def rxn_callback(rxn_info, model):
assert rxn_info.type == m.ReactionType.VOLUME_SURFACE
# we will be moving in the direction
# of the wall's normal
w = model.get_wall(rxn_info.geometry_object, rxn_info.wall_index)
# simplified computtation of offset, valid only for this test, for
# a correct implementation see pymcell4/2321_release_triggered_by_surf_rxn_multiple
pos = rxn_info.pos3d + m.Vec3(-0.005, -0.005, -0.005)
# it is also possible to move it in the direction of the unit normal
#pos = rxn_info.pos3d + w.unit_normal * m.Vec3(-0.005, -0.005, -0.005)
# release molecules
rel_a = m.ReleaseSite(
name = 'rel_c',
complex = subsystem.c.inst(),
shape = m.Shape.SPHERICAL,
location = pos.to_list(),
site_diameter = 0,
number_to_release = 10,
release_time = rxn_info.time
)
model.release_molecules(rel_a)
def rxn_callback(rxn_info, model):
assert rxn_info.type == m.ReactionType.VOLUME_SURFACE
# we will be moving in the direction
# of the wall's normal
w = model.get_wall(rxn_info.geometry_object, rxn_info.wall_index)
# MCell3 (reference model) mdl_mcell3/2310_release_triggered_by_surf_rxn_single
# computes position like this:
pos = rxn_info.pos3d + rotate_about_normal(w.unit_normal,
m.Vec3(-0.005, -0.005, -0.005))
# it is also possible to move it in the direction of the unit normal
#pos = rxn_info.pos3d + w.unit_normal * m.Vec3(-0.005, -0.005, -0.005)
# release molecules
rel_a = m.ReleaseSite(name='rel_c',
complex=subsystem.c.inst(),
shape=m.Shape.SPHERICAL,
location=pos.to_list(),
site_diameter=0,
number_to_release=10,
release_time=rxn_info.time)
model.release_molecules(rel_a)
def rxn_callback(rxn_info, model):
#print(rxn_info)
# release molecules
rel_a = m.ReleaseSite(
name='rel_c',
complex=subsystem.c.inst(),
shape=m.Shape.SPHERICAL,
# MCell3 uses the location as offset
location=(rxn_info.pos3d + m.Vec3(0.005, 0, 0)).to_list(),
site_diameter=0,
number_to_release=10,
release_time=rxn_info.time)
model.release_molecules(rel_a)
# WARNING: This is an automatically generated file and will be overwritten
# by CellBlender on the next model export.
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
Release_of_Syk_ps_a_Y_l_Y_tSH2_pe_CP_at_CP = m.ReleaseSite(
name='Release_of_Syk_ps_a_Y_l_Y_tSH2_pe_CP_at_CP',
complex=m.Complex('Syk(a~Y,l~Y,tSH2)'),
region=CP,
number_to_release=20)
# ---- surface classes assignment ----
# ---- compartments assignment ----
default_compartment.is_bngl_compartment = True
EC.is_bngl_compartment = True
CP.is_bngl_compartment = True
CP.surface_compartment_name = 'PM'
# ---- create instantiation object and add components ----
model = m.Model()
# add geometry
box = m.geometry_utils.create_box('box', 1)
model.add_geometry_object(box)
# load our BNGL file and set directory for BNGL observables
model.load_bngl('model.bngl', './react_data/seed_' + str(SEED).zfill(5) + '/')
# set initial count of molecules so that we won't get to copy nr 0 when removing them
# (remove more than exists is ok - in that case all molecules of given species are removed,
# but this would not give us the nice sinusiodal function)
rel = m.ReleaseSite(
name='rel_A_initial',
complex=m.Complex('A'),
region=box,
number_to_release=1000,
# and do each release each iteration
release_time=0)
model.add_release_site(rel)
# define release pattern
for i in range(ITERATIONS):
rel = m.ReleaseSite(
name='rel_A_' + str(i),
complex=m.Complex('A'),
region=box,
