'/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 ----
