7.1.1.2.1.1. pta.gibbs_estimators.equilibrator_gibbs_estimator

Estimation of Gibbs free energies using eQuilibrator.

7.1.1.2.1.1.1. Module Contents

class pta.gibbs_estimators.equilibrator_gibbs_estimator.EquilibratorGibbsEstimator(rmse_inf: pta.commons.Q = default_rmse)[source]

Bases: pta.gibbs_estimators.gibbs_estimator_interface.GibbsEstimatorInterface

Estimation of Gibbs free energies using equilibrator_api.

Parameters

rmse_inf (Q, optional) – Uncertainty to use for unknown groups or compounds.

property eq_api(self)[source]

Gets the equilibrator API object.

property rmse_inf(self)[source]

Gets the uncertainty used for unknown compounds or groups.

property incorrect_metabolites(self) → List[str][source]

Gets the list of metabolites that are not correctly recognized by equilibrator.

get_dfg0_prime(self, S: numpy.array, metabolites: List[pta.metabolite.Metabolite], parameters: pta.compartment_parameters.CompartmentParameters) → Tuple[pta.commons.Q, pta.commons.Q][source]

Estimates the standard Gibbs free energies for a reaction network using equilibrator_api.

Parameters

  • S (np.array) – n-by-m stoichiometric matrix of the reaction network.

  • metabolites (List[Metabolite]) – A m-elements list describing the compounds in the network.

  • compartment_parameters (CompartmentParameters) – The prior for the physiological parameters of each compartment, such as pH and ionic strength.

Returns

A tuple, whose first element is the vector of the mean estimate, and the second is a square root \(Q\) of the covariance matrix on the estimation uncertainty \(\Sigma\), such that \(QQ^\intercal = \Sigma\).

Return type

Tuple[Q, Q]