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 EnzymeModuleForm
s 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 associatedEnzymeModuleForm
s.Even though
MassReaction
s are also catalyzed by enzymes, an enzyme module reaction in the context of this module will refer to reactions that involveEnzymeModuleForm
(s) and are associated with anEnzymeModule
.
Module Contents
Classes
Class representing an enzyme reaction in an |
- 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 theirreversible_Keq
andirreversible_kr
attributes of theMassConfiguration
. Default isTrue
.- 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
The
bound_metabolites
attribute of the associatedEnzymeModuleForm
is used in generating the name.
- Parameters
update_enzyme (bool) – If
True
, update thename
attribute of the enzyme module reaction in addition to returning the generated name. Default isFalse
.- Returns
String representing the name of the
EnzymeModuleReaction
.- Return type