Merge pull request #210 from ReactionMechanismGenerator/spc_rxn_constructor

Add species and reaction constructors

Author: mjohnson541

src/Reaction.jl

@@ -1,27 +1,31 @@
-using Parameters
 import Base: length,show,print,println
 using StaticArrays
 abstract type AbstractReaction end
 export AbstractReaction
 
-@with_kw struct ElementaryReaction{T<:AbstractRate,Q<:Integer,V1<:AbstractArray,V2<:AbstractArray,V3<:AbstractArray,V4<:AbstractArray,V5<:AbstractArray,V6<:AbstractArray,V7<:AbstractArray,V8<:AbstractArray,V9<:AbstractArray} <: AbstractReaction
+struct ElementaryReaction{T<:AbstractRate,Q<:Integer,V1<:AbstractArray,V2<:AbstractArray,V3<:AbstractArray,V4<:AbstractArray,V5<:AbstractArray,V6<:AbstractArray,V7<:AbstractArray,V8<:AbstractArray,V9<:AbstractArray} <: AbstractReaction
     index::Q
     reactants::V1
     reactantinds::V2
     products::V3
     productinds::V4
     kinetics::T
-    electronchange::Int64 = 0
-    radicalchange::Int64 = -100
-    reversible::Bool = true
-    forwardable::Bool = true
-    pairs::V5 = [[""]]
-    fragmentbasedreactants::V6 = []
-    fragmentbasedproducts::V7 = []
-    fragmentbasedreactantinds::V8 = []
-    fragmentbasedproductinds::V9 = []
-    comment::String = ""
+    electronchange::Int64
+    radicalchange::Int64
+    reversible::Bool
+    forwardable::Bool
+    pairs::V5
+    fragmentbasedreactants::V6
+    fragmentbasedproducts::V7
+    fragmentbasedreactantinds::V8
+    fragmentbasedproductinds::V9
+    comment::String
 end
+
+function ElementaryReaction(; index::Q, reactants::V1, reactantinds::V2, products::V3, productinds::V4, kinetics::T, electronchange::Int64=0, radicalchange::Int64=-100, reversible::Bool=true, forwardable::Bool=true, pairs::V5=[[""]], fragmentbasedreactants::V6=[], fragmentbasedproducts::V7=[], fragmentbasedreactantinds::V8=[], fragmentbasedproductinds::V9=[], comment::String="") where {T<:AbstractRate,Q<:Integer,V1<:AbstractArray,V2<:AbstractArray,V3<:AbstractArray,V4<:AbstractArray,V5<:AbstractArray,V6<:AbstractArray,V7<:AbstractArray,V8<:AbstractArray,V9<:AbstractArray}
+    return ElementaryReaction(index, reactants, reactantinds, products, productinds, kinetics, electronchange, radicalchange, reversible, forwardable, pairs, fragmentbasedreactants, fragmentbasedproducts, fragmentbasedreactantinds, fragmentbasedproductinds, comment)
+end
+
 export ElementaryReaction
 
 getrxnstr(rxn::T) where {T<:AbstractReaction} = join([join(getfield.(rxn.reactants,:name),"+"),join(getfield.(rxn.products,:name),"+")],"<=>")

src/Species.jl

@@ -1,29 +1,38 @@
-using Parameters
 import Base: length
 
 abstract type AbstractSpecies end
 export AbstractSpecies
 
 struct EmptySpecies <: AbstractSpecies end
 
-@with_kw struct Species{T<:AbstractThermo,N<:AbstractDiffusivity,N1<:AbstractHenryLawConstant,N2<:AbstractLiquidVolumetricMassTransferCoefficient} <: AbstractSpecies
+struct Species{T<:AbstractThermo,N<:AbstractDiffusivity,N1<:AbstractHenryLawConstant,N2<:AbstractLiquidVolumetricMassTransferCoefficient} <: AbstractSpecies
     name::String
     index::Integer
-    inchi::String = ""
-    smiles::String = ""
-    adjlist::String = ""
+    inchi::String
+    smiles::String
+    adjlist::String
     thermo::T
-    atomnums::Dict{String,Int64} = Dict()
-    bondnum::Int64=-1
-    diffusion::N = EmptyDiffusivity()
-    radius::Float64 = 0.0
-    radicalelectrons::Int64 = -100
-    molecularweight::Float64 = 0.0
-    henrylawconstant::N1 = EmptyHenryLawConstant()
-    liquidvolumetricmasstransfercoefficient::N2 = EmptyLiquidVolumetricMassTransferCoefficient()
-    comment::String = ""
-    isfragment::Bool = false
-    isfragmentintermediate::Bool = false
+    atomnums::Dict{String,Int64}
+    bondnum::Int64
+    diffusion::N
+    radius::Float64
+    radicalelectrons::Int64
+    molecularweight::Float64
+    henrylawconstant::N1
+    liquidvolumetricmasstransfercoefficient::N2
+    comment::String
+    isfragment::Bool
+    isfragmentintermediate::Bool
+end
+
+function Species(; name::String, index::Integer, inchi::String="", smiles::String="", adjlist::String="", 
+                   thermo::T=nothing, atomnums::Dict{String,Int64}=Dict{String,Int64}(), bondnum::Int64=-1, diffusion::N=EmptyDiffusivity(),
+                   radius::Float64=0.0, radicalelectrons::Int64=-100, molecularweight::Float64=0.0,
+                   henrylawconstant::N1=EmptyHenryLawConstant(), 
+                   liquidvolumetricmasstransfercoefficient::N2=EmptyLiquidVolumetricMassTransferCoefficient(),
+                   comment::String="",isfragment::Bool=false,isfragmentintermediate::Bool=false,
+                   ) where {T<:AbstractThermo,N<:AbstractDiffusivity,N1<:AbstractHenryLawConstant,N2<:AbstractLiquidVolumetricMassTransferCoefficient}
+    return Species(name, index, inchi, smiles, adjlist, thermo, atomnums, bondnum, diffusion, radius, radicalelectrons, molecularweight, henrylawconstant, liquidvolumetricmasstransfercoefficient, comment, isfragment, isfragmentintermediate)
 end
 export Species