# tlbr_hpp.bngl
# Created by BioNetGen 2.2.4
version("2.2.4+")
setOption("SpeciesLabel","HNauty")

begin model
begin parameters
  NA            6.0221e23
  cell_density  1e9
  Rec_cell      3e5
  Lig_conc      8.3e-9
  f             0.001
  Vol           (1/cell_density)*f
  Lig_tot       (Lig_conc*NA)*Vol
  Rec_tot       Rec_cell*f
  K1            0.1084e9
  K2            33.72e9
  koff          0.01
  kp1           K1*koff
  kp2           K2*koff
  rateLaw1      (kp1/NA)/Vol
  rateLaw2      (kp2/NA)/Vol
  rateLaw3      (kp2/NA)/Vol
  k_lump        10000
  rateLaw1_1    3*((kp1/NA)/Vol)
  rateLaw1_2    6*((kp1/NA)/Vol)
  rateLaw2_1    2*((kp2/NA)/Vol)
  rateLaw3_1    2*((kp2/NA)/Vol)
end parameters
begin molecule types
  X0002()              population
  X0001()              population
  R(l,l)             
  L(r,r,r)           
end molecule types
begin observables
  Species Rfree {MatchOnce}R(l,l) X0002()
  Species Lfree {MatchOnce}L(r,r,r) X0001()
  Molecules Ropen R(l) X0002() X0002()
  Molecules Lopen L(r) X0001() X0001() X0001()
  Species Rsingle R()==1 X0002()
  Species Rclusters R()>=2
  Molecules LRmotif L(r!1).R(l!1)
  Molecules RLRmotif R(l!1).L(r!1,r!2).R(l!2)
  Molecules Rtot R() X0002()
  Molecules Ltot L() X0001()
end observables
begin species
  X0002() Rec_tot
  X0001() Lig_tot
end species
begin reaction rules
  Rule1_v1:  L(r!1).R(l!1) -> R(l) + L(r)  koff
  Rule2_v1:  X0001() + R(l) -> L(r,r,r!1).R(l!1)  rateLaw1_1
  Rule2_v2:  X0001() + X0002() -> L(r,r,r!1).R(l,l!1)  rateLaw1_2
  Rule3_v1:  L(r!+,r%T2,r) + R(l) -> L(r!+,r,r%T2!1).R(l!1)  rateLaw2
  Rule3_v2:  L(r!+,r%T2,r) + X0002() -> L(r!+,r,r%T2!1).R(l,l!1)  rateLaw2_1
  Rule4_v1:  L(r!+,r!+,r) + R(l) -> L(r!+,r!+,r!1).R(l!1)  rateLaw3
  Rule4_v2:  L(r!+,r!+,r) + X0002() -> L(r!+,r!+,r!1).R(l,l!1)  rateLaw3_1
  MapRule0:  L(r,r,r) -> X0001()  k_lump
  MapRule1:  R(l,l) -> X0002()  k_lump
end reaction rules
end model


## model actions ##
simulate_nf({ t_end=>500, n_steps=>100, gml=>10000000, complex=>1 })