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 the MassMetabolite(s) found in bound_metabolites. A moiety is also included for the formula using the enzyme_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 EnzymeModuleReactions of the EnzymeModule.

Module Contents

Classes

EnzymeModuleForm

Class representing an enzyme forms of an EnzymeModule.

class mass.enzyme_modules.enzyme_module_form.EnzymeModuleForm(id_or_specie=None, enzyme_module_id='', bound_metabolites=None, **kwargs)

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, with MassMetabolites 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 is False.

property bound_metabolites

Get or set metabolites bound to the enzyme’s site(s).

Notes

Assigning a dict to this property updates the current dict of ligands bound at the enzyme site(s) with the new values.

Parameters

value (dict) – A dict where keys are MassMetabolite and values are the number currently bound to the site(s). An empty dict will reset the bound ligands.

generate_enzyme_module_form_name(update_enzyme=False)

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 the name attribute of the enzyme module form in addition to returning the generated name. Default is False.

Returns

String representing the name of the EnzymeModuleForm.

Return type

str

generate_form_formula(update_enzyme=False)

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 the formula attribute of the enzyme module form in addition to returning the generated formula. Default is False.

Returns

String representing the formula of the EnzymeModuleForm.

Return type

str

generate_form_charge(update_enzyme=False)

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 the charge attribute of the enzyme module form in addition to returning the generated charge. Default is False.

Returns

Value representing the charge of the EnzymeModuleForm.

Return type

float

_set_id_with_model(value)

Set the id of the EnzymeModuleForm to the associated MassModel.

Warning

This method is intended for internal use only.

_repair_bound_obj_pointers()

Repair object pointer for metabolites in bound dict attributes.

Requires a model to be associated with the EnzymeModuleForm.

Warning

This method is intended for internal use only.

_repr_html_()

HTML representation of the overview for the EnzymeModuleForm.

Warning

This method is intended for internal use only.