def main():
# Create the MCell world
world = m.mcell_create()
m.mcell_init_state(world)
# Set iterations, step size
dt = 1e-5
iterations = 100
m.mcell_set_time_step(world, dt)
m.mcell_set_iterations(world, iterations)
# Define volume molecule
vm1_sym = m.create_species(world, "vm1", 1e-6, False)
# Create a scene
scene_name = "Scene"
scene = m.create_instance_object(world, scene_name)
# Create release pattern with a delay
rel_pattern = m.create_release_pattern(world,
"Release Pattern",
delay=5e-4)
# Create box objects
box_name = "Box_Union_Outer"
r = (0.1, 0.1, 0.1)
ctr = (-0.3, 0.3, 0)
box_mesh = create_rectangle(world, scene, r, ctr, box_name)
# List of mols to release
mol_list = m.mcell_add_to_species_list(vm1_sym, False, 0, None)
# Release
rel_object = m.object()
box_rel_object = m.mcell_create_region_release(world, scene, box_mesh,
"Box Release", "ALL",
mol_list, 1000, 0, 1,
rel_pattern, rel_object)
m.mcell_delete_species_list(mol_list)
# Create viz data
viz_list = m.mcell_add_to_species_list(vm1_sym, False, 0, None)
m.mcell_create_viz_output(world, "./viz_data/test", viz_list, 0,
iterations, 1)
m.mcell_init_simulation(world)
m.mcell_init_output(world)
output_freq = 10
for i in range(iterations):
m.mcell_run_iteration(world, output_freq, 0)
m.mcell_flush_data(world)
m.mcell_print_final_warnings(world)
m.mcell_print_final_statistics(world)
def main():
world = m.mcell_create()
m.mcell_init_state(world)
dt = 1e-5
iterations = 100
m.mcell_set_time_step(world, dt)
m.mcell_set_iterations(world, iterations)
# Define one volume molecule
vm1_sym = m.create_species(world, "vm1", 1e-6, False)
sm1_sym = m.create_species(world, "sm1", 1e-6, True)
scene_name = "Scene"
scene = m.create_instance_object(world, scene_name)
# Create box object
box_name = "Box"
box_mesh = m.create_box(world, scene, 1.0, box_name)
# Release site object
# One volume list
(vol_rel_obj, success_vol) = m.create_list_release_site(
world, scene, [vm1_sym, vm1_sym], [1.0, 0.0], [0.0, 0.0], [0.0, 0.0],
"rel_name_vol")
# One surface list
(surf_rel_obj,
success_surf) = m.create_list_release_site(world,
scene, [sm1_sym, sm1_sym],
[1.0, 0.0], [0.0, 1.0],
[0.0, 0.0],
"rel_name_surf",
surf_flags=[True, True],
orientations=[1, 1])
# Create viz data
viz_list = m.mcell_add_to_species_list(vm1_sym, False, 0, None)
viz_list = m.mcell_add_to_species_list(sm1_sym, True, 1, viz_list)
m.mcell_create_viz_output(world, "./test_release_list_viz/test", viz_list,
0, iterations, 1)
m.mcell_init_simulation(world)
m.mcell_init_output(world)
output_freq = 1
for i in range(iterations):
m.mcell_run_iteration(world, output_freq, 0)
m.mcell_flush_data(world)
m.mcell_print_final_warnings(world)
m.mcell_print_final_statistics(world)
def create_region_release_site(world, scene, mesh, release_name, reg_name,
number, number_type, mol_sym):
"""Creates a release site on a specific region
Args:
world (object) -- the world object which has been generated by
mcell create_instance_object
scene (instance object) -- scene for mcell simulation
mesh (mesh object) -- scene object where the release will occur
release_name (string) -- name of the region release site
reg_name (string) -- name of the region for the release site
number (int or float) -- number to be released at the region release
site
number_type (int) -- 0 for NUMBER, 1 for CONCENTRATION
mol_sym (mcell_symbol) -- species to be released
Returns:
release object (object)
"""
mol_list = m.mcell_add_to_species_list(mol_sym, False, 0, None)
rel_object = m.object()
release_object = m.mcell_create_region_release(world, scene, mesh,
release_name,
reg_name, mol_list,
float(number), number_type,
1, None, rel_object)
m.mcell_delete_species_list(mol_list)
return release_object
