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
cplx = m.Complex('A(x~0)')
assert str(cplx) == 'A(x~0)'
assert "elementary_molecule_type=(ElementaryMoleculeType 'A'" in cplx.__str__(all_details=True)
# species
spec = m.Species('A', diffusion_constant_3d = 1e-6)
assert str(spec) == 'A'
assert "diffusion_constant_3d=1e-06" in spec.__str__(True)
# geometry object
box = m.geometry_utils.create_box('box', 1)
#print(len(str(box)))
assert len(str(box)) < 150
#print(len(box.__str__(True)))
assert len(box.__str__(True)) > 150
import mcell as m
from parameters import *
# ---- subsystem ----
b = m.Species(name='b', diffusion_constant_2d=5.00000000000000024e-05)
a = m.Species(name='a', diffusion_constant_3d=9.99999999999999955e-07)
c = m.Species(name='c', diffusion_constant_3d=9.99999999999999955e-07)
react_a_and_b = m.ReactionRule(name='react_a_and_b',
reactants=[
a.inst(orientation=m.Orientation.DOWN),
b.inst(orientation=m.Orientation.UP)
],
products=[],
fwd_rate=1e+08)
subsystem = m.Subsystem()
subsystem.add_species(b)
subsystem.add_species(a)
subsystem.add_species(c)
subsystem.add_reaction_rule(react_a_and_b)
import mcell as m
from parameters import *
# ---- subsystem ----
b = m.Species(name='b', diffusion_constant_3d=4.99999999999999977e-07)
a = m.Species(name='a', diffusion_constant_3d=9.99999999999999955e-07)
c = m.Species(name='c', diffusion_constant_3d=9.99999999999999955e-07)
react_a_and_b = m.ReactionRule(name='react_a_and_b',
reactants=[a.inst(), b.inst()],
products=[],
fwd_rate=5e+08)
subsystem = m.Subsystem()
subsystem.add_species(b)
subsystem.add_species(a)
subsystem.add_species(c)
subsystem.add_reaction_rule(react_a_and_b)
import mcell as m from parameters import * # ---- subsystem ---- a = m.Species(name='a', diffusion_constant_3d=9.99999999999999955e-07) subsystem = m.Subsystem() subsystem.add_species(a)
import os
MCELL_PATH = os.environ.get('MCELL_PATH', '')
if MCELL_PATH:
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
subsystem = m.Subsystem()
model = m.Model()
for o, c in [(subsystem, 's'), (model, 'm')]:
o.add_species(m.Species('A' + c, diffusion_constant_3d=1e-6))
# must give a warning
o.add_species(m.Species('A' + c, diffusion_constant_3d=1e-6))
assert len(o.species) == 1
try:
o.add_species(m.Species('A' + c, diffusion_constant_3d=1e-7))
assert False
except ValueError as err:
print(err)
assert len(o.species) == 1
import sys
import os
MCELL_PATH = os.environ.get('MCELL_PATH', '')
if MCELL_PATH:
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
C = m.Species(name='C(a)')
assert C.to_bngl_str() == 'C(a)'
# there was a bug where setting compartment name in instantiation changed
# the compartment name for Species
inst = C.inst(compartment_name='EC')
assert inst.to_bngl_str() == 'C(a)@EC'
assert C.to_bngl_str() == 'C(a)'
inst = C.inst(compartment_name='EC')
inst.elementary_molecules[0].compartment_name = 'XX'
assert inst.to_bngl_str() == 'C(a)@XX'
assert C.to_bngl_str() == 'C(a)'
# 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 * # ---- subsystem ---- MODEL_PATH = os.path.dirname(os.path.abspath(__file__)) vm = m.Species(name='vm', diffusion_constant_3d=5.00000000000000024e-05) # ---- create subsystem object and add components ---- subsystem = m.Subsystem() subsystem.add_species(vm)
import mcell as m from parameters import * # ---- subsystem ---- vm = m.Species(name='vm', diffusion_constant_3d=1e-05) subsystem = m.Subsystem() subsystem.add_species(vm)
