Example3.bngl

###
#@notes:'This is a plain translation of an SBML model created on 12/01/2016. The original model has 6 molecules and 8 reactions. The translated model has 6 molecules and 8 rules'
###
begin model
begin parameters
end parameters
begin compartments
	default_compartment  3  1.0
end compartments
begin molecule types
	MH()
	MS()
	MD()
	FH()
	FS()
	FD()
end molecule types
begin seed species
	@default_compartment:MH() 50.0 #MH #MH
	@default_compartment:FH() 50.0 #FH #FH
end seed species
begin observables
	Species MH MH() #MH
	Species MS MS() #MS
	Species MD MD() #MD
	Species FH FH() #FH
	Species FS FS() #FS
	Species FD FD() #FD
end observables
begin functions
	functionRate0() = if(0.2>= 0,0.2,0)
	functionRate0m() = if(if(MS>0,MH * 0.2/MS,0)< 0,-(if(MS>0,MH * 0.2/MS,0)),0)
	functionRate1() = if(0.01>= 0,0.01,0)
	functionRate1m() = if(if(MD>0,MH * 0.01/MD,0)< 0,-(if(MD>0,MH * 0.01/MD,0)),0)
	functionRate2() = if(0.1>= 0,0.1,0)
	functionRate2m() = if(if(MH>0,MS * 0.1/MH,0)< 0,-(if(MH>0,MS * 0.1/MH,0)),0)
	functionRate3() = if(0.3>= 0,0.3,0)
	functionRate3m() = if(if(MD>0,MS * 0.3/MD,0)< 0,-(if(MD>0,MS * 0.3/MD,0)),0)
	functionRate4() = if(0.1>= 0,0.1,0)
	functionRate4m() = if(if(FS>0,FH * 0.1/FS,0)< 0,-(if(FS>0,FH * 0.1/FS,0)),0)
	functionRate5() = if(0.01>= 0,0.01,0)
	functionRate5m() = if(if(FD>0,FH * 0.01/FD,0)< 0,-(if(FD>0,FH * 0.01/FD,0)),0)
	functionRate6() = if(0.1>= 0,0.1,0)
	functionRate6m() = if(if(FH>0,FS * 0.1/FH,0)< 0,-(if(FH>0,FS * 0.1/FH,0)),0)
	functionRate7() = if(0.3>= 0,0.3,0)
	functionRate7m() = if(if(FD>0,FS * 0.3/FD,0)< 0,-(if(FD>0,FS * 0.3/FD,0)),0)
end functions
begin reaction rules
	MJ00: MH() <-> MS() functionRate0(),functionRate0m()
	MJ02: MH() <-> MD() functionRate1(),functionRate1m()
	MJ10: MS() <-> MH() functionRate2(),functionRate2m()
	MJ12: MS() <-> MD() functionRate3(),functionRate3m()
	FJ00: FH() <-> FS() functionRate4(),functionRate4m()
	FJ02: FH() <-> FD() functionRate5(),functionRate5m()
	FJ10: FS() <-> FH() functionRate6(),functionRate6m()
	FJ12: FS() <-> FD() functionRate7(),functionRate7m()
end reaction rules
end model

# The following lines were manually added after translation to execute the model
generate_network({overwrite=>1})
simulate({method=>"ssa", t_end=>10, n_steps=>10, verbose=>1, seed=>0})