# receptor_activation_hpp.bngl
# Created by BioNetGen 2.2.5
version("2.2.4+")

begin model
begin parameters
  f       0.01
  NA      6.0221e23
  V       1e-12*f
  L0      (500e-9*NA)*V
  R0      (100e-9*NA)*V
  A0      (100e-9*NA)*V
  B0      (100e-9*NA)*V
  C0      (100e-9*NA)*V
  BC0     (100e-9*NA)*V
  kp1     10e6/(NA*V)
  km1     1.0
  k2      1.0
  k3      1.0
  kp4     10e6/(NA*V)
  km4     1.0
  kp5     10e6/(NA*V)
  km5     1.0
  kp6     10e6/(NA*V)
  km6     1.0
  k7      1.0
  k8      1.0
  kp9     10e6/(NA*V)
  km9     1.0
  k_lump  10000
end parameters
begin molecule types
  A(r,b~0~P)      
  P5()              population
  P7()              population
  P2()              population
  P1()              population
  B(r,c)          
  P6()              population
  P3()              population
  C(b)            
  R(l,a~0~P,b~0~P)
  P8()              population
  P4()              population
  L(r)            
end molecule types
begin observables
  Molecules LR L(r!1).R(l!1)
  Molecules Rp R(a~P!?) R(b~P!?)
  Molecules Ap A(b~P!?) P3() P4() P5()
  Molecules RC R(b~P!1).B(r!1,c!2).C(b!2) R(a~P!1).A(r!1,b~P!2).B(r!2,c!3).C(b!3)
  Molecules Ltot L() P1()
  Molecules Rtot R()
  Molecules Atot A() P2() P3() P4() P5()
  Molecules Btot B() P4() P5() P6() P7()
  Molecules Ctot C() P5() P7() P8()
end observables
begin species
  P1() L0
  R(a~0,b~0,l) R0
  P2() A0
  P6() B0
  P8() C0
  P7() BC0
  A(b~0,r!1).L(r!2).R(a~P!1,b~0,l!2) 0
  A(b~0,r!1).B(c!2,r!3).C(b!2).L(r!4).R(a~P!1,b~P!3,l!4) 0
  A(b~0,r!1).B(c,r!2).L(r!3).R(a~P!1,b~P!2,l!3) 0
  A(b~0,r!1).L(r!2).R(a~P!1,b~P,l!2) 0
  A(b~0,r!1).R(a~P!1,b~0,l) 0
  A(b~0,r!1).B(c!2,r!3).C(b!2).R(a~P!1,b~P!3,l) 0
  A(b~0,r!1).B(c,r!2).R(a~P!1,b~P!2,l) 0
  A(b~0,r!1).R(a~P!1,b~P,l) 0
  A(b~P!1,r!2).B(c!3,r!1).C(b!3).L(r!4).R(a~P!2,b~0,l!4) 0
  A(b~P!1,r!2).B(c,r!1).L(r!3).R(a~P!2,b~0,l!3) 0
  A(b~P!1,r!2).B(c!3,r!1).B(c!4,r!5).C(b!3).C(b!4).L(r!6).R(a~P!2,b~P!5,l!6) 0
  A(b~P!1,r!2).B(c!3,r!1).B(c,r!4).C(b!3).L(r!5).R(a~P!2,b~P!4,l!5) 0
  A(b~P!1,r!2).B(c!3,r!4).B(c,r!1).C(b!3).L(r!5).R(a~P!2,b~P!4,l!5) 0
  A(b~P!1,r!2).B(c,r!1).B(c,r!3).L(r!4).R(a~P!2,b~P!3,l!4) 0
  A(b~P!1,r!2).B(c!3,r!1).C(b!3).L(r!4).R(a~P!2,b~P,l!4) 0
  A(b~P!1,r!2).B(c,r!1).L(r!3).R(a~P!2,b~P,l!3) 0
  A(b~P!1,r!2).B(c!3,r!1).C(b!3).R(a~P!2,b~0,l) 0
  A(b~P!1,r!2).B(c,r!1).R(a~P!2,b~0,l) 0
  A(b~P,r!1).L(r!2).R(a~P!1,b~0,l!2) 0
  A(b~P,r!1).B(c!2,r!3).C(b!2).L(r!4).R(a~P!1,b~P!3,l!4) 0
  A(b~P,r!1).B(c,r!2).L(r!3).R(a~P!1,b~P!2,l!3) 0
  A(b~P,r!1).L(r!2).R(a~P!1,b~P,l!2) 0
  A(b~P,r!1).R(a~P!1,b~0,l) 0
  A(b~P,r!1).B(c!2,r!3).C(b!2).R(a~P!1,b~P!3,l) 0
  A(b~P,r!1).B(c,r!2).R(a~P!1,b~P!2,l) 0
