Merge pull request #425 from TorkelE/problems_from_reaction_systems

Enable the creation of Problems from ReactionSystems

Author: ChrisRackauckas

src/systems/reaction/reactionsystem.jl

@@ -327,3 +327,33 @@ function make_sub!(eq,states_swaps)
 	end
 	return eq
 end
+
+### Converts a reaction system to ODE or SDE problems ###
+
+
+# ODEProblem from AbstractReactionNetwork
+function DiffEqBase.ODEProblem(rs::ReactionSystem, u0::Union{AbstractArray, Number}, tspan, p, args...; kwargs...)
+    u0 = typeof(u0) <: Array{<:Pair} ? u0 : Pair.(rs.states,u0)
+    p = typeof(p) <: Array{<:Pair} ? p : Pair.(rs.ps,p)
+    return ODEProblem(convert(ODESystem,rs),u0,tspan,p, args...; kwargs...)
+end
+
+# SDEProblem from AbstractReactionNetwork
+function DiffEqBase.SDEProblem(rs::ReactionSystem, u0::Union{AbstractArray, Number}, tspan, p, args...; kwargs...)
+    u0 = typeof(u0) <: Array{<:Pair} ? u0 : Pair.(rs.states,u0)
+    p = typeof(p) <: Array{<:Pair} ? p : Pair.(rs.ps,p)
+    p_matrix = zeros(length(rs.states), length(rs.eqs))
+    return SDEProblem(convert(SDESystem,rs),u0,tspan,p,args...; noise_rate_prototype=p_matrix,kwargs...)
+end
+
+# DiscreteProblem from AbstractReactionNetwork
+function DiffEqBase.DiscreteProblem(rs::ReactionSystem, u0::Union{AbstractArray, Number}, tspan::Tuple, p=nothing, args...; kwargs...)
+    u0 = typeof(u0) <: Array{<:Pair} ? u0 : Pair.(rs.states,u0)
+    p = typeof(p) <: Array{<:Pair} ? p : Pair.(rs.ps,p)
+    return DiscreteProblem(convert(JumpSystem,rs), u0,tspan,p, args...; kwargs...)
+end
+
+# JumpProblem from AbstractReactionNetwork
+function DiffEqJump.JumpProblem(rs::ReactionSystem, prob, aggregator, args...; kwargs...)
+    return JumpProblem(convert(JumpSystem,rs), prob, aggregator, args...; kwargs...)
+end