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.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 EnzymeModule
s.
Module Contents
Classes
Container to store |
Attributes
- class mass.enzyme_modules.enzyme_module_dict.EnzymeModuleDict(id_or_enzyme=None)[source]
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 anEnzymeModuleDict
, or an existingEnzymeModuleDict
. If an existingEnzymeModuleDict
is provided, a newEnzymeModuleDict
is instantiated with the same information as the original.
- copy(self)[source]
Copy an
EnzymeModuleDict
.
- _set_missing_to_defaults(self)[source]
Set all of the missing attributes to their default values.
Warning
This method is intended for internal use only.
- _update_object_pointers(self, model=None)[source]
Update objects in the EnzymeModuleDict to point to the given model.
Warning
This method is intended for internal use only.
- _make_enzyme_stoichiometric_matrix(self, update=False)[source]
Return the S matrix based on enzyme forms, reactions, and ligands.
Warning
This method is intended for internal use only.
- _fix_order(self)[source]
Fix the order of the items in the EnzymeModuleDict.
Warning
This method is intended for internal use only.
- _repr_html_(self)[source]
HTML representation of the overview for the EnzymeModuleDict.
Warning
This method is intended for internal use only.
- __getattr__(self, name)[source]
Override of default
getattr
implementation.Warning
This method is intended for internal use only.
- __setattr__(self, name, value)[source]
Override of default
setattr
implementation.Warning
This method is intended for internal use only.
- __delattr__(self, name)[source]
Override of default
delattr
implementation.Warning
This method is intended for internal use only.
- __dir__(self)[source]
Override of default
dir
implementation to include the keys.Warning
This method is intended for internal use only.