# we would like the number of moleucles in the system to follow the sinus curve,
# derivative of that is cos, number to release is truncated to an integer, may be negative
number_to_release=100 * math.cos(i / 10),
# and do each release each iteration
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
Tetrahedron_rel = m.ReleaseSite(
name = 'Tetrahedron_rel',
complex = sm.inst(orientation = m.Orientation.UP),
region = Tetrahedron,
number_to_release = 10
)
# ---- surface classes assignment ----
# ---- instantiation data ----
instantiation = m.Instantiation()
instantiation.add_geometry_object(Tetrahedron)
instantiation.add_release_site(Tetrahedron_rel)
# 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__))
box1_sr1_rel = m.ReleaseSite(name='box1_sr1_rel',
complex=sm.inst(),
region=box1_sr1,
number_to_release=4)
box1_sr2_rel = m.ReleaseSite(name='box1_sr2_rel',
complex=sm.inst(),
region=box1_sr2,
number_to_release=6)
# TODO: release on difference, union, and intersection
box2_rel = m.ReleaseSite(name='box2_rel',
complex=sm.inst(),
region=box2,
number_to_release=8)
# ---- create instantiation object and add components ----
import mcell as m
# numerical attribute
c = m.Color(red=1, green=0, blue=0, alpha=1)
c2 = copy.copy(c)
c2.red = 0.5
# check that the original object is correct
assert c.red == 1
assert c2.red == 0.5
# object
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 = m.Complex('B')
assert rs.complex.to_bngl_str() == 'A'
assert rs2.complex.to_bngl_str() == 'B'
# vector
ct = m.ComponentType('u', states=['0'])
ct2 = copy.copy(ct)
ct2.states = ['X', 'Y']
#!/usr/bin/env python3
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
model = m.Model()
a = m.Species('a', diffusion_constant_3d = 1e-6)
model.add_species(a)
rs = m.ReleaseSite('rel_a', a, location = (0, 0, 0), number_to_release = 1)
model.add_release_site(rs)
model.initialize()
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
model.initialize() # initialize simulation state
model.run_iterations(10) # simulate 10 iterations
model.end_simulation() # final simulation step
# does not check anything
model = m.Model()
a = m.Species(
name = 'a',
diffusion_constant_3d = 9.99999999999999955e-07
)
# ---- create subsystem object and add components ----
model.add_species(a)
rel_a = m.ReleaseSite(
name = 'rel_a',
complex = a.inst(),
# shape = m.Shape.SPHERICAL, # - must work even without this specification
location = (0, 0, 0),
site_diameter = 0,
number_to_release = 2
)
model.add_release_site(rel_a)
sphere = m.geometry_utils.create_icosphere('sphere', 0.1, 3)
model.add_geometry_object(sphere)
viz_output = m.VizOutput(
mode = m.VizMode.ASCII,
output_files_prefix = './viz_data/seed_' + str(parameters.SEED).zfill(5) + '/Scene',
from geometry import *
MODEL_PATH = os.path.dirname(os.path.abspath(__file__))
# ---- instantiation ----
# ---- release sites ----
# ---- surface classes assignment ----
Plane.surface_class = empty
# ---- compartments assignment ----
vol1_rel = m.ReleaseSite(
name = 'vol1_rel',
complex = m.Complex('vol1'),
region = Cube,
number_to_release = 2000
)
# ---- create instantiation object and add components ----
instantiation = m.Instantiation()
instantiation.add_geometry_object(Plane)
instantiation.add_geometry_object(Cube)
instantiation.add_release_site(vol1_rel)
# load seed species information from bngl file
instantiation.load_bngl_compartments_and_seed_species(os.path.join(MODEL_PATH, 'model.bngl'), None, shared.parameter_overrides)