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
subsystem = m.Subsystem()
model = m.Model()
for o, c in [(subsystem, 's'), (model, 'm')]:
# just declarations, expecting that the elementary molecule type
# will be defined before initialization
o.add_species(m.Species('B' + c + '(a,b)'))
# in theory this should not give a warning or error
# but for consistency, we are reporting an error as well
try:
o.add_species(m.Species('B' + c + '(b,a)'))
assert False
except ValueError as err:
print(err)
# this is ok
o.add_species(m.Species('C' + c + '(b,a)'))
# also check that initialization fails
# because we don't know the diffusion constant
try:
import mcell as m
c1_1 = m.ComponentType('C', ['0', '1', 'Z'])
c1_2 = m.ComponentType('C', ['1', '0', 'Z'])
b1 = m.ComponentType('B', ['0', '1', 'Q'])
mt1_1 = m.ElementaryMoleculeType('M', [c1_1, b1], diffusion_constant_3d=1e-6)
mt1_2 = m.ElementaryMoleculeType('M', [b1, c1_2])
mt2 = m.ElementaryMoleculeType('M', [b1, c1_2], diffusion_constant_3d=1e-5)
mt4 = m.ElementaryMoleculeType('N', [b1, b1, c1_1])
mt5 = m.ElementaryMoleculeType('O', [b1, c1_2])
s1_1 = m.Species(
elementary_molecules=[mt1_1.inst([c1_1.inst('0'),
b1.inst('Q')])])
s1_2 = m.Species(
elementary_molecules=[mt1_1.inst([b1.inst('Q'),
c1_1.inst('0')])])
assert s1_1 == s1_2
s1_3 = m.Species(
elementary_molecules=[mt1_2.inst([b1.inst('Q'),
c1_2.inst('0')])])
assert s1_1 == s1_3
s2_1 = m.Species(elementary_molecules=[
mt1_1.inst([c1_1.inst('0'), b1.inst('Q', bond=1)]),
mt4.inst([b1.inst('0'), b1.inst('Q', bond=1),
c1_1.inst('0')])
print("Error: Python module mcell.so or mcell.pyd was not found in "
"directory '" + lib_path + "' constructed from system variable "
"MCELL_PATH.")
sys.exit(1)
else:
print("Error: system variable MCELL_PATH that is used to find the mcell "
"library was not set.")
sys.exit(1)
import mcell as m
subsystem = m.Subsystem()
a = m.Species(
name = 'a', # this species will be called 'a'
diffusion_constant_3d = 1e-6 # 'a' is a volume molecule (diffuses in 3d space)
)
subsystem.add_species(a)
instantiation = m.Instantiation()
rel_a = m.ReleaseSite( # ReleaseSite defines molecule releases
name = 'rel_a',
complex = a,
number_to_release = 10, # 10
location = (0, 0, 0) # all molecules will be released at origin
)
instantiation.add_release_site(rel_a)
model = m.Model()
model.add_subsystem(subsystem) # include information on species
model.add_instantiation(instantiation) # include information on molecule releases
cplx_inst = m.Complex(elementary_molecules=[
CaM.inst([C.inst(2, 1), N.inst(bond=2)]),
CaM.inst([C.inst('Z', 1), N.inst(bond=2)])
])
assert cplx_inst.to_bngl_str() == 'CaM(C~2!1,N!2).CaM(C~Z!1,N!2)'
cplx2 = m.Complex('Ca', compartment_name='CP')
assert cplx2.to_bngl_str() == 'Ca@CP'
cplx3 = m.Complex('A(a!1).B(b!1)', compartment_name='CP')
assert cplx3.to_bngl_str() == '@CP:A(a!1).B(b!1)'
cplx4 = m.Complex('A(a!1)@IN.B(b!1)')
assert cplx4.to_bngl_str() == 'A(a!1)@IN.B(b!1)'
CaMC0N1_species = m.Species(
elementary_molecules=[CaM.inst([C.inst(0), N.inst(1)])])
assert CaMC0N1_species.to_bngl_str() == 'CaM(C~0,N~1)'
d = m.ComponentType('d') # no states
