mass.enzyme_modules.enzyme_module_reaction

EnzymeModuleReaction is a class for holding information regarding enzyme module reactions.

The EnzymeModuleReaction class inherits and extends the MassReaction class. It is designed to represent the reactions and transitions involving EnzymeModuleForms represented in the EnzymeModule class.

The enzyme specific attributes on the EnzymeModuleReaction are the following:

  • enzyme_module_id

Some other important points about the EnzymeModuleReaction include:

  • If the name attribute is not set upon initializing, it is automatically generated using the enzyme specific attributes of the associated EnzymeModuleForms.

  • Even though MassReactions are also catalyzed by enzymes, an enzyme module reaction in the context of this module will refer to reactions that involve EnzymeModuleForm(s) and are associated with an EnzymeModule.

Module Contents

Classes

EnzymeModuleReaction

Class representing an enzyme reaction in an EnzymeModule.
class mass.enzyme_modules.enzyme_module_reaction.EnzymeModuleReaction(id_or_reaction=None, enzyme_module_id='', **kwargs)[source]

Bases: mass.core.mass_reaction.MassReaction

Class representing an enzyme reaction in an EnzymeModule.

Accepted kwargs are passed to the initialization method of the base class, MassReaction.

Parameters

  • id_or_reaction (str, MassReaction, EnzymeModuleReaction) – A string identifier to associate with the enzyme module reaction, or an existing reaction object. If an existing reaction object is provided, a new EnzymeModuleReaction is instantiated with the same properties as the original reaction.

  • enzyme_module_id (str) – The identifier of the associated EnzymeModule.

  • **kwargs –

    name :

    str representing a human readable name for the enzyme module reaction.

    subsystem :

    str representing the subsystem where the enzyme module reaction is meant to occur.

    reversible :

    bool indicating the the kinetic reversibility of the reaction. Irreversible reactions have an equilibrium constant and a reverse rate constant as set in the irreversible_Keq and irreversible_kr attributes of the MassConfiguration. Default is True.

    steady_state_flux :

    float representing the stored (typically steady state) flux for the reaction.

generate_enzyme_module_reaction_name(update_enzyme=False)[source]

Generate name for an enzyme module reaction based on bound ligands.

Notes

Parameters

update_enzyme (bool) – If True, update the name attribute of the enzyme module reaction in addition to returning the generated name. Default is False.

Returns

String representing the name of the EnzymeModuleReaction.

Return type

str