Simulation

Running simulations

Simulation(tileset[, system, states])
Simulation.evolve([state_index, for_events, ...])	Evolve a particular state, with index state_index, subject to some bounds.
Simulation.evolve_all([for_events, ...])	Evolve all states, stopping each as they reach the boundary conditions.
Simulation.evolve_some(state_indices[, ...])	Evolve some states, stopping each as they reach the boundary conditions.

Modifying simulations and getting information

Simulation.add_state()	Add a state to the simulation.
Simulation.add_n_states(n)	Add n states to the simulation.
Simulation.set_system_param(name, value)	Sets a system parameter to a value.
Simulation.get_system_param(name)	Gets a system parameter.
Simulation.canvas_copy([state_index])	Returns a copy of the current canvas for state_index (default 0).
Simulation.canvas_view([state_index])	Returns the current canvas for state_index (default 0), as a direct view of the state array.
Simulation.state_events([state_index])	Returns the number of events simulated for a state.
Simulation.state_time([state_index])	Returns the amount of time simulated (in seconds) for the state.
Simulation.state_ntiles([state_index])	Returns the number of tiles in the state.
Simulation.states_events	Returns the number of events simulated for each state.
Simulation.states_time	Returns the amount of time simulated (in seconds) for each state.
Simulation.states_ntiles	Returns the number of tiles in each state.
Simulation.tile_concs	Returns the concentration of each tile in the system.
Simulation.tile_stoics	Returns the stoichiometry of each tile in the system.
Simulation.tile_names	Returns the names of each tile in the system.
Simulation.tile_colors	Returns the colors of each tile in the system.
Simulation.n_mismatches([state_index])	Returns the number of mismatches in the state.
Simulation.mismatch_array([state_index])	Returns an array of mismatches in the state.
Simulation.plot_state([state_index, ax])	Plot a state as a pcolormesh.
Simulation.tile_cmap()	Returns a matplotlib colormap for tile numbers.