l = m.ComponentType('l')
r = m.ComponentType('r')
Y286 = m.ComponentType('Y286', ['0', 'P'])
S306 = m.ComponentType('S306', ['0', 'P'])
cam = m.ComponentType('cam')
CaMKII = m.ElementaryMoleculeType('CaMKII', [d, r, l, Y286, S306],
diffusion_constant_3d=1e-6)
V = 0.125 * 1e-15 # um^3 -> liters
NA = 6.022e23 / 1e6
k_onCaMKII = 50 / (NA * V) #1/uM 1/s
import mcell as m from parameters import * # ---- subsystem ---- sm = m.Species(name='sm', diffusion_constant_2d=1e-7) subsystem = m.Subsystem() subsystem.add_species(sm)
import sys
import os
MCELL_PATH = os.environ.get('MCELL_PATH', '')
if MCELL_PATH:
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
c1_1 = m.ComponentType('C', ['0', '1', 'Z'])
c1_2 = m.ComponentType('C', ['1', '0', 'Z'])
b1 = m.ComponentType('B', ['0', '1', 'Q'])
mt1_1 = m.ElementaryMoleculeType('M', [c1_1, b1], diffusion_constant_3d=1e-6)
mt2 = m.ElementaryMoleculeType('M', [b1, c1_2], diffusion_constant_3d=1e-5)
# different diffusion constant of used mol type
s5_1 = m.Species(
elementary_molecules=[mt1_1.inst([c1_1.inst('0'),
b1.inst('Q')])])
s5_2 = m.Species(
elementary_molecules=[mt2.inst([c1_1.inst('0'),
b1.inst('Q')])])
assert s5_1 != s5_2
#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
#0000-4)
species_a = m.Species(name='a', diffusion_constant_3d=1e-6)
#0000-5)
release_site_a = m.ReleaseSite(name='rel_a',
complex=species_a,
location=(0, 0, 0),
number_to_release=1)
#0000-6)
viz_output = m.VizOutput(output_files_prefix='./viz_data/seed_00001/Scene', )
#0010-1)
"""
0020-1)
In the previous section we created a simple box inside the
simulation. Simple primitives (cube and icosphere) can
if MCELL_PATH:
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
ITERATIONS = 1000
TIME_STEP = 1e-06
model = m.Model()
a = m.Species(name='a', diffusion_constant_3d=0)
rel_a = m.ReleaseSite(name='rel_a',
complex=a.inst(),
shape=m.Shape.SPHERICAL,
location=(0, 0, 0),
site_diameter=0,
number_to_release=100000)
# ---- configuration ----
model.config.total_iterations = ITERATIONS
model.add_species(a)
model.config.memory_limit_gb = 1
import os
MCELL_PATH = os.environ.get('MCELL_PATH', '')
if MCELL_PATH:
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
model = m.Model()
a = m.Species('a', diffusion_constant_3d=1e-6)
model.add_species(a)
s1 = model.find_species('a')
assert s1 is not None and s1.name == 'a'
s2 = model.find_species('b')
assert s2 is None
r = m.ReactionRule('r', [a.inst()], [], 0)
model.add_reaction_rule(r)
r1 = model.find_reaction_rule('r')
assert r1 is not None and r1.name == 'r'
r2 = model.find_reaction_rule('s')
assert r2 is None
sc = m.SurfaceClass('sc',
type=m.SurfacePropertyType.TRANSPARENT,
print(
"Error: variable MCELL_PATH that is used to find the mcell library was not set."
)
sys.exit(1)
import mcell as m
from parameters import *
SEED = 1
ITERATIONS = 20
model = m.Model()
# subsystem
species_a = m.Species(name='a', diffusion_constant_3d=1e-06)
species_b = m.Species(name='b', diffusion_constant_3d=1e-06)
subsystem = m.Subsystem()
model.add_species(species_a)
model.add_species(species_b)
# geometry
box_inner = m.geometry_utils.create_box('box_inner', 0.3)
box_outer = m.geometry_utils.create_box('box_outer', 0.6)
model.add_geometry_object(box_inner)
model.add_geometry_object(box_outer)
# instantiation