def release_into_mesh_obj(self, relobj) -> None:
""" Release the specified amount of species into an object. """
mesh_obj = relobj.mesh_obj
species = relobj.spec
region = relobj.region
if isinstance(species, m.OrientedSpecies):
orient = species.orient_num
species = species.spec
else:
orient = None
if species.surface and orient is None:
logging.info(
"Error: must specify orientation when releasing surface "
"molecule")
if region:
rel_name = "%s_%s_%s_rel" % (species.name, mesh_obj.name,
region.reg_name)
else:
rel_name = "%s_%s_rel" % (species.name, mesh_obj.name)
mol_sym = self._species[species.name]
if orient:
mol_list = m.mcell_add_to_species_list(mol_sym, True, orient, None)
else:
mol_list = m.mcell_add_to_species_list(mol_sym, False, 0, None)
rel_object = m.object()
if relobj.number:
number_type = 0
rel_amt = relobj.number
elif relobj.conc:
number_type = 1
rel_amt = relobj.conc
if region:
reg_name = region.reg_name
else:
reg_name = "ALL"
release_object = m.mcell_create_region_release(
self._world, self._scene,
self._mesh_objects[mesh_obj.name], rel_name, reg_name, mol_list,
float(rel_amt), number_type, 1, None, rel_object)
if rel_name not in self._releases:
self._releases[rel_name] = release_object
m.mcell_delete_species_list(mol_list)
def add_viz(self, species: Iterable[Species]) -> None:
""" Set all the species in an Iterable to be visualized. """
viz_list = None
for spec in species:
viz_list = m.mcell_add_to_species_list(self._species[spec.name],
False, 0, viz_list)
logging.info("Output '%s' for viz data." % spec.name)
m.mcell_create_viz_output(self._world,
"./viz_data/seed_%04i/Scene" % self._seed,
viz_list, 0, self._iterations, 1)
def add_reaction(self, rxn: Reaction) -> None:
""" Add a Reaction object to the simulation. """
r_spec_list = None
p_spec_list = None
# Figure out if it's an iterable of reactants or a single reactant
try:
for r in rxn.reactants:
if isinstance(r, m.OrientedSpecies):
r_sym = self._species[r.spec.name]
r_spec_list = m.mcell_add_to_species_list(
r_sym, True, r.orient_num, r_spec_list)
else:
r_sym = self._species[r.name]
r_spec_list = m.mcell_add_to_species_list(
r_sym, False, 0, r_spec_list)
except TypeError:
r = rxn.reactants
if isinstance(r, m.OrientedSpecies):
r_sym = self._species[r.spec.name]
r_spec_list = m.mcell_add_to_species_list(
r_sym, True, r.orient_num, r_spec_list)
else:
r_sym = self._species[r.name]
r_spec_list = m.mcell_add_to_species_list(
r_sym, False, 0, r_spec_list)
try:
for p in rxn.products:
if isinstance(r, m.OrientedSpecies):
p_sym = self._species[p.spec.name]
p_spec_list = m.mcell_add_to_species_list(
p_sym, True, p.orient_num, p_spec_list)
else:
p_sym = self._species[p.name]
p_spec_list = m.mcell_add_to_species_list(
p_sym, False, 0, p_spec_list)
except TypeError:
p = rxn.products
if isinstance(r, m.OrientedSpecies):
p_sym = self._species[p.spec.name]
p_spec_list = m.mcell_add_to_species_list(
p_sym, True, p.orient_num, p_spec_list)
else:
p_sym = self._species[p.name]
p_spec_list = m.mcell_add_to_species_list(
p_sym, False, 0, p_spec_list)
logging.info("Add reaction '%s' to simulation" %
rxn.print_friendly_repr)
m.create_reaction(self._world,
r_spec_list,
p_spec_list,
rxn.rate_constant,
rxn.bkwd_rate_constant,
name=rxn.name)
def create_release_site(world, scene, pos, diam, shape, number, number_type,
mol_sym, name):
"""Creates a molecule release site
Args:
world (object) -- the world object which has been generated by
mcell create_instance_object
scene (instance object) -- scene for mcell simulation
pos (vector3) -- position of release site
diam (vector3) -- diameter of release site
number (int or float) -- number to be release at release site
number_type (int) -- 0 for NUMBER, 1 for CONCENTRATION
