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 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 create_instance_object(world, name):
"""Creates an instance object. Simple translation from wrapped code
to python function. Frees the user from having to initialize the
scene object and then pass it in and generate the object.
Args:
world (object) -- the world object which has been generated by
mcell create_instance_object
name (string) -- name of the instance object
Returns:
instance object
"""
scene_temp = m.object()
return m.mcell_create_instance_object(world, name, scene_temp)
def create_polygon_object(world,
vert_list,
face_list,
scene,
name,
translation=None):
"""Creates a polygon object from a vertex and element lest
Args:
world (object) -- the world object which has been generated by
mcell create_instance_object
vert_list (vertex list) -- verteces for the polygon
face_list (element connection list) -- faces for the polygon
scene (instance object) -- scene for mcell simulation
name (string) -- name of polygon object that will be created
Returns:
polygon object
"""
verts = None
vert_list = vert_list[::-1]
t = translation
if t:
for x, y, z in vert_list:
verts = m.mcell_add_to_vertex_list(x + t[0], y + t[1], z + t[2],
verts)
else:
for x, y, z in vert_list:
verts = m.mcell_add_to_vertex_list(x, y, z, verts)
elems = None
face_list = face_list[::-1]
for x, y, z in face_list:
elems = m.mcell_add_to_connection_list(x, y, z, elems)
pobj = m.poly_object()
pobj.obj_name = name
pobj.vertices = verts
pobj.num_vert = len(vert_list)
pobj.connections = elems
pobj.num_conn = len(face_list)
mesh_temp = m.object()
mesh = m.mcell_create_poly_object(world, scene, pobj, mesh_temp)
return mesh
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 create_box(world, scene, half_length, name):
"""Creates the verteces and lines of a cube object at the origin
Args:
half_length (double) -- half length of the cube
Returns:
vertex list and element connection list
"""
hl = half_length
verts = m.mcell_add_to_vertex_list(hl, hl, -hl, None)
verts = m.mcell_add_to_vertex_list(hl, -hl, -hl, verts)
verts = m.mcell_add_to_vertex_list(-hl, -hl, -hl, verts)
verts = m.mcell_add_to_vertex_list(-hl, hl, -hl, verts)
verts = m.mcell_add_to_vertex_list(hl, hl, hl, verts)
verts = m.mcell_add_to_vertex_list(hl, -hl, hl, verts)
verts = m.mcell_add_to_vertex_list(-hl, -hl, hl, verts)
verts = m.mcell_add_to_vertex_list(-hl, hl, hl, verts)
elems = m.mcell_add_to_connection_list(1, 2, 3, None)
elems = m.mcell_add_to_connection_list(7, 6, 5, elems)
elems = m.mcell_add_to_connection_list(0, 4, 5, elems)
elems = m.mcell_add_to_connection_list(1, 5, 6, elems)
elems = m.mcell_add_to_connection_list(6, 7, 3, elems)
elems = m.mcell_add_to_connection_list(0, 3, 7, elems)
elems = m.mcell_add_to_connection_list(0, 1, 3, elems)
elems = m.mcell_add_to_connection_list(4, 7, 5, elems)
elems = m.mcell_add_to_connection_list(1, 0, 5, elems)
elems = m.mcell_add_to_connection_list(2, 1, 6, elems)
elems = m.mcell_add_to_connection_list(2, 6, 3, elems)
elems = m.mcell_add_to_connection_list(4, 0, 7, elems)
pobj = m.poly_object()
pobj.obj_name = name
pobj.vertices = verts
pobj.num_vert = 8
pobj.connections = elems
pobj.num_conn = 12
mesh_temp = m.object()
mesh = m.mcell_create_poly_object(world, scene, pobj, mesh_temp)
return mesh
def create_rectangle(world, scene, r, ctr, name):
xp = ctr[0] + r[0]
yp = ctr[1] + r[1]
zp = ctr[2] + r[2]
xm = ctr[0] - r[0]
ym = ctr[1] - r[1]
zm = ctr[2] - r[2]
verts = m.mcell_add_to_vertex_list(xp, yp, zm, None)
verts = m.mcell_add_to_vertex_list(xp, ym, zm, verts)
verts = m.mcell_add_to_vertex_list(xm, ym, zm, verts)
verts = m.mcell_add_to_vertex_list(xm, yp, zm, verts)
verts = m.mcell_add_to_vertex_list(xp, yp, zp, verts)
verts = m.mcell_add_to_vertex_list(xp, ym, zp, verts)
verts = m.mcell_add_to_vertex_list(xm, ym, zp, verts)
verts = m.mcell_add_to_vertex_list(xm, yp, zp, verts)
elems = m.mcell_add_to_connection_list(1, 2, 3, None)
elems = m.mcell_add_to_connection_list(7, 6, 5, elems)
elems = m.mcell_add_to_connection_list(0, 4, 5, elems)
elems = m.mcell_add_to_connection_list(1, 5, 6, elems)
elems = m.mcell_add_to_connection_list(6, 7, 3, elems)
elems = m.mcell_add_to_connection_list(0, 3, 7, elems)
elems = m.mcell_add_to_connection_list(0, 1, 3, elems)
elems = m.mcell_add_to_connection_list(4, 7, 5, elems)
elems = m.mcell_add_to_connection_list(1, 0, 5, elems)
elems = m.mcell_add_to_connection_list(2, 1, 6, elems)
elems = m.mcell_add_to_connection_list(2, 6, 3, elems)
elems = m.mcell_add_to_connection_list(4, 0, 7, elems)
pobj = m.poly_object()
pobj.obj_name = name
pobj.vertices = verts
pobj.num_vert = 8
pobj.connections = elems
pobj.num_conn = 12
mesh_temp = m.object()
mesh = m.mcell_create_poly_object(world, scene, pobj, mesh_temp)
return mesh
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)
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)