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
rel_a = m.ReleaseSite(name='rel_a',
complex=a.inst(),
shape=m.Shape.SPHERICAL,
location=(0, 0, 0),
site_diameter=0,
number_to_release=100)
rel_a120 = m.ReleaseSite(name='rel_a120',
complex=a.inst(),
shape=m.Shape.SPHERICAL,
location=(0, 0, 0),
site_diameter=0,
number_to_release=100,
release_time=120 * TIME_STEP)
# ---- surface classes assignment ----
# ---- compartments assignment ----
# ---- instantiation data ----
from subsystem import *
from geometry import *
MODEL_PATH = os.path.dirname(os.path.abspath(__file__))
# ---- instantiation ----
# ---- release sites ----
# ---- surface classes assignment ----
box_bottom.surface_class = reflect_edge
# ---- compartments assignment ----
rel_m = m.ReleaseSite(
name = 'rel_m',
complex = m.Complex('M'),
region = box_bottom,
number_to_release = 3755
)
# ---- create instantiation object and add components ----
instantiation = m.Instantiation()
instantiation.add_geometry_object(box)
instantiation.add_release_site(rel_m)
# load seed species information from bngl file
instantiation.load_bngl_compartments_and_seed_species(os.path.join(MODEL_PATH, 'model.bngl'), None, shared.parameter_overrides)
output_files_prefix='./viz_data/seed_' +
str(SEED).zfill(5) + '/Scene',
every_n_timesteps=5000)
model.add_viz_output(viz_output)
gdat_file = ''
if 'GDAT' in params and params['GDAT'] == 1:
gdat_file = os.path.splitext(bngl_file)[0] + '.gdat'
model.load_bngl(bngl_file,
'./react_data/seed_' + str(SEED).zfill(5) + '/' + gdat_file,
default_compartment)
rel_site = m.ReleaseSite(
name='x',
complex=m.Complex('A@PM'),
#shape = model.find_geometry_object('CP'),
number_to_release=12345678900)
model.add_release_site(rel_site)
# ---- configuration ----
model.config.time_step = TIME_STEP
model.config.seed = SEED
model.config.total_iterations = ITERATIONS
model.config.partition_dimension = MCELL_DEFAULT_COMPARTMENT_EDGE_LENGTH
model.config.subpartition_dimension = MCELL_DEFAULT_COMPARTMENT_EDGE_LENGTH
model.initialize()
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__))
instantiation = m.Instantiation()
for mol in ['A', 'B']:
cplx = m.Complex(mol)
box1_only_rel = m.ReleaseSite(name='box1_only_rel_' + mol,
complex=cplx,
region=box1 - box2,
number_to_release=50)
box2_only_rel = m.ReleaseSite(name='box2_only_rel_' + mol,
complex=cplx,
region=box2 - box1,
number_to_release=60)
both_only_rel = m.ReleaseSite(name='both_only_rel_' + mol,
complex=cplx,
region=box1 * box2,
number_to_release=80)
instantiation.add_release_site(box1_only_rel)
instantiation.add_release_site(box2_only_rel)
instantiation.add_release_site(both_only_rel)
lipid_raft_A = m.SurfaceClass(name='lipid_raft_A',
type=m.SurfacePropertyType.REFLECTIVE,
affected_complex_pattern=m.Complex('A'))
lipid_raft_B = m.SurfaceClass(name='lipid_raft_B',
type=m.SurfacePropertyType.REFLECTIVE,
affected_complex_pattern=m.Complex('B'))
model.add_surface_class(lipid_raft_A)
model.add_surface_class(lipid_raft_B)
Sphere1_right.surface_class = lipid_raft_A
Sphere2_left.surface_class = lipid_raft_B
# release molecules in specified regions
rel_A = m.ReleaseSite(name='rel_A',
complex=m.Complex('A', orientation=m.Orientation.UP),
region=Sphere1_right,
number_to_release=350)
rel_B = m.ReleaseSite(name='rel_B',
complex=m.Complex('B', orientation=m.Orientation.UP),