mol_sym (mcell_symbol) -- species to be released
name (string) -- name of the release site
Returns:
void -- generates a species release site
"""
position = m.vector3()
position.x = pos.x
position.y = pos.y
position.z = pos.z
diameter = m.vector3()
diameter.x = diam.x
diameter.y = diam.y
diameter.z = diam.z
mol_list = m.mcell_add_to_species_list(mol_sym, False, 0, None)
rel_object = m.object()
release_object = m.mcell_create_geometrical_release_site(
world, scene, name, shape, position, diameter, mol_list, float(number),
number_type, 1, None, rel_object)
m.mcell_delete_species_list(mol_list)
return (position, diameter, release_object)
def main(lexer, parser):
# Create the MCell world
world = m.mcell_create()
m.mcell_init_state(world)
# Set iterations, step size
dt = 1e-5
iterations = 100
m.mcell_set_time_step(world, dt)
m.mcell_set_iterations(world, iterations)
# Define volume molecule
vm1_sym = m.create_species(world, "vm1", 1e-6, False)
# Create a scene
scene_name = "Scene"
scene = m.create_instance_object(world, scene_name)
##########
# Create each of the three binary operations
# Each example consists of two box objects
##########
# Dictionary of release evaluator objects
rel_eval_dict = {}
##########
# Union
##########
# Create box objects
box_union_outer_name = "Box_Union_Outer"
r_union_outer = (0.1, 0.1, 0.1)
ctr_union_outer = (-0.3, 0.3, 0)
box_union_outer_mesh = create_rectangle(world, scene, r_union_outer,
ctr_union_outer,
box_union_outer_name)
box_union_inner_name = "Box_Union_Inner"
r_union_inner = (0.1, 0.1, 0.12)
ctr_union_inner = (-0.3 + 0.1, 0.3 + 0.1, 0.0)
box_union_inner_mesh = create_rectangle(world, scene, r_union_inner,
ctr_union_inner,
box_union_inner_name)
# Add to the dictionary of objects for the parser to see
lexer.obj_dict[box_union_outer_name] = box_union_outer_mesh
lexer.obj_dict[box_union_inner_name] = box_union_inner_mesh
# We will use the "ALL" region specification
# We could also define a surface region using the following code
'''
box_union_outer_region_name = "Box_Union_Outer_Reg"
box_union_outer_face_list = [0,1,2,3,4,5,6,7,8,9,10,11]
box_union_outer_region = m.create_surface_region(world, box_union_outer_mesh, box_union_outer_face_list, box_union_outer_region_name)
box_union_inner_region_name = "Box_Union_Inner_Reg"
box_union_inner_face_list = [0,1,2,3,4,5,6,7,8,9,10,11]
box_union_inner_region = m.create_surface_region(world, box_union_inner_mesh, box_union_inner_face_list, box_union_inner_region_name)
'''
# Parse a string to create a release_evaluator
s_union = box_union_outer_name + "[ALL]" + " + " + box_union_inner_name + "[ALL]"
print("> Parsing: " + s_union)
lexer.mcell_world = world
parser.parse(s_union)
rel_eval_dict[s_union] = lexer.release_evaluator
print("> Finished parsing.")
##########
# Subtraction
##########
# Create box objects
box_sub_outer_name = "Box_Sub_Outer"
r_sub_outer = (0.1, 0.1, 0.1)
ctr_sub_outer = (0.3, 0.3, 0)
box_sub_outer_mesh = create_rectangle(world, scene, r_sub_outer,
ctr_sub_outer, box_sub_outer_name)
box_sub_inner_name = "Box_Sub_Inner"
r_sub_inner = (0.1, 0.1, 0.12)
ctr_sub_inner = (0.3 + 0.1, 0.3 + 0.1, 0.0)
box_sub_inner_mesh = create_rectangle(world, scene, r_sub_inner,
ctr_sub_inner, box_sub_inner_name)
# Add to the dictionary of objects for the parser to see
lexer.obj_dict[box_sub_outer_name] = box_sub_outer_mesh
lexer.obj_dict[box_sub_inner_name] = box_sub_inner_mesh
# Parse a string to create a release_evaluator
s_sub = box_sub_outer_name + "[ALL]" + " - " + box_sub_inner_name + "[ALL]"
print("> Parsing: " + s_sub)
lexer.mcell_world = world
parser.parse(s_sub)
rel_eval_dict[s_sub] = lexer.release_evaluator
print("> Finished parsing.")
