2.1.1.3.1.1. `enkie.estimators.bmm_kinetic_estimator`

Estimator of kinetic parameters based on Bayesian Multilevel Models.

2.1.1.3.1.1.1. Module Contents

class enkie.estimators.bmm_kinetic_estimator.BmmKineticEstimator[source]

An estimator of kinetic parameters based on Bayesian Multilevel Models.

get_parameters(reactions: List[enkie.miriam_reaction.MiriamReaction], enzymes: List[enkie.enzyme.Enzyme], parameter_types: List[enkie.estimators.kinetics_estimator_interface.KineticParameterType], substrates: List[enkie.miriam_metabolite.MiriamMetabolite]) → Tuple[numpy.ndarray, numpy.ndarray][source]

Estimate kinetic parameter values for the given reaction-enzyme pairs.

Parameters:

reactions (List[MiriamReaction]) – The reactions to predict parameters for.
enzymes (List[Enzyme]) – The enzymes associated with the reactions.
parameter_types (List[KineticParameterType]) – The type of the parameters to predict.
substrates (List[MiriamMetabolite]) – For KM parameters, the metabolite to predict the KM for. This is ignored for kcat.

Returns:

The vector of mean parameter ln-values and the covariance of the uncertainty of the estimated parameter ln-values.

Return type:

Tuple[np.ndarray, np.ndarray]

predict(query_df: pandas.DataFrame) → Tuple[numpy.ndarray, numpy.ndarray][source]

Predict kinetic parameters for the given query.

Parameters:: query_df (pd.DataFrame) – DataFrame containing the query data.
Returns:: The mean and covariance of the predicted parameters, in natural log scale.
Return type:: Tuple[np.ndarray, np.ndarray]