Source code for cobra.core.Species

from warnings import warn
from copy import deepcopy
from .Object import Object

[docs]class Species(Object): """Species is a class for holding information regarding a chemical Species """ def __init__(self, id=None, name=None): """ id: A string. name: String. A human readable name. """ Object.__init__(self, id, name) self._model = None # references to reactions that operate on this species self._reaction = set() @property def reactions(self): return frozenset(self._reaction)
[docs] def __getstate__(self): """Remove the references to container reactions when serializing to avoid problems associated with recursion. """ state = Object.__getstate__(self) state['_reaction'] = set() return state
[docs] def copy(self): """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.__deecopy__ if possible """ return deepcopy(self)
@property def model(self): return(self._model)