mass.enzyme_modules.enzyme_module_dict

EnzymeModuleDict is a class representing the EnzymeModule after merging.

This object is intended to represent the EnzymeModule once merged into a MassModel in order to retain EnzymeModule specific attributes of the EnzymeModule without the need of storing the EnzymeModule object itself.

When merging an EnzymeModule into another model, the EnzymeModule is converted into an EnzymeModuleDict, allowing for most of the enzyme specific attribute information of the EnzymeModule to be preserved during the merging process, and accessed after the merging. All keys of the EnzymeModuleDict can be used as attribute accessors. Additionally EnzymeModuleDict is a subclass of an OrderedDictWithID which in turn is a subclass of an OrderedDict, thereby inheriting its methods and behavior.

The EnzymeModule attributes preserved in the EnzymeModuleDict are the following:

• EnzymeModule.id

• EnzymeModule.name

• EnzymeModule.subsystem

• EnzymeModule.enzyme_module_ligands

• EnzymeModule.enzyme_module_forms

• EnzymeModule.enzyme_module_reactions

• EnzymeModule.enzyme_module_ligands_categorized

• EnzymeModule.enzyme_module_forms_categorized

• EnzymeModule.enzyme_module_reactions_categorized

• EnzymeModule.enzyme_concentration_total

• EnzymeModule.enzyme_rate

• EnzymeModule.enzyme_concentration_total_equation

• EnzymeModule.enzyme_rate_equation

• EnzymeModule.S

If one of the above attributes has not been set, it will be added to the EnzymeModuleDict as its default value. This means that the above attributes can always be found in an EnzymeModuleDict.

Note that this class is not intended to be used for construction of an EnzymeModule, but rather a representation of one after construction. See the enzyme_module documentation for more information on constructing EnzymeModules.

Module Contents

Classes

EnzymeModuleDict

Container to store EnzymeModule information after merging.

Attributes

_ORDERED_ENZYMEMODULE_DICT_DEFAULTS

class mass.enzyme_modules.enzyme_module_dict.EnzymeModuleDict(id_or_enzyme=None)

Bases: mass.util.dict_with_id.OrderedDictWithID

Container to store EnzymeModule information after merging.

Parameters

enzyme (EnzymeModule or EnzymeModuleDict) – The EnzymeModule to be converted into an EnzymeModuleDict, or an existing EnzymeModuleDict. If an existing EnzymeModuleDict is provided, a new EnzymeModuleDict is instantiated with the same information as the original.

copy()

Copy an EnzymeModuleDict.

_set_missing_to_defaults()

Set all of the missing attributes to their default values.

Warning

This method is intended for internal use only.

_update_object_pointers(model=None)

Update objects in the EnzymeModuleDict to point to the given model.

Warning

This method is intended for internal use only.

_make_enzyme_stoichiometric_matrix(update=False)

Return the S matrix based on enzyme forms, reactions, and ligands.

Warning

This method is intended for internal use only.

_fix_order()

Fix the order of the items in the EnzymeModuleDict.

Warning

This method is intended for internal use only.

_repr_html_()

HTML representation of the overview for the EnzymeModuleDict.

Warning

This method is intended for internal use only.

__getattr__(name)

Override of default getattr implementation.

Warning

This method is intended for internal use only.

__setattr__(name, value)

Override of default setattr implementation.

Warning

This method is intended for internal use only.

__delattr__(name)

Override of default delattr implementation.

Warning

This method is intended for internal use only.

__dir__()

Override of default dir implementation to include the keys.

Warning

This method is intended for internal use only.

__copy__()

Create a copy of the EnzymeModuleDict.

Warning

This method is intended for internal use only.

__deepcopy__(memo)

Create a deepcopy of the EnzymeModuleDict.

Warning

This method is intended for internal use only.

mass.enzyme_modules.enzyme_module_dict._ORDERED_ENZYMEMODULE_DICT_DEFAULTS