2.1.1.3.1.3. enkie.estimators.fixed_kinetics_estimator

Mock estimator of kinetic parameters.

2.1.1.3.1.3.1. Module Contents

class enkie.estimators.fixed_kinetics_estimator.FixedKineticsEstimator(ln_km_mean: float = np.log(0.0001), ln_km_std: float = 5, ln_kcat_fw_mean: float = np.log(1), ln_kcat_fw_std: float = 5, ln_kcat_bw_mean: float = np.log(1), ln_kcat_bw_std: float = 5)[source]

Bases: enkie.estimators.kinetics_estimator_interface.KineticsEstimatorInterface

Mock estimator of kinetic parameters that returns predefined values.

Parameters:

  • ln_km_mean (float, optional) – Default value for KM parameters.

  • ln_km_std (float, optional) – Default uncertainty for KM parameters.

  • ln_kcat_fw_mean (float, optional) – Default value for forward kcat parameters.

  • ln_kcat_fw_std (float, optional) – Default uncertainty for forward kcat parameters.

  • ln_kcat_bw_mean (float, optional) – Default value for backward kcat parameters.

  • ln_kcat_bw_std (float, optional) – Default uncertainty for backward kcat parameters.

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]

Return default kinetic parameters for teh 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]