API Reference

This is the API reference for stochastix. For usage examples and guides see Home.

Core

Models

• stochastix.Reaction : A reaction.
• stochastix.kinetics : Kinetics of a reaction.
• stochastix.ReactionNetwork : A network of reactions.
• stochastix.generators : Generators of ReactionNetwork models for some common kinetic models.

Simulation

• stochastix.stochsimsolve : Main simulation entry point. Solve a stochastic initial value problem with a given solver.
• stochastix.faststochsimsolve : Fast simulation entry point. Solve a stochastic initial value problem with a given solver, but stop early if the simulation finishes before reaching max_steps.
• stochastix.SimulationResults : Results of a stochastic simulation with utilities (interpolation and cleaning results).
• stochastix.solvers : Solvers for stochastic simulations.
• stochastix.controllers : Controllers for stochastic simulations.

Systems

• stochastix.System : Convenience wrappers. Bundle a ReactionNetwork with a forward solver.

Analysis

• stochastix.analysis : Analysis utilities (e.g. correlation functions, KDE, and mutual information).

Utilities

• stochastix.utils.optimization : Optimization utilities.
• stochastix.utils.visualization : Visualization utilities.
• stochastix.utils.nn : Neural network utilities for neural kinetics.
• stochastix.utils.misc : Miscellaneous utilities.