add space for kineticLaw math rules

src/SBML.jl

@@ -6,6 +6,7 @@ using SparseArrays
 include("structs.jl")
 include("version.jl")
 include("readsbml.jl")
+include("math.jl")
 include("utils.jl")
 
 sbml = (sym::Symbol) -> dlsym(SBML_jll.libsbml_handle, sym)

src/math.jl

+
+"""
+    parseMath(ast::VPtr)::Math
+
+This attempts to parse out a decent Julia-esque ([`Math`](@ref) AST from a
+pointer to `ASTNode_t`.
+"""
+function parseMath(ast::VPtr)::Math
+    @info "got $ast"
+    MathIdent("placeholder")
+end

src/readsbml.jl

@@ -216,6 +216,7 @@ function extractModel(mdl::VPtr)::Model
         lb = (-Inf, "") # (bound value, unit id)
         ub = (Inf, "")
         oc = 0.0
+        math = nothing
 
         # kinetic laws store a second version of the bounds and objectives
         kl = ccall(sbml(:Reaction_getKineticLaw), VPtr, (VPtr,), re)
@@ -233,6 +234,10 @@ function extractModel(mdl::VPtr)::Model
                     oc = pval()
                 end
             end
+
+            if ccall(sbml(:KineticLaw_isSetMath), Cint, (VPtr,), kl) != 0
+                math = parseMath(ccall(sbml(:KineticLaw_getMath), VPtr, (VPtr,), kl))
+            end
         end
 
         # TRICKY: SBML spec is completely silent about what should happen if
@@ -272,6 +277,7 @@ function extractModel(mdl::VPtr)::Model
             add_stoi(sr, 1)
         end
 
+        # gene product associations
         association = nothing
         if re_fbc != C_NULL
             gpa = ccall(
@@ -294,6 +300,7 @@ function extractModel(mdl::VPtr)::Model
             ub,
             haskey(objectives_fbc, reid) ? objectives_fbc[reid] : oc,
             association,
+            math,
             getNotes(re),
             getAnnotation(re),
         )

src/structs.jl

@@ -55,6 +55,33 @@ struct GPAOr <: GeneProductAssociation
     terms::Vector{GeneProductAssociation}
 end
 
+"""
+A simplified representation of MathML-specified math AST
+"""
+abstract type Math end
+
+"""
+A literal value (usually a numeric constant) in mathematical expression
+"""
+struct MathVal{T} <: Math where {T}
+    val::T
+end
+
+"""
+An identifier (usually a variable name) in mathematical expression
+"""
+struct MathIdent <: Math
+    id::String
+end
+
+"""
+Function application ("call by name", no tricks allowed) in mathematical expression
+"""
+struct MathApply <: Math
+    fn::String
+    attributes::Dict{String,String}
+    args::Vector{Math}
+end
 
 """
 Reaction with stoichiometry that assigns reactants and products their relative
@@ -68,9 +95,10 @@ struct Reaction
     ub::Tuple{Float64,String}
     oc::Float64
     gene_product_association::Maybe{GeneProductAssociation}
+    kinetic_math::Maybe{Math}
     notes::Maybe{String}
     annotation::Maybe{String}
-    Reaction(s, l, u, o, as, n = nothing, an = nothing) = new(s, l, u, o, as, n, an)
+    Reaction(s, l, u, o, as, km, n = nothing, an = nothing) = new(s, l, u, o, as, km, n, an)
 end
 
 """