from parameters import *
from subsystem import *
from geometry import *
MODEL_PATH = os.path.dirname(os.path.abspath(__file__))
# ---- observables ----
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
output_files_prefix='./viz_data/seed_' +
str(SEED).zfill(5) + '/Scene',
every_n_timesteps=1)
rxn = subsystem.find_reaction_rule('a_plus_b')
assert rxn
count_all = m.Count(expression=m.CountTerm(reaction_rule=rxn),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/rxn.all.dat',
every_n_timesteps=1)
count_box1 = m.Count(expression=m.CountTerm(reaction_rule=rxn, region=box1),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/rxn.box1.dat',
every_n_timesteps=1)
count_box1_sr1 = m.Count(expression=m.CountTerm(reaction_rule=rxn,
region=box1_sr1),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/rxn.box1_sr1.dat',
every_n_timesteps=1)
# ---- default configuration overrides ----
if customization and 'custom_config' in dir(customization):
# user-defined model configuration
customization.custom_config(model)
# ---- add components ----
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
output_files_prefix='./viz_data/seed_' +
str(parameters.SEED).zfill(5) + '/Scene',
every_n_timesteps=1)
model.add_viz_output(viz_output)
count_Syk_CP = m.Count(
expression=m.CountTerm(molecules_pattern=m.Complex('Syk@CP')),
file_name='./react_data/seed_' + str(parameters.SEED).zfill(5) +
'/Syk.dat',
every_n_timesteps=1)
model.add_count(count_Syk_CP)
model.add_subsystem(subsystem.subsystem)
model.add_instantiation(instantiation.instantiation)
# ---- initialization and execution ----
if customization and 'custom_init_and_run' in dir(customization):
customization.custom_init_and_run(model)
else:
model.initialize()
sys.path.append(os.path.join(MCELL_PATH, 'lib'))
else:
print(
"Error: variable MCELL_PATH that is used to find the mcell library was not set."
)
sys.exit(1)
import mcell as m
params = m.bngl_utils.load_bngl_parameters('test.bngl')
box1 = m.geometry_utils.create_box('box1', 0.5)
box2 = m.geometry_utils.create_box('box2', 1)
box3 = m.geometry_utils.create_box('box3', 1.5)
ct_box2 = m.CountTerm(species_pattern=m.Complex('A'), region=box2)
ct_box1 = m.CountTerm(species_pattern=m.Complex('A'), region=box1)
ct_box2_minus_ct_box1 = ct_box2 - ct_box1
# setting region that will be ignored
ct_box2_minus_ct_box1.region = box3
count = m.Count(name='z', expression=ct_box2_minus_ct_box1, file_name='x.dat')
# ---- load bngl file ----
# must be checked during initialization
model = m.Model()
model.load_bngl('test.bngl')
import shared
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
MODEL_PATH = os.path.dirname(os.path.abspath(__file__))
# ---- observables ----
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
output_files_prefix='./viz_data/seed_' +
str(SEED).zfill(5) + '/Scene',
every_n_timesteps=1)
count_all = m.Count(expression=m.CountTerm(species_pattern=sm.inst()),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/sm.all.dat',
every_n_timesteps=1)
count_box1 = m.Count(expression=m.CountTerm(species_pattern=sm.inst(),
region=box1),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/sm.box1.dat',
every_n_timesteps=1)
count_box1_sr1 = m.Count(expression=m.CountTerm(species_pattern=sm.inst(),
region=box1_sr1),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/sm.box1_sr1.dat',
every_n_timesteps=1)
assert ct.states == ['0']
assert ct2.states == ['X', 'Y']
# vector2
ct3 = m.ComponentType('u', states=['0', '1'])
ct4 = copy.copy(ct3)
ct4.states[0] = 'X'
assert ct3.states == ['0', '1']
assert ct4.states == ['X', '1']
# object that has all defaults set but requires
# to be set to pass sematic check
# checking only that cloning passes
cnt = m.Count(expression=m.CountTerm(species_pattern=m.Complex('Z')),
file_name='x.dat')
cnt2 = copy.copy(cnt)
# checking that we are not doing deep copy
rs = m.ReleaseSite(name='test',
complex=m.Complex('A'),
shape=m.Shape.SPHERICAL,
location=(1, 2, 3),
number_to_release=1000)
rs2 = copy.copy(rs)
rs2.complex.name = 'B'
# both variants must stay the same
assert rs.complex.name == 'B'
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- observables ----
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
output_files_prefix='./viz_data/seed_' +
str(get_seed()).zfill(5) + '/Scene',
every_n_timesteps=1)
# declaration of rxn rules defined in BNGL and used in counts
count_react_a_plus_b = m.Count(
expression=m.CountTerm(
reaction_rule=subsystem.find_reaction_rule('a_plus_b')),
file_name='./react_data/seed_' + str(get_seed()).zfill(5) +
'/react_a_plus_b.World.dat',
every_n_timesteps=9.99999999999999955e-07 / 1e-06)
observables = m.Observables()
observables.add_viz_output(viz_output)
observables.add_count(count_react_a_plus_b)
