Source code for cobra.core.species

"""Define the Species class, used as a base for Gene and Metabolite."""

from copy import deepcopy
from typing import TYPE_CHECKING, FrozenSet, Optional

from ..core.object import Object

    from .. import Model

[docs]class Species(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. """ # noinspection PyShadowingBuiltins def __init__( self, id: Optional[str] = None, name: Optional[str] = None, **kwargs ) -> None: """Initialize a Species. Parameters ---------- id : string, optional, default None An identifier for the chemical species name : string, optional, default None A human readable name. A species also contains a _model, reference to a cobra.model (initialized as None) and a self._reaction, a set of cobra.reactions (initialized as empty set). """ super().__init__(id=id, name=name, **kwargs) self._model = None # references to reactions that operate on this species self._reaction = set() @property
[docs] def reactions(self) -> FrozenSet: """Return a frozenset of reactions. Returns ------- FrozenSet A frozenset that includes the reactions of the species. """ return frozenset(self._reaction)
[docs] def __getstate__(self) -> dict: """Return the state of the species. Remove the references to container reactions when serializing to avoid problems associated with recursion. Returns ------- dict A dictionary describing the state, without the self._reaction to avoid recursion. """ state = Object.__getstate__(self) state["_reaction"] = set() return state
[docs] def copy(self) -> "Species": """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 ------- Species A copy of the species. """ return deepcopy(self)
[docs] def model(self) -> Optional["Model"]: """Return the model. Returns ------- model Returns the cobra model that the species is associated with. None if there is no model associated with this species. """ return self._model