partial progress

Author: TorkelE

src/reactionsystem.jl

@@ -538,6 +538,11 @@ struct ReactionSystem{V <: NetworkProperties} <:
         checks && validate(rs)
         rs
     end
+
+    # Copies a reaction system, but with the option of having some fields replaced
+    function ReactionSystem(rs::ReactionSystem; eqs = rs.eqs, rxs = rs.rxs, iv = rs.iv, sivs = rs.sivs, states = rs.states, species = rs.species, ps = rs.ps, var_to_name = rs.var_to_name, observed = rs.observed, name = rs.name, systems = rs.systems, defaults = rs.defaults, connection_type = rs.connection_type, networkproperties = rs.networkproperties, combinatoric_ratelaws = rs.combinatoric_ratelaws, continuous_events = rs.continuous_events, discrete_events = rs.discrete_events, complete = rs.complete)
+        new{typeof(networkproperties)}(eqs, rxs, ModelingToolkit.unwrap(iv), ModelingToolkit.unwrap.(sivs), ModelingToolkit.unwrap.(states), ModelingToolkit.unwrap.(species), ModelingToolkit.unwrap.(ps), var_to_name, observed, name, systems, defaults, connection_type, networkproperties, combinatoric_ratelaws, continuous_events, discrete_events, complete)
+    end
 end
 
 function get_speciestype(iv, states, systems)

src/registered_functions.jl

@@ -109,11 +109,11 @@ function Symbolics.derivative(::typeof(hillar), args::NTuple{5, Any}, ::Val{5})
 end
 
 """
-expand_registered_functions!(expr)
+expand_registered_functions(expr)
 
 Takes an expression, and expands registered function expressions. E.g. `mm(X,v,K)` is replaced with v*X/(X+K). Currently supported functions: `mm`, `mmr`, `hill`, `hillr`, and `hill`.
 """
-function expand_registered_functions!(expr)
+function expand_registered_functions(expr)
     istree(expr) || return expr
     args = arguments(expr)
     if operation(expr) == Catalyst.mm
@@ -131,4 +131,8 @@ function expand_registered_functions!(expr)
         args[i] = expand_registered_functions!(args[i])
     end
     return expr
-end
+end
+# If applied to a reaction, return a reaction with its rate modified.
+function expand_registered_functions(rx::Reaction)
+    Reaction(expand_registered_functions(rx.rate), rx.substrates, rx.products, rx.substoich, rx.prodstoich, rx.netstoich, rx.only_use_rate)
+end