"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,
affected_complex_pattern=a)
model.add_surface_class(sc)
sc1 = model.find_surface_class('sc')
assert sc1 is not None and sc1.name == 'sc'
sc2 = model.find_surface_class('scx')
assert sc2 is None
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)
# 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__))
react_a_plus_b = m.ReactionRule(name='react_a_plus_b',
reactants=[m.Complex('a'),
m.Complex('b')],
products=[m.Complex('c')],
variable_rate=var_rate_react_a_plus_b_0)
# ---- create subsystem object and add components ----
subsystem = m.Subsystem()
subsystem.add_reaction_rule(react_a_plus_b)
# load subsystem information from bngl file
subsystem.load_bngl_molecule_types_and_reaction_rules(
os.path.join(MODEL_PATH, 'model.bngl'), shared.parameter_overrides)
# set additional information about species and molecule types that cannot be stored in BNGL,
# elementary molecule types are already in the subsystem after they were loaded from BNGL
import os
import shared
import mcell as m
from parameters import *
# ---- subsystem ----
MODEL_PATH = os.path.dirname(os.path.abspath(__file__))
empty = m.SurfaceClass(name='empty', type=m.SurfacePropertyType.REACTIVE)
unnamed_reaction_rule_0 = m.ReactionRule(
name='unnamed_reaction_rule_0',
reactants=[
m.Complex('vol1', orientation=m.Orientation.DOWN),
m.Complex('empty', orientation=m.Orientation.UP)
],
products=[m.Complex('vol2', orientation=m.Orientation.UP)],
fwd_rate=1e7)
# ---- create subsystem object and add components ----
subsystem = m.Subsystem()
subsystem.add_surface_class(empty)
subsystem.add_reaction_rule(unnamed_reaction_rule_0)
# load subsystem information from bngl file
subsystem.load_bngl_molecule_types_and_reaction_rules(
os.path.join(MODEL_PATH, 'model.bngl'), shared.parameter_overrides)
# ---- add components ----
model.add_geometry_object(Cube)
model.load_bngl('model.bngl', '', Cube)
surf = m.SurfaceClass(
name = 'surf',
type = m.SurfacePropertyType.REACTIVE
)
rxn = m.ReactionRule(
name = 'rxn',
reactants = [ m.Complex('v', orientation = m.Orientation.DOWN), m.Complex('surf', orientation = m.Orientation.UP) ],
products = [ m.Complex('s', orientation = m.Orientation.UP) ],
fwd_rate = 1e+07
)
Cube_membrane.surface_class = surf
model.add_surface_class(surf)
model.add_reaction_rule(rxn)
# ---- initialization and execution ----
model.initialize()
if DUMP:
model.dump_internal_state()
rxn_rule = m.ReactionRule(
name="sixth rxn",
rev_name="sixth rxn rev",
reactants=[
m.Complex(elementary_molecules=[
CaMKII.inst([
l.inst(),
r.inst(),
Y286.inst('0'),
cam.inst(bond=m.BOND_BOUND)
])
]),
m.Complex(elementary_molecules=[
CaMKII.inst([l.inst(
), r.inst(), cam.inst(bond=m.BOND_BOUND)])
])
],
products=[
m.Complex(elementary_molecules=[
CaMKII.inst([
l.inst(1, bond=1),
r.inst(),
Y286.inst('0'),
cam.inst(bond=m.BOND_BOUND)
]),
CaMKII.
inst([l.inst(
), r.inst(
bond=1), cam.inst(bond=m.BOND_BOUND)])
])
],
fwd_rate=k_onCaMKII,
rev_rate=k_offCaMKII)
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)
react_a_to_b = m.ReactionRule(name='react_a_to_b',
reactants=[a.inst()],
products=[b.inst()],
variable_rate=var_rate_react_a_to_b_1)
subsystem = m.Subsystem()
subsystem.add_species(b)
subsystem.add_species(a)
subsystem.add_reaction_rule(react_a_to_b)
