2.1.1.3.1.4. enkie.estimators.gibbs_estimator_interface

Interface for an estimator of Gibbs free energies.

2.1.1.3.1.4.1. Module Contents

class enkie.estimators.gibbs_estimator_interface.GibbsEstimatorInterface[source]

Interface for a class implementing estimation of Gibbs free energies

abstract get_dfg0_prime(S: numpy.array, metabolites: List[enkie.miriam_metabolite.MiriamMetabolite], parameters: enkie.compartment_parameters.CompartmentParameters) → Tuple[enkie.commons.Q, enkie.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.