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_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 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_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 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)