##########
# Intersection
##########
# Create box objects
box_inter_outer_name = "Box_Inter_Outer"
r_inter_outer = (0.1, 0.1, 0.1)
ctr_inter_outer = (0.0, -0.3, 0.0)
box_inter_outer_mesh = create_rectangle(world, scene, r_inter_outer,
ctr_inter_outer,
box_inter_outer_name)
box_inter_inner_name = "Box_Inter_Inner"
r_inter_inner = (0.1, 0.1, 0.12)
ctr_inter_inner = (0.1, -0.3 + 0.1, 0.0)
box_inter_inner_mesh = create_rectangle(world, scene, r_inter_inner,
ctr_inter_inner,
box_inter_inner_name)
# Add to the dictionary of objects for the parser to see
lexer.obj_dict[box_inter_outer_name] = box_inter_outer_mesh
lexer.obj_dict[box_inter_inner_name] = box_inter_inner_mesh
# Parse a string to create a release_evaluator
s_inter = box_inter_outer_name + "[ALL]" + " * " + box_inter_inner_name + "[ALL]"
print("> Parsing: " + s_inter)
lexer.mcell_world = world
parser.parse(s_inter)
rel_eval_dict[s_inter] = lexer.release_evaluator
print("> Finished parsing.")
##########
# Set up all the release sites for each: union/subtraction/intersection
##########
# List of mols to release
mol_list = m.mcell_add_to_species_list(vm1_sym, False, 0, None)
# Union
rel_object = m.object()
box_union_outer_rel_object = m.mcell_create_region_release_boolean(
world, scene, "Box Union Outer Release", mol_list, 1000, 0, 1, None,
rel_eval_dict[s_union], rel_object)
# Subtraction
rel_object = m.object()
box_sub_outer_rel_object = m.mcell_create_region_release_boolean(
world, scene, "Box Subtraction Outer Release", mol_list, 1000, 0, 1,
None, rel_eval_dict[s_sub], rel_object)
# Union
mol_list = m.mcell_add_to_species_list(vm1_sym, False, 0, None)
rel_object = m.object()
box_inter_outer_rel_object = m.mcell_create_region_release_boolean(
world, scene, "Box Intersection Outer Release", mol_list, 1000, 0, 1,
None, rel_eval_dict[s_inter], rel_object)
m.mcell_delete_species_list(mol_list)
##########
# Create viz data
##########
viz_list = m.mcell_add_to_species_list(vm1_sym, False, 0, None)
m.mcell_create_viz_output(world, "./viz_data/test", viz_list, 0,
iterations, 1)
m.mcell_init_simulation(world)
m.mcell_init_output(world)
output_freq = 10
for i in range(iterations):
m.mcell_run_iteration(world, output_freq, 0)
m.mcell_flush_data(world)
m.mcell_print_final_warnings(world)
m.mcell_print_final_statistics(world)
if __name__ == "__main__":
# Create pyMCell instance
world = m.mcell_create()
m.mcell_init_state(world)
dt = 1e-6
iterations = 300
m.mcell_set_time_step(world, dt)
m.mcell_set_iterations(world, iterations)
# Define one surface molecule and three volume molecules
vm1_sym = m.create_species(world, "vm1", 1e-6, False)
# vm1 -> NULL [1e5]
reactants2 = m.mcell_add_to_species_list(vm1_sym, False, 0, None)
m.create_reaction(world, reactants2, None, 0.01, name="rxn")
# Create Scene for simulation
scene_name = "Scene"
scene = m.create_instance_object(world, scene_name)
# Create a spherical release site
pos_vec3 = m.Vector3()
diam_vec3 = m.Vector3(0.015, 0.015, 0.015)
position, diameter, sphere_release_object = m.create_release_site(
world, scene, pos_vec3, diam_vec3, m.SHAPE_SPHERICAL, 500, 0, vm1_sym,
"vm1_rel")
obj_name = "Torus"
def create_list_release_site(world,
scene,
mol_list,
xpos,
ypos,
zpos,
name,
surf_flags=None,
orientations=None,
diameter=1e-4):
'''
Creates a list release site
All is self explanatory except mol_list:
This is a list of "mol_sym" that you get back when you create the species.
