'/rxn.box2.dat', every_n_timesteps=1) count_box1_or_box2 = m.Count(expression=m.CountTerm(reaction_rule=rxn, region=box1 + box2), file_name='./react_data/seed_' + str(SEED).zfill(5) + '/rxn.box1_or_box2.dat', every_n_timesteps=1) count_box1_minus_box2 = m.Count(expression=m.CountTerm(reaction_rule=rxn, region=box1 - box2), file_name='./react_data/seed_' + str(SEED).zfill(5) + '/rxn.box1_or_box2.dat', every_n_timesteps=1) # ---- create observables object and add components ---- observables = m.Observables() observables.add_viz_output(viz_output) observables.add_count(count_all) observables.add_count(count_box1) observables.add_count(count_box1_sr1) observables.add_count(count_box1_sr2) observables.add_count(count_box2) observables.add_count(count_box1_or_box2) observables.add_count(count_box1_sr1_only) observables.add_count(count_box1_sr2_only) observables.add_count(count_box1_sr1_and_sr2)
box_no_compartment = m.geometry_utils.create_box('box_no_compartment', MCELL_NO_COMPARTMENT_SIZE) instantiation = m.Instantiation() instantiation.load_bngl_compartments_and_seed_species('test.bngl', box_no_compartment) instantiation.add_geometry_object(box_no_compartment) assert (len(instantiation.release_sites) == 2) viz_output = m.VizOutput(mode=m.VizMode.ASCII, output_files_prefix='./viz_data/seed_' + str(SEED).zfill(5) + '/Scene', every_n_timesteps=1) observables = m.Observables() observables.load_bngl_observables( 'test.bngl', './react_data/seed_' + str(SEED).zfill(5) + '/counts.gdat') observables.add_viz_output(viz_output) observables2 = m.Observables() observables2.load_bngl_observables( 'test.bngl', './react_data/seed_' + str(SEED).zfill(5) + '/counts2.gdat') for c in observables2.counts: c.name = c.name + '2' assert (len(observables.counts) == 6) model = m.Model() # ---- configuration ----