def setUp(self):
reactor = aggsim.Reactor(volume_uL=1e-9 * 45, temperature_C=40)
self.reactor = reactor
n_monomers = aggsim.numberOfMolecules(1e-15 * 45, 1e-6 * 10)
monomers = aggsim.ActivatableReactant('monomer', n_monomers)
self.monomer = monomers
reactor.addReactant(monomers)
#print monomer.getProportionActivated(reactor.temperature)
ensemble = aggsim.SphericalAssemblyEnsemble('ensemble',
monomers,
1.0,
packing_fraction=sp.pi /
(3 * sp.sqrt(2)))
self.ens = ensemble
reactor.addReactant(ensemble)
# Nucleation
nuc_reaction = aggsim.EnsembleNucleationReaction(
'monomer', 'ensemble', 1e-13 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(nuc_reaction)
# Nucleation
denuc_reaction = aggsim.EnsembleDenucleationReaction(
'monomer', 'ensemble', 1e-3 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(denuc_reaction)
# Assembly
asmb_reaction = aggsim.SphericalAssemblyReaction(
'monomer', 'ensemble', 1e-8 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(asmb_reaction)
# Disassembly
disasmb_reaction = aggsim.SphericalDisassemblyReaction(
'monomer', 'ensemble', 1e-6 * 1e-6) # convert rate to (uM s)^-1
reactor.addReaction(disasmb_reaction)
def test_steps(self):
"""advancing n steps"""
reactor = aggsim.Reactor()
A = aggsim.Reactant('A', 1000)
Deg = aggsim.DegradationReaction('A', 2.0)
reactor.addReactant(A)
reactor.addReaction(Deg)
reactor.step(10)
self.assertTrue(reactor.num_steps == 10)
def test_single_assembly(self):
"""monomers at surface, single assembly"""
reactor = aggsim.Reactor()
n = 9
mon = aggsim.Reactant('monomer', n)
nuc = aggsim.Reactant('nucleus', 0)
amb = aggsim.SphericalAssembly('assembly', n, 1.0)
self.assertTrue(amb.monomers_at_surface == n - 1)
amb.inc(10)
self.assertTrue(amb.monomers_at_surface > n - 1)
def test_deg(self):
"""degradation"""
reactor = aggsim.Reactor()
A = aggsim.Reactant('A', 1000)
Deg = aggsim.DegradationReaction('A', 2.0)
reactor.addReactant(A)
reactor.addReaction(Deg)
while not reactor.exhausted:
reactor.step()
self.assertTrue(reactor['A'].number == 0)
def test_asmb(self):
"""nucleation, into assembly"""
reactor = aggsim.Reactor()
n = 1001
mon = aggsim.Reactant('monomer', n)
nuc = aggsim.SphericalAssembly('nucleus', 0, 1.0, 0.74)
nucr = aggsim.NucleationReaction('monomer', 'nucleus', 2.0)
reactor.addReactant(mon)
reactor.addReactant(nuc)
reactor.addReaction(nucr)
while not reactor.exhausted:
reactor.step()
self.assertTrue(reactor['nucleus'].number == (n - 1) / 2)
self.assertTrue(reactor['monomer'].number == 1)
def test_odd(self):
"""nucleation, odd number of monomers"""
reactor = aggsim.Reactor()
n = 1001
mon = aggsim.Reactant('monomer', n)
nuc = aggsim.Reactant('nucleus', 0)
nucr = aggsim.NucleationReaction('monomer', 'nucleus', 2.0)
reactor.addReactant(mon)
reactor.addReactant(nuc)
reactor.addReaction(nucr)
while not reactor.exhausted:
reactor.step()
self.assertTrue(reactor['nucleus'].number == (n - 1) / 2)
self.assertTrue(reactor['monomer'].number == 1)
def setUp(self):
self.n_initial_mrnas = 10
self.n_initial_prots = 0
reactor = aggsim.Reactor(volume_uL=1e-9 * 45, temperature_C=25)
self.reactor = reactor
n_prot_A = self.n_initial_prots #aggsim.numberOfMolecules(1e-15 * 45, 1e-6 * 10)
prot_A = aggsim.ActivatableReactant('prot-A', n_prot_A)
reactor.addReactant(prot_A)
n_mrna_A = self.n_initial_mrnas #aggsim.numberOfMolecules(1e-15 * 45, 1e-6 * 10)
mrna_A = aggsim.Reactant('mrna-A', n_mrna_A)
#self.prot_A = monomers
reactor.addReactant(mrna_A)
transl_reaction = aggsim.TranslationReaction('mrna-A', 'prot-A', 1e-7)
reactor.addReaction(transl_reaction)
def test_assembly_by_area(self):
"""add monomers to largest assembly"""
reactor = aggsim.Reactor()
large_n = 10000
#mon = aggsim.Reactant('monomer', n)
ens = aggsim.SphericalAssemblyEnsemble('nucleus', 1.0, 0.74)
small = ens.newAssembly(1)
large = ens.newAssembly(large_n)
# Add a single monomer
ens.inc(1)
for a in ens.assemblies:
#print a.id, a.number, a.monomers_at_surface
if a.id == large.id:
self.assertTrue(a.number == large_n + 1)
elif a.id == small.id:
self.assertTrue(a.number == 1)
def setUp(self):
self.reactor = aggsim.Reactor()
self.large_n = 10000
self.ens = aggsim.SphericalAssemblyEnsemble('nucleus', 1.0, 0.74)
# By default, write to stdout
data_outs.addStream(sys.stdout)
# Write out parameters
data_outs.write("# Run started {}\n".format(util.timestamp()))
data_outs.write("# Command: {}\n".format(' '.join(sys.argv)))
data_outs.write("# Parameters:\n")
optdict = vars(options)
for (k, v) in optdict.items():
data_outs.write("#\t{k}: {v}\n".format(k=k, v=v))
# Set seed
sp.random.seed(options.random_seed)
# Set up reaction
reactor = aggsim.Reactor(volume_uL=1e-9 * options.volume_fL,
temperature_C=options.initial_temperature_C)
n_monomers = aggsim.numberOfMolecules(
1e-15 * options.volume_fL, 1e-6 * options.initial_concentration_uM)
monomers = aggsim.ActivatableReactant('monomer', n_monomers)
reactor.addReactant(monomers)
#print monomer.getProportionActivated(reactor.temperature)
ensemble = aggsim.SphericalAssemblyEnsemble('ensemble',
monomers,
options.monomer_radius_nm,
packing_fraction=sp.pi /
(3 * sp.sqrt(2)))
reactor.addReactant(ensemble)
# Nucleation
nuc_reaction = aggsim.EnsembleNucleationReaction(
'monomer', 'ensemble',
options.k_nucleation * 1e-6) # convert rate to (uM s)^-1
