7.1.1.2.1.2. pta.gibbs_estimators.gibbs_estimator_interface

Interface for an estimator of Gibbs free energies

7.1.1.2.1.2.1. Module Contents

class pta.gibbs_estimators.gibbs_estimator_interface.GibbsEstimatorInterface[source]

Interface for a class implementing estimation of Gibbs free energies

abstract 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

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.

  • 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]

Raises

NotImplementedError – An metaclass does not implement methods. Please use an implementation of this interface.