Exemplo n.º 1
0
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)
Exemplo n.º 2
0
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)
Exemplo n.º 3
0
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)
Exemplo n.º 4
0
# 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 ----
Exemplo n.º 5
0
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
Exemplo n.º 6
0
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)
Exemplo n.º 7
0
# 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 ----
Exemplo n.º 8
0
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']
Exemplo n.º 9
0
#!/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() 
Exemplo n.º 10
0


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
Exemplo n.º 11
0
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',
Exemplo n.º 12
0
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)

Exemplo n.º 13
0
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 ----
Exemplo n.º 14
0
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)

Exemplo n.º 15
0
                         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()
Exemplo n.º 16
0
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)
Exemplo n.º 17
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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,
Exemplo n.º 18
0
# 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)
Exemplo n.º 19
0
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)
Exemplo n.º 20
0
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)
Exemplo n.º 21
0
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)
Exemplo n.º 22
0
#          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',
Exemplo n.º 23
0
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 ----

Exemplo n.º 24
0
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),
Exemplo n.º 25
0
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)
Exemplo n.º 26
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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()
Exemplo n.º 27
0
# 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)
Exemplo n.º 28
0
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
Exemplo n.º 29
0
    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
Exemplo n.º 30
0
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()