Package abstochkin

Agent-based (or Particle-based) Stochastic Kinetics.

""" Agent-based (or Particle-based) Stochastic Kinetics. """

#  Copyright (c) 2023, Alex Plakantonakis.
#
#  This program is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#
#  This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.

from .base import AbStochKin

__version__ = '0.1.0'
__license__ = "GPL-3.0"

Sub-modules

abstochkin.agentstatedata

Class for storing the state of all agents of a certain species during an AbStochKin simulation.

abstochkin.base

Base class, AbStochKin, for initializing and storing all data for performing stochastic simulations using the Agent-based Kinetics method. A …

abstochkin.de_calcs

Perform deterministic calculations on a set of processes. Construct the ordinary differential equations (ODEs) describing the system and obtain a …

abstochkin.graphing

Graphing for AbStochKin simulations.

abstochkin.het_calcs

Some functions for calculating metrics of population heterogeneity.

abstochkin.process

Define a process of the form Reactants -> Products.

abstochkin.simulation

Perform an Agent-based Kinetics simulation …

abstochkin.utils

Some utility functions on generating random number streams, measuring a function's runtime, calculating a statistic measuring the goodness of fit when …