This is a Python list - it is converted to a species list in this function
for you. By default, assumes all molecules are volume molecules. Else, need
to pass surf_flags=[True,True,False,...] and their orientations =
[1,0,1,...] Diameter is the diameter we search for to place a surface mol
It can be None (= NULL in C) but then we do a poor job of placing surface
mols
'''
# Check that they're all the same length
n = len(mol_list)
if len(xpos) != n or len(ypos) != n or len(zpos) != n:
raise ValueError("All lists must have the same length.")
# Check that if there are surface molecules
if surf_flags is not None:
# Check that there are enough
if len(surf_flags) != n or len(orientations) != n:
raise ValueError(
"surf_flags and orientations lists must have the same lengths "
"as the others.")
# Convert to floats (can't be int)
xpos = [float(q) for q in xpos]
ypos = [float(q) for q in ypos]
zpos = [float(q) for q in zpos]
# Diameter
diam = m.vector3()
diam.x = diameter
diam.y = diameter
diam.z = diameter
# Mols
mol_list.reverse()
species_list = None
# All volume molecules
if surf_flags is None:
for mol_sym in mol_list:
species_list = m.mcell_add_to_species_list(mol_sym, False, 0,
species_list)
else:
for i, mol_sym in enumerate(mol_list):
species_list = m.mcell_add_to_species_list(mol_sym, surf_flags[i],
orientations[i],
species_list)
rel_object = m.object()
ret = m.mcell_create_list_release_site(world, scene, name, species_list,
xpos, ypos, zpos, n, diam,
rel_object)
# Delete the species list
m.mcell_delete_species_list(species_list)
# VERY IMPORTANT HERE - MUST RETURN "ret"
# If we throw this away, all is lost....
return (rel_object, ret)
def create_reaction(world,
reactants,
products,
rate_constant,
backward_rate_constant=0.0,
surf_class=None,
name=None):
"""Creates a molecular reaction
Args:
world (object) -- the world object which has been generated by
mcell create_instance_object
reactants (mcell_species_list) -- list of species that are the
reactants for the reaction
products (mcell_species_list) -- list of species that are the
products for the reaction
rate_constant (double) -- the rate constant for the forward
direction reaction -> product
backward_rate_constant (double)(optional) -- the rate constant
for the backward direction reaction <- product
surf_class (mcell species list surface class)(optional) -- the
surface class upon which the reaction will happen
name (string)(optional) -- Name of the reaction
Returns:
void -- creates a reaction, by generating reaction_rates
structure
"""
if surf_class:
# Do nothing, surf_class has been added and a null object is not needed
pass
else:
surf_class = m.mcell_add_to_species_list(None, False, 0, None)
arrow = m.reaction_arrow()
# reversible reaction e.g. A<->B
if backward_rate_constant:
arrow.flags = m.ARROW_BIDIRECTIONAL
rate_constant = m.mcell_create_reaction_rates(m.RATE_CONSTANT,
rate_constant,
m.RATE_CONSTANT,
backward_rate_constant)
# irreversible reaction e.g. A->B
else:
arrow.flags = m.REGULAR_ARROW
rate_constant = m.mcell_create_reaction_rates(m.RATE_CONSTANT,
rate_constant,
m.RATE_UNSET, 0)
arrow.catalyst = m.mcell_species()
arrow.catalyst.next = None
arrow.catalyst.mol_type = None
arrow.catalyst.orient_set = 0
arrow.catalyst.orient = 0
if (name):
name_sym = m.mcell_new_rxn_pathname(world, name)
else:
name_sym = None
m.mcell_add_reaction_simplified(world, reactants, arrow, surf_class,
products, rate_constant, name_sym)
