ecoli.processes.complexation

Complexation

This process encodes molecular simulation of macromolecular complexation, in which monomers are assembled into complexes. Macromolecular complexation is done by identifying complexation reactions that are possible (which are reactions that have sufficient counts of all sub-components), performing one randomly chosen possible reaction, and re-identifying all possible complexation reactions. This process assumes that macromolecular complexes form spontaneously, and that complexation reactions are fast and complete within the time step of the simulation.

class ecoli.processes.complexation.Complexation(parameters=None)[source]

Bases: PartitionedProcess

Complexation PartitionedProcess

calculate_request(timestep, states)[source]
defaults: Dict[str, Any]
{   'complex_ids': [],
    'molecule_names': [],
    'rates': array([], dtype=float64),
    'reaction_ids': [],
    'seed': 0,
    'stoichiometry': array([], shape=(1, 0), dtype=float64),
    'time_step': 1}
evolve_state(timestep, states)[source]
name = 'ecoli-complexation'
ports_schema()[source]
topology
{'bulk': ('bulk',), 'listeners': ('listeners',), 'timestep': ('timestep',)}