region=Sphere2_left,
number_to_release=350)
model.add_release_site(rel_A)
model.add_release_site(rel_B)
# must be 1 for visualization to work correctly (for now)
VIZ_FREQUENCY = 1
# viz output to visualize molecules
viz_output = m.VizOutput(mode=m.VizMode.ASCII,
# 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__))
box1_only_rel = m.ReleaseSite(name='box1_only_rel',
complex=vm.inst(),
region=box1 - box2,
number_to_release=4)
box2_only_rel = m.ReleaseSite(name='box2_only_rel',
complex=vm.inst(),
region=box2 - box1,
number_to_release=6)
both_only_rel = m.ReleaseSite(name='both_only_rel',
complex=vm.inst(),
region=box1 * box2,
number_to_release=8)
# ---- create instantiation object and add components ----
instantiation = m.Instantiation()
instantiation.add_geometry_object(box1)
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
rel_a = m.ReleaseSite(name='rel_a',
complex=vm,
shape=m.Shape.SPHERICAL,
location=(0, 0, 0),
site_diameter=0,
number_to_release=100)
# ---- surface classes assignment ----
# ---- instantiation data ----
instantiation = m.Instantiation()
instantiation.add_geometry_object(Tetrahedron)
instantiation.add_release_site(rel_a)
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
rel_a1 = m.ReleaseSite(name='rel_a1',
complex=m.Complex('a'),
shape=m.Shape.SPHERICAL,
location=(0, 0, 0),
site_diameter=0,
number_to_release=20)
rel_a2 = m.ReleaseSite(name='rel_a2',
complex=m.Complex('a'),
shape=m.Shape.SPHERICAL,
location=(0.14999999999999999, 0, 0),
site_diameter=0,
number_to_release=20)
rel_a3 = m.ReleaseSite(name='rel_a3',
complex=m.Complex('a'),
shape=m.Shape.SPHERICAL,
location=(0.25, 0, 0),
site_diameter=0,
number_to_release=20)
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__))
instantiation = m.Instantiation()
for mol in ['A', 'B']:
cplx = m.Complex(mol)
box1_sr1_rel = m.ReleaseSite(name='box1_sr1_rel_' + mol,
complex=cplx,
region=box1_sr1,
number_to_release=40)
box1_sr2_rel = m.ReleaseSite(name='box1_sr2_rel' + mol,
complex=cplx,
region=box1_sr2,
number_to_release=60)
box2_rel = m.ReleaseSite(name='box2_rel' + mol,
complex=cplx,
region=box2,
number_to_release=30)
instantiation.add_release_site(box1_sr1_rel)
instantiation.add_release_site(box1_sr2_rel)
instantiation.add_release_site(box2_rel)
# by CellBlender on the next model export.
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
rel_a = m.ReleaseSite(
name = 'rel_a',
complex = a.inst(),
shape = m.Shape.SPHERICAL,
location = (0, 0, 0),
site_diameter = 0,
number_to_release = 100
)
rel_b = m.ReleaseSite(
name = 'rel_b',
complex = b.inst(),
shape = m.Shape.SPHERICAL,
location = (5.0000000000000001e-03, 0, 0),
site_diameter = 0,
number_to_release = 100
)
rel_sd = m.ReleaseSite(
name = 'rel_sd',
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
rel_a = m.ReleaseSite(
name = 'rel_a',
complex = a.inst(),
shape = m.Shape.SPHERICAL,
location = (0, 0, 0),
site_diameter = 0,
number_to_release = 9
)
rel_b = m.ReleaseSite(
name = 'rel_b',
complex = b.inst(),
shape = m.Shape.SPHERICAL,
location = (1.00000000000000002e-02, 0, 0),
site_diameter = 0,
number_to_release = 9
)
# ---- surface classes assignment ----
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
# single property
rs1 = m.ReleaseSite('rel1',
complex=m.Complex('X(y!1).Y(x!1)'),
shape=m.Shape.SPHERICAL,
location=(1, 1, 1),
number_to_release=10)
rs2 = m.ReleaseSite('rel1',
