# command line: # KaDE kin_phos_1.ka -print-efficiency -ode-backend DOTNET -dotnet-output network_kin_phos_9_wo_sym.net -propagate-constants # THINGS THAT ARE KNOWN FROM KAPPA FILE AND KaSim OPTIONS: # # init - the initial abundances of each species and token # tinit - the initial simulation time (likely 0) # tend - the final simulation time # initialstep - initial time step at the beginning of numerical integration # maxstep - maximal time step for numerical integration # reltol - relative error tolerance; # abstol - absolute error tolerance; # period - the time period between points to return # # variables (init(i),y(i)) denote numbers of embeddings # rule rates are corrected by the number of automorphisms in the lhs of rules begin species 1 S(x1~u) 100 2 P(s) 100 3 K(s) 100 4 K(s!1).S(x1~u!1) 0 5 S(x1~p) 0 6 S(x1~p!1).P(s!1) 0 end species begin reactions # rule : P(s!1), S(x1~p!1) -> P(s), S(x1~u) # S(x1~p!1), P(s!1) -> S(x1~u) + P(s) 1 6 1,2 0.01 # rule : P(s!1), S(x1~p!1) -> P(s), S(x1~p) # S(x1~p!1), P(s!1) -> S(x1~p) + P(s) 2 6 2,5 0.1 # rule : P(s), S(x1~p) -> P(s!1), S(x1~p!1) # S(x1~p) + P(s) -> S(x1~p!1), P(s!1) 3 2,5 6 0.001 # rule : K(s!1), S(x1~u!1) -> K(s), S(x1~p) # K(s!1), S(x1~u!1) -> S(x1~p) + K(s) 4 4 3,5 0.1 # rule : K(s!1), S(x1~u!1) -> K(s), S(x1~u) # K(s!1), S(x1~u!1) -> S(x1~u) + K(s) 5 4 1,3 1 # rule : K(s), S(x1~u) -> K(s!1), S(x1~u!1) # S(x1~u) + K(s) -> K(s!1), S(x1~u!1) 6 1,3 4 0.01 end reactions