Merge pull request #854 from SciML/add_nonreaction_function

Add `nonreaction` function

Author: TorkelE

docs/src/api.md

@@ -157,6 +157,7 @@ species
 nonspecies
 reactionparams
 reactions
+nonreactions
 numspecies
 numparams
 numreactions

src/Catalyst.jl

@@ -98,7 +98,7 @@ export get_noise_scaling, has_noise_scaling
 # The `ReactionSystem` structure and its functions.
 include("reactionsystem.jl")
 export ReactionSystem, isspatial
-export species, nonspecies, reactionparams, reactions, speciesmap, paramsmap
+export species, nonspecies, reactionparams, reactions, nonreactions, speciesmap, paramsmap
 export numspecies, numreactions, numreactionparams, setdefaults!
 export make_empty_network, reactionparamsmap
 export dependants, dependents, substoichmat, prodstoichmat, netstoichmat

src/reactionsystem.jl

@@ -811,6 +811,18 @@ function numreactions(network)
     nr
 end
 
+"""
+    nonreactions(network)
+
+Return the non-reaction equations within the network (i.e. algebraic and differnetial equations).
+
+Notes:
+- Allocates a new array to store the non-species variables.
+"""
+function nonreactions(network)
+    equations(network)[(numreactions(network) + 1):end]
+end
+
 """
     numreactionparams(network)
 

test/reactionsystem_core/coupled_equation_crn_systems.jl

@@ -211,6 +211,55 @@ let
 end
 
 
+### Accessor Tests ###
+
+# Checks basic accessor functions for a basic coupled CRN/equation model.
+let
+    # Creates a reaction system.
+    t = default_t()
+    D = default_time_deriv()
+    @parameters p d v
+    @species X(t)
+    @variables V(t) W(t)
+
+    eqs = [
+        Reaction(p, [], [X]),
+        Reaction(d, [X], []),
+        Reaction(d, [X], nothing, [2], nothing),
+        D(V) ~ X - v*V,
+        W^2 ~ log(V) + X 
+    ]
+    @named coupled_rs = ReactionSystem(eqs, t)
+
+    # Check unknowns-related accessors.
+    @test Catalyst.has_species(coupled_rs)
+    @test issetequal(Catalyst.get_species(coupled_rs), [X])
+    @test issetequal(species(coupled_rs), [X])
+    @test issetequal(ModelingToolkit.get_unknowns(coupled_rs), [X, V, W])
+    @test issetequal(unknowns(coupled_rs), [X, V, W])
+    @test issetequal(nonspecies(coupled_rs), [V, W])
+    @test numspecies(coupled_rs) == 1
+
+    # Check parameters-related accessors.
+    @test Catalyst.has_rxs(coupled_rs)
+    @test issetequal(Catalyst.get_rxs(coupled_rs), eqs[1:3])
+    @test issetequal(reactions(coupled_rs), eqs[1:3])
+    @test issetequal(equations(coupled_rs), eqs)
+    @test issetequal(nonreactions(coupled_rs), eqs[4:5])
+    @test issetequal(reactionrates(coupled_rs), [p, d, d])
+    @test numreactions(coupled_rs) == 3
+
+    # Check parameters-related accessors.
+    @test issetequal(parameters(coupled_rs), [p, d, v])
+    @test issetequal(reactionparams(coupled_rs), [p, d, v])
+    @test numparams(coupled_rs) == 3
+    @test numreactionparams(coupled_rs) == 3
+
+    # Check other accessors.
+    @test !isspatial(coupled_rs)
+end
+
+
 ### Species, Variables, and Parameter Handling ###
 
 # Checks that coupled systems contain the correct species, variables, and parameters.