pH 7. Molfiles should be named with the metabolite identifiers in model.mets (without compartment assignments). Not required if cid is specified.

  • cid – m x 1 cell array of KEGG Compound identifiers. Not required if molFileDir is specified.

  • printLevel – verbosity level (default 1)

OUTPUTS:

model – Model structure with the following additional fields:

  • .inchi - structure containing four m x 1 cell arrays of IUPAC InChI strings for metabolites, with varying levels of structural detail

  • .pseudoisomers - p x 4 matrix with columns: metabolite index; estimated pseudoisomer standard Gibbs energy; number of hydrogen atoms in the pseudoisomer chemical formula; charge on the pseudoisomer

Note

Writes MetStructures.sdf, an SDF containing all structures input to the component contribution method for estimation of standard Gibbs energies.