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fix default handling #19

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merged 3 commits into from
Jul 20, 2021
Merged

fix default handling #19

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aba1f14
fix default handling. remove checksupport(::Model)
anandijain Jul 20, 2021
a27d416
remove some duplicate code
anandijain Jul 20, 2021
667bbdc
defaults dispatch for Model
anandijain Jul 20, 2021
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29 changes: 8 additions & 21 deletions src/reactionsystem.jl
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Original file line number Diff line number Diff line change
@@ -1,32 +1,16 @@
""" ReactionSystem constructor """
function ModelingToolkit.ReactionSystem(model::SBML.Model; kwargs...) # Todo: requires unique parameters (i.e. SBML must have been imported with localParameter promotion in libSBML)
checksupport(model)
rxs = mtk_reactions(model)
species = []
for k in keys(model.species)
push!(species, create_var(k,Catalyst.DEFAULT_IV))
end
params = vcat([create_param(k) for k in keys(model.parameters)], [create_param(k) for (k,v) in model.compartments if !isnothing(v.size)])
ReactionSystem(rxs,Catalyst.DEFAULT_IV,species,params; kwargs...)
u0map = get_u0map(model)
parammap = get_paramap(model)
defs = ModelingToolkit._merge(u0map, parammap)
ReactionSystem(rxs,Catalyst.DEFAULT_IV,first.(u0map),first.(parammap); defaults=defs, kwargs...)
end

""" ODESystem constructor """
function ModelingToolkit.ODESystem(model::SBML.Model; kwargs...)
rs = ReactionSystem(model; kwargs...)
u0map = [create_var(k,Catalyst.DEFAULT_IV) => v for (k,v) in SBML.initial_amounts(model, convert_concentrations = true)]
parammap = get_paramap(model)
defaults = Dict(vcat(u0map, parammap))
convert(ODESystem, rs, defaults=defaults)
end

""" Check if conversion to ReactionSystem is possible """
function checksupport(model::SBML.Model)
# for s in values(model.species)
# if s.boundary_condition
# @warn "Species $(s.name) has `boundaryCondition` or is `constant`. This will lead to wrong results when simulating the `ReactionSystem`."
# end
# end
return nothing
convert(ODESystem, rs)
end

""" Check if conversion to ReactionSystem is possible """
Expand Down Expand Up @@ -216,6 +200,9 @@ function get_paramap(model)
paramap
end

get_u0map(model) = [create_var(k,Catalyst.DEFAULT_IV) => v for (k,v) in SBML.initial_amounts(model, convert_concentrations = true)]
ModelingToolkit.defaults(model::SBML.Model) = ModelingToolkit._merge(get_u0map(model), get_paramap(model))

""" Get rate constant of mass action kineticLaws """
function getmassaction(kl::Num, reactants::Union{Vector{Num},Nothing}, stoich::Union{Vector{<:Real},Nothing})
function check_args(x::SymbolicUtils.Symbolic{Real})
Expand Down
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