  P5() 0
  P4() 0
  P3() 0
  B(c!1,r!2).C(b!1).L(r!3).R(a~0,b~P!2,l!3) 0
  B(c!1,r!2).C(b!1).L(r!3).R(a~P,b~P!2,l!3) 0
  B(c!1,r!2).C(b!1).R(a~0,b~P!2,l) 0
  B(c!1,r!2).C(b!1).R(a~P,b~P!2,l) 0
  B(c,r!1).L(r!2).R(a~0,b~P!1,l!2) 0
  B(c,r!1).L(r!2).R(a~P,b~P!1,l!2) 0
  B(c,r!1).R(a~0,b~P!1,l) 0
  B(c,r!1).R(a~P,b~P!1,l) 0
  L(r!1).R(a~0,b~0,l!1) 0
  L(r!1).R(a~0,b~P,l!1) 0
  L(r!1).R(a~P,b~0,l!1) 0
  L(r!1).R(a~P,b~P,l!1) 0
  R(a~0,b~P,l) 0
  R(a~P,b~0,l) 0
  R(a~P,b~P,l) 0
end species
begin reaction rules
  Rule1_v1:  P1() + R(l) -> L(r!1).R(l!1)  kp1
  Rule1r_v1:  L(r!1).R(l!1) -> P1() + R(l)  km1 DeleteMolecules
  Rule2_v1:  L(r!1).R(a~0,l!1) -> L(r!1).R(a~P,l!1)  k2
  Rule3_v1:  L(r!1).R(b~0,l!1) -> L(r!1).R(b~P,l!1)  k2
  Rule4_v1:  R(a~P) -> R(a~0)  k3
  Rule5_v1:  R(b~P) -> R(b~0)  k3
  Rule6_v1:  R(a~P) + A(r) -> A(r!1).R(a~P!1)  kp4
  Rule6_v2:  R(a~P) + P2() -> A(b~0,r!1).R(a~P!1)  kp4
  Rule6_v3:  R(a~P) + P3() -> A(b~P,r!1).R(a~P!1)  kp4
  Rule6_v4:  R(a~P) + P4() -> A(b~P!1,r!2).B(c,r!1).R(a~P!2)  kp4
  Rule6_v5:  R(a~P) + P5() -> A(b~P!1,r!2).B(c!3,r!1).C(b!3).R(a~P!2)  kp4
  Rule6r_v1:  A(r!1).R(a~P!1) -> R(a~P) + A(r)  km4
  Rule7_v1:  R(b~P) + B(r) -> B(r!1).R(b~P!1)  kp5
  Rule7_v2:  R(b~P) + P6() -> B(c,r!1).R(b~P!1)  kp5
  Rule7_v3:  R(b~P) + P7() -> B(c!1,r!2).C(b!1).R(b~P!2)  kp5
  Rule7r_v1:  B(r!1).R(b~P!1) -> R(b~P) + B(r)  km5
  Rule8_v1:  B(c) + P8() -> B(c!1).C(b!1)  kp6
  Rule8_v2:  P4() + P8() -> P5()  kp6
  Rule8_v3:  P6() + P8() -> P7()  kp6
  Rule8r_v1:  B(c!1).C(b!1) -> B(c) + P8()  km6 DeleteMolecules
  Rule8r_v2:  P5() -> P4() + P8()  km6
  Rule8r_v3:  P7() -> P6() + P8()  km6
  Rule9_v1:  A(b~0,r!1).R(a~P!1) -> A(b~P,r!1).R(a~P!1)  k7
  Rule10_v1:  A(b~P) -> A(b~0)  k8
  Rule10_v2:  P3() -> P2()  k8
  Rule11_v1:  A(b~P) + B(r) -> A(b~P!1).B(r!1)  kp9
  Rule11_v2:  A(b~P) + P6() -> A(b~P!1).B(c,r!1)  kp9
  Rule11_v3:  A(b~P) + P7() -> A(b~P!1).B(c!2,r!1).C(b!2)  kp9
  Rule11_v4:  P3() + B(r) -> A(b~P!1,r).B(r!1)  kp9
  Rule11_v5:  P3() + P6() -> P4()  kp9
  Rule11_v6:  P3() + P7() -> P5()  kp9
  Rule11r_v1:  A(b~P!1).B(r!1) -> A(b~P) + B(r)  km9
  Rule11r_v2:  P4() -> P3() + P6()  km9
  Rule11r_v3:  P5() -> P3() + P7()  km9
  MapRule0:  L(r) -> P1()  k_lump
  MapRule1:  A(b~0,r) -> P2()  k_lump
  MapRule2:  A(b~P,r) -> P3()  k_lump
  MapRule3:  A(b~P!1,r).B(c,r!1) -> P4()  k_lump
  MapRule4:  A(b~P!1,r).B(c!2,r!1).C(b!2) -> P5()  k_lump
  MapRule5:  B(c,r) -> P6()  k_lump
  MapRule6:  B(c!1,r).C(b!1) -> P7()  k_lump
  MapRule7:  C(b) -> P8()  k_lump
end reaction rules
end model


## model actions ##
simulate_nf({ suffix=>'nf', t_end=>40, n_steps=>120, gml=>1000000, verbose=>1 })