#---------------------------------------------------------------------------
#
# Cell.py: hierarchical compartments containing molecules that react,
# and possibly other compartments too, like in P Systems
#
# by Lidia Yamamoto, July 2013
#
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
# Copyright (C) 2015 Lidia A. R. Yamamoto
# Contact: http://www.artificial-chemistries.org/
#
# This file is part of PyCellChemistry.
#
# PyCellChemistry is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# version 3, as published by the Free Software Foundation.
#
# PyCellChemistry is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with PyCellChemistry, see file COPYING. If not, see
# http://www.gnu.org/licenses/
#

Modules
		numpy sys

Classes
		Cell class Cell Methods defined here: __init__(self) initialize empty cell add(self, c) add a new internal compartment c to this cell clear_cells() delete all the internal compartments from this cell dissolve(self, i) dissolve internal compartment [i], and release its content to the cytoplasm divide(self) cell division: approximately half of the objects (chosen randomly) goes to the daughter cell; returns the newly created daughter cell get_cells() get list of internal compartments for this cell get_cytoplasm(self) get cytoplasm object for this cell gillespie(self) hierarchical gillespie for cell and its subcells inert(self) true if none of the vessels in this cell (including the cytoplasm and all the subcells, recursively) has reactions to perform propensity(self) calculate propensities for the elements within this cell run(self, niter) run 'niter' iterations of gillespie for this cell, or until cell becomes inert set_cytoplasm(self, c) assign a cytoplasm object to this cell; a cytoplasm represents the set of molecules floating inside the cell, which are not inside another subcell; it is typically implemented as a Multiset or a more elaborated class derived from it.

Generated automatically by pydoc, July 10, 2015

Generated automatically by pydoc, July 10, 2015