mass.enzyme_modules.enzyme_module_form
EnzymeModuleForm is a class for holding information regarding enzyme module forms.
The EnzymeModuleForm
class inherits and extends the
MassMetabolite
class. It is designed to represent various bound
states and conformations of the enzymes represented through the
EnzymeModule
class.
The enzyme specific attributes on the EnzymeModuleForm
are the
following:
enzyme_module_id
"bound_metabolites"
The EnzymeModuleForm
contains the attribute
MassMetabolite
(s) that could be bound to the sites on the enzyme.
Some other important points about the EnzymeModuleForm
include:
If the
name
attribute is not set upon initializing, it is automatically generated using the enzyme specific attributes.If the
formula
or charge attributes are not set upon initialization, it is inferred using the formulas and charges set on theMassMetabolite
(s) found inbound_metabolites
. A moiety is also included for the formula using theenzyme_module_id
.The purpose of the generated formula and charge is to ensure reactions remained mass and charge balanaced as metabolite species are bound and altered by the
EnzymeModuleReaction
s of theEnzymeModule
.
Module Contents
Classes
Class representing an enzyme forms of an |
- class mass.enzyme_modules.enzyme_module_form.EnzymeModuleForm(id_or_specie=None, enzyme_module_id='', bound_metabolites=None, **kwargs)[source]
Bases:
mass.core.mass_metabolite.MassMetabolite
Class representing an enzyme forms of an
EnzymeModule
.Accepted
kwargs
are passed to the initialization method of the base class,MassMetabolite
.- Parameters
id_or_specie (str, MassMetabolite, EnzymeModuleForm) – A string identifier to associate with the enzyme module forms, or an existing metabolite object. If an existing metabolite object is provided, a new
EnzymeModuleForm
is instantiated with the same properties as the original metabolite.enzyme_module_id (str) – The identifier of the associated
EnzymeModule
.bound_metabolites (dict) – A
dict
representing the ligands bound to the enzyme, withMassMetabolite
s or their identifiers as keys and the number bound as values.**kwargs –
- name :
str
representing a human readable name for the enzyme module form.- formula :
str
representing a chemical formula associated with the enzyme module form.- charge :
float
representing the charge number associated with the enzyme module form.- compartment :
str
representing the compartment where the enzyme module form is located.- fixed :
bool
indicating whether the enzyme module form concentration should remain at a fixed value. Default isFalse
.
- property bound_metabolites[source]
Get or set metabolites bound to the enzyme’s site(s).
Notes
Assigning a
dict
to this property updates the currentdict
of ligands bound at the enzyme site(s) with the new values.- Parameters
value (dict) – A
dict
where keys areMassMetabolite
and values are the number currently bound to the site(s). An emptydict
will reset the bound ligands.
- generate_enzyme_module_form_name(update_enzyme=False)[source]
Generate name for the enzyme module form based on bound ligands.
Notes
The
bound_metabolites
attribute is used in generating the name.If the
enzyme_module_id
attributes are not set, the string'Enzyme'
will be used in its place.
- Parameters
update_enzyme (bool) – If
True
, update thename
attribute of the enzyme module form in addition to returning the generated name. Default isFalse
.- Returns
String representing the name of the
EnzymeModuleForm
.- Return type
- generate_form_formula(update_enzyme=False)[source]
Generate the chemical formula for the enzyme module form.
This function is primarily utilized for keeping reactions between
EnzymeModuleForm
mass and charge balanced.Notes
The
bound_metabolites
attribute is used in generating the formula.- Parameters
update_enzyme (bool) – If
True
, update theformula
attribute of the enzyme module form in addition to returning the generated formula. Default isFalse
.- Returns
String representing the formula of the
EnzymeModuleForm
.- Return type
- generate_form_charge(update_enzyme=False)[source]
Generate the charge for the enzyme module form.
This function is primarily utilized for keeping reactions between
EnzymeModuleForm
mass and charge balanced.Notes
The
bound_metabolites
attribute is used in generating the charge.- Parameters
update_enzyme (bool) – If
True
, update thecharge
attribute of the enzyme module form in addition to returning the generated charge. Default isFalse
.- Returns
Value representing the charge of the
EnzymeModuleForm
.- Return type
- _set_id_with_model(value)[source]
Set the id of the EnzymeModuleForm to the associated MassModel.
Warning
This method is intended for internal use only.