componentContribution

addThermoToModel(model, params, printLevel)

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.use_cached_kegg_inchis: params.use_model_pKas_by_default: params.uf: maximum uncertainty

OUTPUTS:

model: COBRA model structure with 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.

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

setupComponentContribution(model, molFileDir, cid, printLevel)

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. See details on availability at the end of help text.

modelT = setupThermoModel(model,molfileDir,cid,T,cellCompartments,ph,…

is,chi,concMin,concMax,confidenceLevel)

INPUTS model Model structure with following fields: .S m x n stoichiometric matrix. .mets m x 1 array of metabolite identifiers. .rxns n x 1 array of reaction identifiers. .metFormulas m x 1 cell array of metabolite formulas. Formulas for

protons should be H, and formulas for water should be 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 are specified.

cid m x 1 cell array of KEGG Compound identifiers.

Not required if molfiledir is specified.

model.metCompartments m x 1 array of metabolite compartment

assignments. Not required if metabolite identifiers are strings of the format ID[*] where * is the appropriate compartment identifier.

OUTPUTS model Model structure with following additional fields: .inchi Structure containing four m x 1 cell array’s of

IUPAC InChI strings for metabolites, with varying levels of structural detail.

.pKa m x 1 structure containing metabolite pKa values

estimated with ChemAxon’s Calculator Plugins.

.pseudoisomers p x 4 matrix with the following columns:

  1. Metabolite index.

  2. Estimated pseudoisomer standard Gibbs energy.

3. Number of hydrogen atoms in pseudoisomer chemical formula. 4. Charge on pseudoisomer.

WRITTEN OUTPUTS MetStructures.sdf An SDF containing all structures input to the

component contribution method for estimation of standard Gibbs energies.

Ronan M. T. Fleming, Sept. 2012 Version 1.0 Hulda S. H., Dec. 2012 Version 2.0