Merge pull request #142 from anandijain/aj/substoich_prodstoich

separate reactants and product stoichiometries

src/readsbml.jl

@@ -358,24 +358,23 @@ function extractModel(mdl::VPtr)::SBML.Model
         end
 
         # extract stoichiometry
-        stoi = Dict{String,Float64}()
-        add_stoi(sr, factor) = begin
+        reactants = Dict{String,Float64}()
+        products = Dict{String,Float64}()
+
+        add_stoi(sr, coll) = begin
             s = get_string(sr, :SpeciesReference_getSpecies)
-            stoi[s] =
-                get(stoi, s, 0) +
-                ccall(sbml(:SpeciesReference_getStoichiometry), Cdouble, (VPtr,), sr) *
-                factor
+            coll[s] =
+                ccall(sbml(:SpeciesReference_getStoichiometry), Cdouble, (VPtr,), sr)
         end
 
-        # reactants and products
         for j = 1:ccall(sbml(:Reaction_getNumReactants), Cuint, (VPtr,), re)
             sr = ccall(sbml(:Reaction_getReactant), VPtr, (VPtr, Cuint), re, j - 1)
-            add_stoi(sr, -1)
+            add_stoi(sr, reactants)
         end
 
         for j = 1:ccall(sbml(:Reaction_getNumProducts), Cuint, (VPtr,), re)
             sr = ccall(sbml(:Reaction_getProduct), VPtr, (VPtr, Cuint), re, j - 1)
-            add_stoi(sr, 1)
+            add_stoi(sr, products)
         end
 
         # gene product associations
@@ -399,7 +398,8 @@ function extractModel(mdl::VPtr)::SBML.Model
 
         reid = get_string(re, :Reaction_getId)
         reactions[reid] = Reaction(
-            stoi,
+            reactants,
+            products,
             lb,
             ub,
             haskey(objectives_fbc, reid) ? objectives_fbc[reid] : oc,

src/structs.jl

@@ -99,15 +99,16 @@ end
 $(TYPEDEF)
 
 Reaction with stoichiometry that assigns reactants and products their relative
-consumption/production rates (accessible in field `stoichiometry`), lower/upper
-bounds (in tuples `lb` and `ub`, with unit names), and objective coefficient
-(`oc`). Also may contains `notes` and `annotation`.
+consumption/production rates, lower/upper bounds (in tuples `lb` and `ub`, with
+unit names), and objective coefficient (`oc`). Also may contains `notes` and
+`annotation`.
 
 # Fields
 $(TYPEDFIELDS)
 """
 struct Reaction
-    stoichiometry::Dict{String,Float64}
+    reactants::Dict{String,Float64}
+    products::Dict{String,Float64}
     lb::Tuple{Float64,String}
     ub::Tuple{Float64,String}
     oc::Float64
@@ -116,8 +117,8 @@ struct Reaction
     reversible::Bool
     notes::Maybe{String}
     annotation::Maybe{String}
-    Reaction(s, l, u, o, as, km, r, n = nothing, an = nothing) =
-        new(s, l, u, o, as, km, r, n, an)
+    Reaction(rs, ps, l, u, o, as, km, r, n = nothing, an = nothing) =
+        new(rs, ps, l, u, o, as, km, r, n, an)
 end
 
 """

src/utils.jl

@@ -18,8 +18,10 @@ function stoichiometry_matrix(
     rowsd = Dict(k => i for (i, k) in enumerate(rows))
     S = zeros(Float64, length(rows), length(cols))
     for col = 1:length(cols)
-        stoi = m.reactions[cols[col]].stoichiometry
-        S[getindex.(Ref(rowsd), keys(stoi)), col] .= values(stoi)
+        s = m.reactions[cols[col]].reactants
+        S[getindex.(Ref(rowsd), keys(s)), col] .-= values(s)
+        s = m.reactions[cols[col]].products
+        S[getindex.(Ref(rowsd), keys(s)), col] .+= values(s)
     end
     return rows, cols, S
 end