cobra.core.species
¶
Define the Species class, used as a base for Gene and Metabolite.
Module Contents¶
Classes¶
Species is a base class in Cobrapy. |
- class cobra.core.species.Species(id: Optional[str] = None, name: Optional[str] = None, **kwargs)[source]¶
Bases:
cobra.core.object.Object
Species is a base class in Cobrapy.
Species is a class for holding information regarding a chemical Species
- Parameters
id (string) – An identifier for the chemical species
name (string) – A human readable name.
- property reactions: FrozenSet[source]¶
Return a frozenset of reactions.
- Returns
A frozenset that includes the reactions of the species.
- Return type
FrozenSet
- property model: Optional[cobra.Model][source]¶
Return the model.
- Returns
Returns the cobra model that the species is associated with. None if there is no model associated with this species.
- Return type
model
- __getstate__() dict [source]¶
Return the state of the species.
Remove the references to container reactions when serializing to avoid problems associated with recursion.
- Returns
A dictionary describing the state, without the self._reaction to avoid recursion.
- Return type
- copy() Species [source]¶
Copy a species.
When copying a reaction, it is necessary to deepcopy the components so the list references aren’t carried over.
Additionally, a copy of a reaction is no longer in a cobra.Model.
This should be fixed with self.__deepcopy__ if possible
- Returns
A copy of the species.
- Return type