# 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)
# WARNING: This is an automatically generated file and will be overwritten
# by CellBlender on the next model export.
import os
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.CELLBLENDER,
output_files_prefix='./viz_data/seed_' +
str(SEED).zfill(5) + '/Scene',
every_n_timesteps=SAMPLING_PERIODICITY)
# ---- create observables object and add components ----
observables = m.Observables()
observables.load_bngl_observables(
os.path.join(MODEL_PATH, 'model.bngl'),
'./react_data/seed_' + str(SEED).zfill(5) + '/')
#observables.add_viz_output(viz_output)
for count in observables.counts:
count.every_n_timesteps = SAMPLING_PERIODICITY
except EOFError:
mol_file.close()
break
return mol_dict
# create main model object (empty)
model = m.Model()
model.load_bngl('model.bngl')
SEED = 0
prefix = './viz_data/seed_' + str(SEED).zfill(5) + '/Scene'
viz_output = m.VizOutput(mode=m.VizMode.CELLBLENDER,
output_files_prefix=prefix)
model.add_viz_output(viz_output)
model.config.total_iterations = 1
# ---- initialization and execution ----
model.initialize()
model.run_iterations(1)
model.end_simulation()
# read cellbnder viz output
mol_dict = read_cellblender_viz_output(prefix + '.cellbin.1.dat')
def assert_eq(a, b):
#0000-2)
MCELL_PATH = os.environ.get('MCELL_PATH', '')
if MCELL_PATH:
lib_path = os.path.join(MCELL_PATH, 'lib')
sys.path.append(lib_path)
else:
print("Error: system variable MCELL_PATH that is used to find the mcell "
"library was not set.")
sys.exit(1)
#0000-3)
import mcell as m
#0000-6)
viz_output = m.VizOutput(output_files_prefix='./viz_data/seed_00001/Scene', )
#0030-1)
o1v = m.geometry_utils.create_icosphere(name='O1V', radius=0.3, subdivisions=4)
#0030-2)
o1v.translate((0, -0.2, 0))
#0040-1)
cyt = m.geometry_utils.create_icosphere(name='CYT', radius=0.6, subdivisions=4)
"""
0060-1)
We will add a second organelle and move it a bit to the right.
"""
o2v = m.geometry_utils.create_icosphere(name='O2V', radius=0.2, subdivisions=4)
o2v.translate((0, 0.35, 0))
