vivarium.processes.complexation module

class vivarium.processes.complexation.Complexation(initial_parameters=None)

Bases: vivarium.core.process.Process

defaults = {'complex_ids': ['flhDC', 'flagellar motor switch', 'flagella', 'flagellar export apparatus subunit', 'flagellar export apparatus', 'flagellar hook', 'flagellar motor'], 'mass_deriver_key': 'mass_deriver', 'monomer_ids': ['fliG', 'fliM', 'fliN', 'flhA', 'flhB', 'flhD', 'flhC', 'fliO', 'fliP', 'fliQ', 'fliR', 'fliJ', 'fliI', 'fliH', 'fliL', 'flgH', 'motA', 'motB', 'flgB', 'flgC', 'flgF', 'flgG', 'flgI', 'fliF', 'fliE', 'fliC', 'flgL', 'flgK', 'fliD', 'flgE'], 'rates': {'flagellar export apparatus reaction 1': 0.0001, 'flagellar export apparatus reaction 2': 0.0001, 'flagellar hook reaction': 0.0001, 'flagellar motor reaction': 0.0001, 'flagellar motor switch reaction': 0.0001, 'flagellum reaction': 0.0001, 'flhDC': 0.0001}, 'stoichiometry': {'flagellar export apparatus reaction 1': {'flagellar export apparatus subunit': 1.0, 'flhA': -1.0, 'flhB': -1.0, 'fliI': -6.0, 'fliJ': -1.0, 'fliO': -1.0, 'fliP': -1.0, 'fliQ': -1.0, 'fliR': -1.0}, 'flagellar export apparatus reaction 2': {'flagellar export apparatus': 1.0, 'flagellar export apparatus subunit': -1.0, 'fliH': -12.0}, 'flagellar hook reaction': {'flagellar hook': 1, 'flgE': -120.0}, 'flagellar motor reaction': {'flagellar motor': 1.0, 'flagellar motor switch': -1.0, 'flgB': -1.0, 'flgC': -1.0, 'flgF': -1.0, 'flgG': -1.0, 'flgH': -1.0, 'flgI': -1.0, 'fliE': -1.0, 'fliF': -1.0, 'fliL': -2.0, 'motA': -1.0, 'motB': -1.0}, 'flagellar motor switch reaction': {'flagellar motor switch': 1.0, 'fliG': -26.0, 'fliM': -34.0, 'fliN': -1.0}, 'flagellum reaction': {'flagella': 1.0, 'flagellar export apparatus': -1.0, 'flagellar hook': -1, 'flagellar motor': -1.0, 'flgK': -1.0, 'flgL': -1.0, 'fliC': -1.0, 'fliD': -5.0}, 'flhDC': {'flhC': -2.0, 'flhD': -4.0, 'flhDC': 1.0}}, 'time_step': 1.0}

derivers()

name = 'complexation'

next_update(timestep, states)

ports_schema()

vivarium.processes.complexation.build_complexation_stoichiometry(stoichiometry, rates, reaction_ids, monomer_ids, complex_ids)

vivarium.processes.complexation.test_complexation()