Merge pull request #98 from LCSB-BioCore/mk-aj-math

comprehensive math

src/symbolics.jl

@@ -11,22 +11,57 @@ unambiguously represented in Julia; it is supposed to be extended by the user
 if more functions need to be supported.
 """
 const default_symbolics_mapping = Dict{String,Any}(
+    "*" => :*,
     "+" => :+,
     "-" => :-,
-    "*" => :*,
     "/" => :/,
-    "power" => :^,
-    "lt" => :<,
-    "leq" => :<=,
-    "geq" => :>=,
-    "gt" => :>,
+    "abs" => :abs,
+    "arccos" => :acos,
+    "arccosh" => :acosh,
+    "arccot" => :acot,
+    "arccoth" => :acoth,
+    "arccsc" => :acsc,
+    "arccsch" => :acsch,
+    "arcsec" => :asec,
+    "arcsech" => :asech,
+    "arcsin" => :asin,
+    "arcsinh" => :asinh,
+    "arctan" => :atan,
+    "arctanh" => :atanh,
     "ceiling" => :ceil,
+    "cos" => :cos,
+    "cosh" => :cosh,
+    "cot" => :cot,
+    "coth" => :coth,
+    "csc" => :csc,
+    "csch" => :csch,
+    "eq" => :isequal,
+    "exp" => :exp,
+    "factorial" => :factorial,
     "floor" => :floor,
-    "piecewise" => :(Core.ifelse),
+    "geq" => :>=,
+    "gt" => :>,
+    "leq" => :<=,
     "ln" => :log,
-    "exp" => :exp,
+    "log" => :sbmlLog,
+    "lt" => :<,
+    "piecewise" => :(Core.ifelse),
+    "power" => :^,
+    "root" => :sbmlRoot,
+    "sech" => :sech,
+    "sec" => :sec,
+    "sinh" => :sinh,
+    "sin" => :sin,
+    "tanh" => :tanh,
+    "tan" => :tan,
 )
 
+sbmlLog(x) = log(x, 10)
+sbmlLog(base, x) = log(base, x)
+
+sbmlRoot(x) = sqrt(x)
+sbmlRoot(power, x) = x^(1 / power)
+
 allowed_sym(x, allowed_funs) =
     haskey(allowed_funs, x) ? allowed_funs[x] :
     throw(DomainError(x, "Unknown SBML function"))

test/loadmodels.jl

@@ -40,6 +40,14 @@ sbmlfiles = [
         4,
         2,
     ),
+    # this contains some special math
+    (
+        joinpath(@__DIR__, "data", "sbml01565.xml"),
+        "https://raw.githubusercontent.com/sbmlteam/sbml-test-suite/master/cases/semantic/01565/01565-sbml-l3v1.xml",
+        "14a80fbce316eea2adb566f67b4668ad151db8954e487309852ece7f730c8c99",
+        104,
+        52,
+    ),
 ]
 
 @testset "Loading of models from various sources" begin
@@ -108,3 +116,12 @@ end
     @test subterm.args[1] == SBML.MathIdent("S1")
     @test isapprox(subterm.args[2].val, 1.0)
 end
+
+@testset "logBase and root math functions" begin
+    m = readSBML(joinpath(@__DIR__, "data", "sbml01565.xml"))
+
+    @test convert(Num, m.reactions["J23"].kinetic_math) == 0.0
+
+    @variables S29 S29b
+    @test isequal(convert(Num, m.reactions["J29"].kinetic_math), 2.0 * S29 * S29b)
+end