Source code for cobra.core.species

# -*- coding: utf-8 -*-

from __future__ import absolute_import

from copy import deepcopy

from cobra.core.object import Object

[docs]class Species(Object): """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. """ def __init__(self, id=None, name=None): Object.__init__(self, id, name) self._model = None # references to reactions that operate on this species self._reaction = set() @property
[docs] 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.__deepcopy__ if possible """ return deepcopy(self)
[docs] def model(self): return self._model