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support kinetic laws with only cn elements #131

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support kinetic laws with only cn elements #131

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0ed1869
support kinetic laws with only cn elements
Jul 24, 2023
80c1ee8
add test
Jul 24, 2023
fe2a939
update patcch version
Jul 24, 2023
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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "SBMLToolkit"
uuid = "86080e66-c8ac-44c2-a1a0-9adaadfe4a4e"
authors = ["paulflang", "anandijain"]
version = "0.1.24"
version = "0.1.25"

[deps]
Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
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7 changes: 6 additions & 1 deletion src/reactions.jl
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Expand Up @@ -53,7 +53,7 @@ function get_unidirectional_components(bidirectional_math)
end

function add_reaction!(rxs::Vector{Reaction},
kl::Num,
kl::Union{Num, Float64},
reactant_references::Vector{SBML.SpeciesReference},
product_references::Vector{SBML.SpeciesReference},
model::SBML.Model;
Expand Down Expand Up @@ -157,6 +157,11 @@ function use_rate(kl::Num, react::Union{Vector{Num}, Nothing},
return (kl, our)
end

function use_rate(kl::Float64, ::Union{Vector{Num}, Nothing},
::Union{Vector{<:Real}, Nothing})
(kl, true)
end

"""
Get rate constant of mass action kineticLaws
"""
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11 changes: 11 additions & 0 deletions test/reactions.jl
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Expand Up @@ -51,6 +51,17 @@ model = SBML.Model(parameters = Dict("k1" => PARAM1),
reactions = Dict("r1" => reac))
@test isequal(IV, SBMLToolkit.get_reactions(model)[1].rate)

km = SBML.MathVal(1.0)
reac = SBML.Reaction(products = [
SBML.SpeciesReference(species = "s1", stoichiometry = 1),
],
kinetic_math = km,
reversible = false)
model = SBML.Model(compartments = Dict("c1" => COMP1),
species = Dict("s1" => SPECIES1),
reactions = Dict("r2" => reac))
@test isequal(1, SBMLToolkit.get_reactions(model)[1].rate)

# Test get_unidirectional_components
km = SBML.MathApply("-", SBML.Math[KINETICMATH1, SBML.MathIdent("c1")])
sm = SBMLToolkit.interpret_as_num(km, MODEL1)
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