# WARNING: This is an automatically generated file and will be overwritten
# by CellBlender on the next model export.
import os
import mcell as m
MODEL_PATH = os.path.dirname(os.path.abspath(__file__))
from parameters import *
from subsystem import *
from geometry import *
# ---- observables ----
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
output_files_prefix='./viz_data/seed_' +
str(SEED).zfill(5) + '/Scene',
every_n_timesteps=1)
count_a = m.Count(expression=m.CountTerm(species_pattern=m.Complex('a')),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/a.dat')
# ---- create observables object and add components ----
observables = m.Observables()
observables.add_count(count_a)
observables.add_viz_output(viz_output)
location=(0, 0, 0),
site_diameter=0,
number_to_release=2)
model.add_release_site(rel_a)
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
output_files_prefix='./viz_data/seed_' +
str(parameters.SEED).zfill(5) + '/Scene',
every_n_timesteps=1)
model.add_viz_output(viz_output)
count = m.Count(name='a',
file_name='./react_data/seed_' +
str(parameters.SEED).zfill(5) + '/a.gdat',
expression=m.CountTerm(species_pattern=a.inst(), ))
model.add_count(count)
# ---- configuration ----
model.config.time_step = parameters.TIME_STEP
model.config.seed = parameters.SEED
model.config.total_iterations = parameters.ITERATIONS
model.notifications.rxn_and_species_report = True
model.config.partition_dimension = 10
model.config.subpartition_dimension = 2.5
# ---- default configuration overrides ----
from geometry import *
MODEL_PATH = os.path.dirname(os.path.abspath(__file__))
# ---- observables ----
viz_output = m.VizOutput(
mode = m.VizMode.ASCII,
output_files_prefix = './viz_data/seed_' + str(SEED).zfill(5) + '/Scene',
every_n_timesteps = 1
)
# ---- declaration of rxn rules defined in BNGL and used in counts ----
cterm_count_react_a_plus_b = m.CountTerm(
reaction_rule = react_a_plus_b
)
count_react_a_plus_b_World = m.Count(
name = 'react_a_plus_b.World',
expression = cterm_count_react_a_plus_b,
file_name = './react_data/seed_' + str(SEED).zfill(5) + '/react_a_plus_b.World.dat',
every_n_timesteps = 9.99999999999999955e-07/1e-06
)
# ---- create observables object and add components ----
observables = m.Observables()
observables.add_viz_output(viz_output)
observables.add_count(count_react_a_plus_b_World)
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
MODEL_PATH = os.path.dirname(os.path.abspath(__file__))
# ---- observables ----
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
output_files_prefix='./viz_data/seed_' +
str(SEED).zfill(5) + '/Scene',
every_n_timesteps=1)
count_all = m.Count(expression=m.CountTerm(species_pattern=vm.inst()),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/vm.all.dat',
every_n_timesteps=1)
count_box1 = m.Count(expression=m.CountTerm(species_pattern=vm.inst(),
region=box1),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/vm.box1.dat',
every_n_timesteps=1)
count_box2 = m.Count(expression=m.CountTerm(species_pattern=vm.inst(),
region=box2),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/vm.box2.dat',
every_n_timesteps=1)
from parameters import *
from subsystem import *
from geometry import *
MODEL_PATH = os.path.dirname(os.path.abspath(__file__))
# ---- observables ----
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
output_files_prefix='./viz_data/seed_' +
str(SEED).zfill(5) + '/Scene',
every_n_timesteps=1)
rxn = subsystem.find_reaction_rule('a_plus_b')
assert rxn
count_all = m.Count(expression=m.CountTerm(reaction_rule=rxn),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/rxn.all.dat',
every_n_timesteps=1)
count_box1 = m.Count(expression=m.CountTerm(reaction_rule=rxn, region=box1),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/rxn.box1.dat',
every_n_timesteps=1)
count_box2 = m.Count(expression=m.CountTerm(reaction_rule=rxn, region=box2),
file_name='./react_data/seed_' + str(SEED).zfill(5) +
'/rxn.box2.dat',
every_n_timesteps=1)
count_only_box1 = m.Count(expression=m.CountTerm(reaction_rule=rxn,
# ---- observables ----
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
output_files_prefix='./viz_data/seed_' +
str(get_seed()).zfill(5) + '/Scene',
every_n_timesteps=1)
# declaration of rxn rules defined in BNGL and used in counts
react_a_plus_b = subsystem.find_reaction_rule('react_a_plus_b')
assert react_a_plus_b, "Reaction rule 'react_a_plus_b' was not found"
react_b_plus_c = subsystem.find_reaction_rule('react_b_plus_c')
assert react_b_plus_c, "Reaction rule 'react_b_plus_c' was not found"
count_a_Cube1 = m.Count(
expression=m.CountTerm(molecules_pattern=m.Complex('a'), region=Cube1),
file_name='./react_data/seed_' + str(get_seed()).zfill(5) + '/a.Cube1.dat',
every_n_timesteps=0 # used only manually
)
count_a_Cube2 = m.Count(
expression=m.CountTerm(molecules_pattern=m.Complex('a'), region=Cube2),
file_name='./react_data/seed_' + str(get_seed()).zfill(5) + '/a.Cube2.dat',
every_n_timesteps=0 # used only manually
)
count_a_Cube3 = m.Count(
expression=m.CountTerm(molecules_pattern=m.Complex('a'), region=Cube3),
file_name='./react_data/seed_' + str(get_seed()).zfill(5) + '/a.Cube3.dat',
every_n_timesteps=0 # used only manually
)