ecoli.composites.ecoli_engine_process

Composite for simulations with EngineProcess cells in an environment.

Note

This composite requires a config with the spatial environment enabled.

class ecoli.composites.ecoli_engine_process.EcoliEngineProcess(config=None)

Bases: Composer

Base class for composer classes.

Composers generate composites.

All composer classes must inherit from this class.

Parameters:

config (dict | None) – Dictionary of configuration options that can override the class defaults.

defaults: Dict[str, Any]

{   'agent_id': '0',
    'divide': False,
    'division_threshold': True,
    'emit_paths': (),
    'experiment_id': '',
    'inner_composer_config': {},
    'inner_emitter': 'null',
    'inner_same_timestep': True,
    'lysis_config': {},
    'parallel': False,
    'seed': 0,
    'start_time': 0,
    'stub_schemas': {},
    'tunnel_out_schemas': {},
    'tunnels_in': ()}

generate_processes(config)

generate_topology(config)

class ecoli.composites.ecoli_engine_process.EcoliInnerSim(config=None)

Bases: Composer

Base class for composer classes.

Composers generate composites.

All composer classes must inherit from this class.

Parameters:

config (dict | None) – Dictionary of configuration options that can override the class defaults.

defaults: Dict[str, Any]

{   'agent_id': '0',
    'chromosome_path': None,
    'division_threshold': None,
    'division_variable': None,
    'initial_state': None,
    'seed': 0}

generate(config=None)

generate_processes(config)

generate_topology(config)

class ecoli.composites.ecoli_engine_process.EcoliInnerWrapper(config=None, store=None, processes=None, steps=None, flow=None, topology=None, state=None)

Bases: Composite

Helper class to ensure calling initial_state() on the composite generated by EcoliInnerSim returns the cached initial state and removes the internal reference to this state.

Parameters:

• config (Dict[str, Any] | None) –

• store (Store | None) –

• processes (Dict[str, Any]) –

• steps (Dict[str, Any]) –

• flow (Dict[str, Sequence[Tuple[str, ...]]]) –

• topology (Dict[str, Tuple[str, ...] | dict | object]) –

• state (Dict[str, Any]) –

initial_state(config)

ecoli.composites.ecoli_engine_process.colony_save_states(engine, config)

Runs the simulation while saving the states of the colony at specific timesteps to jsons.

ecoli.composites.ecoli_engine_process.run_simulation(config)