# 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']
assert ct.states == ['0']
assert ct2.states == ['X', 'Y']
# vector2
ct3 = m.ComponentType('u', states=['0', '1'])
ct4 = copy.copy(ct3)
ct4.states[0] = 'X'
assert ct3.states == ['0', '1']
assert ct4.states == ['X', '1']
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
# checking that .append and other modifications works
ct_u = m.ComponentType('u', states=['0'])
#print(type(ct_u.states))
assert len(ct_u.states) == 1
ct_u.states.append('1')
assert len(ct_u.states) == 2
ct_u.states[1] = '2'
assert ct_u.states[1] == '2'
rs = m.ReleaseSite(name='test',
complex=m.Complex('A'),
shape=m.Shape.SPHERICAL,
location=(1, 2, 3),
number_to_release=1000)
assert c.red == 1
assert c2.red == 0.5
# object - first level copy
rs = m.ReleaseSite(name='test',
complex=m.Complex('A'),
shape=m.Shape.SPHERICAL,
location=(1, 2, 3),
number_to_release=1000)
rs2 = copy.deepcopy(rs)
rs2.complex.name = 'B'
assert rs.complex.name == 'A'
assert rs2.complex.name == 'B'
# object in vector
cplx = m.Complex('X(a~0!1).Y(b~Q!1)')
ct = m.ComponentType('z', ['E', 'R'])
cplx2 = copy.deepcopy(cplx)
cplx2.elementary_molecules[0].elementary_molecule_type.components[0] = ct
cplx2.elementary_molecules[0].components[0] = ct.inst('E', 1)
assert cplx.elementary_molecules[0].elementary_molecule_type.components[
0].name == 'a'
assert cplx.to_bngl_str() == 'X(a~0!1).Y(b~Q!1)'
assert cplx2.to_bngl_str() == 'X(z~E!1).Y(b~Q!1)'
def convert_species_file(file_name):
# read the .species file and parse complexes to the internal MCell
# representation
complex_counts = species_reader.read_species_file(file_name)
# prepare the component type that we will append to the CaMKII molecules
# the new component means 'upper' and has a boolean state
ct_u = m.ComponentType('u', ['0', '1'])
# process the data by adding component 'u' to the CaMKII elementary molecules
for (complex, count) in complex_counts:
# if this a CaMKII dodecamer?
camkiis = []
for em in complex.elementary_molecules:
em_name = em.elementary_molecule_type.name
if em_name == 'CaMKII':
camkiis.append(em)
if len(camkiis) != 12:
# output it directly
print(complex.to_bngl_str() + " " + str(count))
continue
# ok, we have the holoenzyme, how can we figure out which
# of the CaMKIIs belong to the upper and the lower
# ring?
# let's say that the first one is in the upper ring,
# go along the 'r'
upper_first = camkiis[0]
upper_ring = [upper_first]
curr = upper_first
for i in range(1, 6):
curr = get_bound_em(complex, curr, 'r')
upper_ring.append(curr)
assert upper_first is get_bound_em(complex, curr,
'r'), "A ring must be formed"
# then go down along 'c' and go again along 'r' to get molecules of the lower ring
lower_first = get_bound_em(complex, camkiis[0], 'c')
lower_ring = [lower_first]
curr = lower_first
for i in range(1, 6):
curr = get_bound_em(complex, curr, 'r')
lower_ring.append(curr)
assert lower_first is get_bound_em(complex, curr,
'r'), "A ring must be formed"
# now the modifications - add components by instatiating the component type 'u'
# the way how the complexes were is parsed was that each complex has its own instance
# of the elementary molecule type for CaMKII so lets change one of them
upper_first.elementary_molecule_type.components.append(ct_u)
for em in upper_ring:
em.components.append(ct_u.inst('1'))
for em in lower_ring:
em.components.append(ct_u.inst('0'))
print(complex.to_bngl_str() + " " + str(count))
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
subsystem = m.Subsystem()
model = m.Model()
d = m.ComponentType('d', ['X', 'Y'])
e = m.ComponentType('e', ['0', '1'])
for o, c in [(subsystem, 's'), (model, 'm')]:
mt1 = m.ElementaryMoleculeType('A' + c, [e, d], diffusion_constant_3d=1e-6)
o.add_elementary_molecule_type(mt1)
# must be siletnly ignored
mt2 = m.ElementaryMoleculeType('A' + c, [d, e], diffusion_constant_3d=1e-6)
o.add_elementary_molecule_type(mt2)
assert len(o.elementary_molecule_types) == 1
try:
o.add_elementary_molecule_type(
m.ElementaryMoleculeType('A' + c, [e, d],
diffusion_constant_3d=1e-5))
# 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 *
Syk_a = m.ComponentType(name='a', states=['Y', 'pY'])
Syk_l = m.ComponentType(name='l', states=['Y', 'pY'])
Syk_tSH2 = m.ComponentType(name='tSH2')
Syk = m.ElementaryMoleculeType(name='Syk',
components=[Syk_a, Syk_l, Syk_tSH2],
diffusion_constant_3d=8.50999999999999984e-07)
# ---- create subsystem object and add components ----
subsystem = m.Subsystem()
subsystem.add_elementary_molecule_type(Syk)
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
c1_1 = m.ComponentType('C', ['0', '1', 'Z'])
c1_2 = m.ComponentType('C', ['1', '0', 'Z'])
b1 = m.ComponentType('B', ['0', '1', 'Q'])
mt1_1 = m.ElementaryMoleculeType('M', [c1_1, b1], diffusion_constant_3d=1e-6)
mt1_2 = m.ElementaryMoleculeType('M', [b1, c1_2])
mt2 = m.ElementaryMoleculeType('M', [b1, c1_2], diffusion_constant_3d=1e-5)
mt4 = m.ElementaryMoleculeType('N', [b1, b1, c1_1])
mt5 = m.ElementaryMoleculeType('O', [b1, c1_2])
s1_1 = m.Species(
elementary_molecules=[mt1_1.inst([c1_1.inst('0'),
b1.inst('Q')])])
s1_2 = m.Species(
elementary_molecules=[mt1_1.inst([b1.inst('Q'),
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
C = m.ComponentType('C', ['0', '1', 'Z'])
N = m.ComponentType('N')
assert C.to_bngl_str() == 'C~0~1~Z'
assert N.to_bngl_str() == 'N'
C_inst = C.inst('1', 2)
C_inst2 = C.inst(1)
assert C_inst.to_bngl_str() == 'C~1!2'
assert C_inst2.to_bngl_str() == 'C~1'
CaM = m.ElementaryMoleculeType('CaM', [C, N], diffusion_constant_3d=1e-6)
assert CaM.to_bngl_str() == 'CaM(C~0~1~Z,N)'
CaM_inst = CaM.inst([C.inst(0), N.inst(1)])
assert CaM_inst.to_bngl_str() == 'CaM(C~0,N~1)'
cplx_inst = m.Complex(elementary_molecules=[