update

Author: TorkelE

docs/src/catalyst_functionality/chemistry_related_functionality.md

@@ -7,12 +7,12 @@ While Catalyst has primarily been designed around the modelling of biological sy
 ## Modelling with compound species
 
 #### Creating compound species programmatically
-We will first show how to create compound species through [programmatic construction](@ref programmatic_CRN_construction), and then demonstrate using the DSL. To create a compound species, use the `@compound` macro, first designating the compound, followed by its components (and stoichiometries). In this example, we will create a CO₂ compound species, consisting of one C species and two O species. First, we create species corresponding to the components:
+We will first show how to create compound species through [programmatic construction](@ref programmatic_CRN_construction), and then demonstrate using the DSL. To create a compound species, use the `@compound` macro, first designating the compound, followed by its components (and stoichiometries). In this example, we will create a CO₂ molecule, consisting of one C atom and two O atoms. First, we create species corresponding to the components:
 ```@example chem1
 @variables t
 @species C(t) O(t) 
 ```
-Next, we create the `CO2` compound:
+Next, we create the `CO2` compound species:
 ```@example chem1
 @compound CO2(t) = C + 2O
 ```
@@ -76,10 +76,10 @@ rn = @reaction_network begin
     (k1,k2), H2O+ CO2 <--> H2CO3
 end
 ```
-as the components `C`, `H`, and `O` are not explicitly declared as a species anywhere. Please also note that only `@compounds` can be used as an option in the DSL, not `@compound`.
+as the components `C`, `H`, and `O` are not declared as a species anywhere. Please also note that only `@compounds` can be used as an option in the DSL, not `@compound`.
 
 ## Balancing chemical reactions
-One use of defining a species as a compound is that they can be used to balance reactions to that the number of compounds are the same on both sides. Catalyst provides the `balance_reaction` function, which takes a reaction, and returns a balanced version. E.g. let us consider a reaction when carbon dioxide is formed from carbon and oxide `C + O --> CO2`. Here, `balance_reaction` enables us to find coefficients creating a balanced reaction (in this case, where the number of carbon and oxygen atoms are the same on both sides). To demonstrate, we first created the unbalanced reactions:
+One use of defining a species as a compound is that they can be used to balance reactions to that the number of components are the same on both sides. Catalyst provides the `balance_reaction` function, which takes a reaction, and returns a balanced version. E.g. let us consider a reaction when carbon dioxide is formed from carbon and oxide `C + O --> CO2`. Here, `balance_reaction` enables us to find coefficients creating a balanced reaction (in this case, where the number of carbon and oxygen atoms are the same on both sides). To demonstrate, we first created the unbalanced reactions:
 ```@example chem1
 rx = @reaction k, C + O --> $CO2
 ```

src/chemistry_functionality.jl

@@ -55,14 +55,6 @@ function make_compound(expr)
     components_designation_expr = Expr(:escape, :($species_name = ModelingToolkit.setmetadata($species_name, Catalyst.CompoundComponents, $components)))        # E.g. `CO2 = ModelingToolkit.setmetadata(CO2, Catalyst.CompoundSpecies, [C, O])`
     coefficients_designation_expr = Expr(:escape, :($species_name = ModelingToolkit.setmetadata($species_name, Catalyst.CompoundCoefficients, $coefficients)))  # E.g. `CO2 = ModelingToolkit.setmetadata(CO2, Catalyst.CompoundSpecies, [1, 2])`
 
-    println(
-        return quote
-            $species_declaration_expr
-            $compound_designation_expr
-            $components_designation_expr
-            $coefficients_designation_expr
-        end)
-
     # Returns the rephrased expression.
     return quote
         $species_declaration_expr

src/reaction_network.jl

@@ -468,11 +468,11 @@ end
 
 # When compound species are declared using the "@compound begin ... end" option, get a list of the compound species, and also the expression that crates them.
 function read_compound_options(opts)
-    # If the compound option is used retrive a list of compound species, and the option that creeates them
+    # If the compound option is used retrive a list of compound species (need to be added to teh reaction system's species), and the option that creates them (used to declare them as compounds at the end).
     if haskey(opts, :compounds)
         compound_expr = opts[:compounds]
         compound_species = [arg.args[1].args[1] for arg in compound_expr.args[3].args] # Loops through where in the "@compound begin ... end" the compound species names are.
-    else
+    else  # If option is not used, return empty vectors and expressions.
         compound_expr = :()
         compound_species = Union{Symbol, Expr}[]
     end

test/miscellaneous_tests/compound_macro.jl

@@ -106,7 +106,7 @@ let
     @compound H2_1(t) = 2*H
     @compound H2_2(t) = alpha*H
     @compound H2_3(t) = 2*h
-    @compound H2_4(t) = alpha*2H
+    @compound H2_4(t) = alpha*H
 
     @test iscompound(H2_1)
     @test iscompound(H2_2)