2.1.1.3.1.7. enkie.estimators.parameter_balancer

Estimate kinetic and thermodynamic parameters using parameter balancing.

2.1.1.3.1.7.1. Module Contents

exception enkie.estimators.parameter_balancer.NoEstimateError[source]

Bases: Exception

Raised when no estimate was returned for a parameter.

class enkie.estimators.parameter_balancer.ParameterBalancer(gibbs_estimator: enkie.estimators.gibbs_estimator_interface.GibbsEstimatorInterface = None, kinetics_estimator: enkie.estimators.kinetics_estimator_interface.KineticsEstimatorInterface = None, prior_file: Union[pathlib.Path, str] = None)[source]

Bases: object

An estimator of kinetic and thermodynamic parameter values based on parameter balancing.

Parameters:

  • gibbs_estimator (GibbsEstimatorInterface, optional) – The estimator of Gibbs free energies, by default None

  • kinetics_estimator (KineticsEstimatorInterface, optional) – The estimator of kinetic parameters, by default None

  • prior_file (Union[Path, str], optional) – Path to the file defining priors for the Michaelis and velocity constants, by default None

Raises:

FileNotFoundError – If the specified file does not exist.

property gibbs_estimator: enkie.estimators.gibbs_estimator_interface.GibbsEstimatorInterface[source]

The object used to estimate Gibbs free energies.

property kinetics_estimator: enkie.estimators.kinetics_estimator_interface.KineticsEstimatorInterface[source]

The object used to estimate kinetic parameters.

property kv_prior: enkie.distributions.LogNormalDistribution[source]

Prior distribution of velocity constants.

property km_prior: enkie.distributions.LogNormalDistribution[source]

Prior distribution of affinity constants.

estimate_parameters(reactions: List[enkie.reaction.Reaction], rate_laws: List[enkie.modular_rate_law.ModularRateLaw], enzymes: List[enkie.enzyme.Enzyme], metabolites: List[enkie.metabolite.Metabolite], parameters: enkie.compartment_parameters.CompartmentParameters = None) → Tuple[pandas.Series, pandas.DataFrame][source]

Estimate kinetic and thermodynamic parameter values for the given reactions and metabolites.

Parameters:

  • reactions (List[Reaction]) – The reactions for which reaction energies should be estimated.

  • rate_laws (List[ModularRateLaw]) – The rate laws for which kinetic parameter values should be estimated.

  • enzymes (List[Enzyme]) – The enzymes associated with the rate laws.

  • metabolites (List[Metabolite]) – The metabolites participating to the reactions.

  • parameters (CompartmentParameters, optional) – The physiological parameters of the reaction compartments, by default None

Returns:

The mean and covariance (representing the uncertainty) of the predicted parameter values.

Return type:

Tuple[pd.Series, pd.DataFrame]