def add_reactions(self):
A = self.A
B = self.B
C = self.C
r = model.create_unimolecular_reaction_rule(A, B, self.kf_1)
self.m.network_rules.add_reaction_rule(r)
r = model.create_unimolecular_reaction_rule(B, A, self.kb_1)
self.m.network_rules.add_reaction_rule(r)
r = model.create_binding_reaction_rule(A, B, C, self.kf_2)
self.m.network_rules.add_reaction_rule(r)
r = model.create_unbinding_reaction_rule(C, A, B, self.kb_2)
self.m.network_rules.add_reaction_rule(r)
r = model.create_decay_reaction_rule(C, self.kb_1)
self.m.network_rules.add_reaction_rule(r)
def test_three_particles_in_contact(self):
place_particle(self.s.world, self.S, [0.0,0.0,0.0])
place_particle(self.s.world, self.S, [1e-7,0.0,0.0])
# dummy
place_particle(self.s.world, self.S, [2e-7,0.0,0.0])
r = model.create_unimolecular_reaction_rule(self.S, self.A, 1e10)
self.m.network_rules.add_reaction_rule(r)
t = self.s.t
for i in range(5):
self.s.step()
# Check if species ids are consistent after unimolecular
# multi reaction.
for species in self.s.world.species:
for pid in self.s.world.get_particle_ids(species.id):
particle = self.s.world.get_particle(pid)[1]
self.failIf(particle.sid != species.id)
self.failIf(t == self.s.t)
m.add_species_type(O) m.add_species_type(R) m.add_species_type(P) m.add_species_type(OR) m.add_species_type(ORp) m.add_species_type(ORpa) m.add_species_type(T) m.add_species_type(M) m.add_species_type(Mribo) # Reaction rules r1 = model.create_binding_reaction_rule(O, R, OR, k_fR) m.network_rules.add_reaction_rule(r1) r2 = model.create_unbinding_reaction_rule(OR, O, R, k_bR) m.network_rules.add_reaction_rule(r2) r3 = model.create_unimolecular_reaction_rule(O, ORp, k_f_rp) m.network_rules.add_reaction_rule(r3) r4 = model.create_unimolecular_reaction_rule(ORp, O, k_b_rp) m.network_rules.add_reaction_rule(r4) r5 = model.create_unimolecular_reaction_rule(ORp, ORpa, k_OC) m.network_rules.add_reaction_rule(r5) r6 = model.create_unbinding_reaction_rule(ORpa, T, O, 1 / t_clear) m.network_rules.add_reaction_rule(r6) r7 = model.create_decay_reaction_rule(M, k_dm) m.network_rules.add_reaction_rule(r7) r8 = model.create_unbinding_reaction_rule(M, M, Mribo, k_ribo) m.network_rules.add_reaction_rule(r8) r9 = model.create_unimolecular_reaction_rule(Mribo, P, 1 / t_trans) m.network_rules.add_reaction_rule(r9) r10 = model.create_decay_reaction_rule(P, k_dp) m.network_rules.add_reaction_rule(r10)
m.add_species_type(O) m.add_species_type(R) m.add_species_type(P) m.add_species_type(OR) m.add_species_type(ORp) m.add_species_type(ORpa) m.add_species_type(T) m.add_species_type(M) m.add_species_type(Mribo) # Reaction rules r1 = model.create_binding_reaction_rule(O, R, OR, k_fR) m.network_rules.add_reaction_rule(r1) r2 = model.create_unbinding_reaction_rule(OR, O, R, k_bR) m.network_rules.add_reaction_rule(r2) r3 = model.create_unimolecular_reaction_rule(O, ORp, k_f_rp) m.network_rules.add_reaction_rule(r3) r4 = model.create_unimolecular_reaction_rule(ORp, O, k_b_rp) m.network_rules.add_reaction_rule(r4) r5 = model.create_unimolecular_reaction_rule(ORp, ORpa, k_OC) m.network_rules.add_reaction_rule(r5) r6 = model.create_unbinding_reaction_rule(ORpa, T, O, 1/t_clear) m.network_rules.add_reaction_rule(r6) r7 = model.create_decay_reaction_rule(M, k_dm) m.network_rules.add_reaction_rule(r7) r8 = model.create_unbinding_reaction_rule(M, M, Mribo, k_ribo) m.network_rules.add_reaction_rule(r8) r9 = model.create_unimolecular_reaction_rule(Mribo, P, 1/t_trans) m.network_rules.add_reaction_rule(r9) r10 = model.create_decay_reaction_rule(P, k_dp) m.network_rules.add_reaction_rule(r10)