complex=m.Complex('X(y!1).Y(x!1)'),
shape=m.Shape.SPHERICAL,
location=(0.1, 0.1, 0.1),
number_to_release=10)
assert rs1 != rs2
rs3 = m.ReleaseSite('rel1',
complex=m.Complex('Y(x!1).X(y!1)'),
shape=m.Shape.SPHERICAL,
location=(1, 1, 1),
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
rel_a = m.ReleaseSite(name='rel_a',
complex=a.inst(),
shape=m.Shape.SPHERICAL,
location=(0, 0, 0),
site_diameter=0,
number_to_release=10)
rel_b = m.ReleaseSite(name='rel_b',
complex=b.inst(orientation=m.Orientation.UP),
region=Cube,
number_to_release=80)
# ---- surface classes assignment ----
# ---- compartments assignment ----
# ---- instantiation data ----
instantiation = m.Instantiation()
instantiation.add_geometry_object(Cube)
instantiation.add_release_site(rel_a)
model.config.time_step = TIME_STEP
model.config.seed = SEED
model.config.total_iterations = ITERATIONS
model.config.partition_dimension = 10
model.config.subpartition_dimension = 2.5
# ---- add components ----
# TODO viz without any molecules does not work yet
a = m.Species(name='a', diffusion_constant_3d=1e-6)
model.add_species(a)
rel = m.ReleaseSite(name='rel',
complex=a,
shape=m.Shape.SPHERICAL,
location=(8, 8, 8),
site_diameter=0,
number_to_release=1)
model.add_release_site(rel)
model.add_geometry_object(Sphere1)
model.add_geometry_object(Sphere2)
model.add_observables(observables)
# ---- initialization and execution ----
model.initialize()
if DUMP:
model.dump_internal_state()
# WARNING: This is an automatically generated file and will be overwritten
# by CellBlender on the next model export.
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
rel_A = m.ReleaseSite(name='rel_A',
complex=m.Complex('A', orientation=m.Orientation.UP),
region=up,
number_to_release=100)
rel_B = m.ReleaseSite(name='rel_B',
complex=m.Complex('B', orientation=m.Orientation.UP),
region=bottom,
number_to_release=100)
# ---- surface classes assignment ----
# ---- compartments assignment ----
# ---- create instantiation object and add components ----
instantiation = m.Instantiation()
instantiation.add_geometry_object(up)
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)
rs = m.ReleaseSite(
'rel_a', a,
shape = m.Shape.SPHERICAL,
location = (0, 0, 0),
number_to_release = 10
)
model.add_release_site(rs)
model.initialize()
model.run_iterations(1)
all_ids = model.get_molecule_ids()
a_ids = model.get_molecule_ids(a)
assert len(all_ids) == 10
assert all_ids == a_ids
m0 = model.get_molecule(a_ids[1])
assert m0.id == a_ids[1] # id should be 1
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
be also created using methods provided in a submodule
geometry_utils.
There are two commonly used types of spheres in computer
graphics: UV spheres and icospheres. The reason why we are
using icospheres here is that all of their triangles have
import mcell as m
from parameters import *
from subsystem import *
from geometry import *
# ---- instantiation ----
# ---- release sites ----
rel_a = m.ReleaseSite(name='rel_a',
complex=m.Complex('a'),
shape=m.Shape.SPHERICAL,
location=(0, 0, 0),
site_diameter=0,
number_to_release=1000)
rel_b = m.ReleaseSite(name='rel_b',
complex=m.Complex('b'),
shape=m.Shape.SPHERICAL,
location=(5.0000000000000001e-03, 0, 0),
site_diameter=0,
number_to_release=1000)
# ---- surface classes assignment ----
# ---- compartments assignment ----
# ---- instantiation data ----
instantiation = m.Instantiation()
