Old

checkForMissingStereo(model, nist)

INPUTS model.mets model.inchi.standard model.inchi.standardWithStereo nist.std_inchi nist.std_inchi_stereo

OUTPUTS missingStereo

loadTrainingData(formation_weight)

Generates the structure that contains all the training data needed for Component Contribution.

Input

formation_weight - the relative weight to give the formation energies (Alberty’s data) – compared to the reaction measurements (TECRDB)

prepareTrainingData(model, printLevel, params)

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

INPUTS model

OPTIONAL INPUTS params.use_cached_kegg_inchis params.use_model_pKas_by_default params.uf maximum uncertainty

OUTPUTS: model .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.