2.1.2.9. enkie.modular_rate_law

Description of modular rate laws.

2.1.2.9.1. Module Contents

class enkie.modular_rate_law.RateLawDenominator[source]

Bases: enum.Enum

The type of a modular rate law.

COMMON = 1[source]
DIRECT_BINDING = 2[source]
SIMULTANEOUS_BINDING = 3[source]
POWER_LAW = 4[source]
FORCE_DEPENDENT = 5[source]
enkie.modular_rate_law.DEFAULT_RATE_LAW_TYPE[source]
class enkie.modular_rate_law.ModularRateLaw(rid: str, reaction: enkie.reaction.Reaction, denominator: RateLawDenominator = DEFAULT_RATE_LAW_TYPE, cooperativity: float = 1)[source]

Bases: object

A reaction following modular rate law kinetics.

Parameters:

  • rid (str) – Unique identifier of the ate law.

  • reaction (Reaction) – The reaction whose kinetics are described by this rate law.

  • denominator (RateLawDenominator, optional) – The denominator of the rate law.

  • cooperativity (float, optional) – The cooperativity of the reaction.

property id: str[source]

The identifier of the rate law.

property reaction: enkie.reaction.Reaction[source]

The reaction associated to the rate law.

property num_independent_params: int[source]

The number of independent parameters in the rate law.

property metabolites_kin: List[enkie.metabolite.Metabolite][source]

The reaction metabolites participating to the reaction that have an effect on kinetics.

property metabolite_ids_kin: List[str][source]

The identifiers of the metabolites participating to the reaction that have an effect on kinetics.

property num_metabolites_kin: int[source]

The number of metabolites (substrates or products) in this reaction that have an effect on the reaction kinetics.

NO_KM_MNX_IDS[source]

MetaNetX identifiers of metabolites that are assumed not to affect the kinetics of the reaction.

get_dependence(parameter: enkie.estimators.kinetic_parameter_types.KineticParameterType, temperature: enkie.commons.Q, metabolite: enkie.metabolite.Metabolite = None) → numpy.ndarray[source]

Gets the dependence vector between the independent parameters and the selected parameter of the rate law.

Parameters:

  • parameter (KineticParameterType) – The type of parameter to get the dependence vector for.

  • temperature (Q) – The temperature at which the dependence vector is evaluated.

  • metabolite (Metabolite, optional) – The metabolite a KM parameter refers to. Only meaningful for KM parameters.

Returns:

The dependence vector. The format is [DfG’°, ln kV, ln kMs].

Return type:

np.ndarray