Commit 5ad8c293 authored by Miroslav Kratochvil's avatar Miroslav Kratochvil
Browse files

explain the problematic distinction of reactions right at the source

parent 1e9347be
Pipeline #56519 failed with stages
in 9 minutes and 31 seconds
......@@ -12,7 +12,14 @@ _missing_impl_error(m, a) = throw(MethodError(m, a))
"""
reactions(a::MetabolicModel)::Vector{String}
Return a vector of reaction identifiers in a model.
Return a vector of reaction identifiers in a model. The vector precisely
corresponds to the columns in [`stoichiometry`](@ref) matrix.
For technical reasons, the "reactions" may sometimes not be true reactions but
various virtual and helper pseudo-reactions that are used in the metabolic
modeling, such as metabolite exchanges, separate forward and reverse reactions,
supplies of enzymatic and genetic material and virtual cell volume, etc. To
simplify the view of the model contents use [`reaction_flux`](@ref).
"""
function reactions(a::MetabolicModel)::Vector{String}
_missing_impl_error(reactions, (a,))
......@@ -21,7 +28,11 @@ end
"""
metabolites(a::MetabolicModel)::Vector{String}
Return a vector of metabolite identifiers in a model.
Return a vector of metabolite identifiers in a model. The vector precisely
corresponds to the rows in [`stoichiometry`](@ref) matrix.
As with [`reaction`](@ref)s, some metabolites in models may be virtual,
representing purely technical equality constraints.
"""
function metabolites(a::MetabolicModel)::Vector{String}
_missing_impl_error(metabolites, (a,))
......
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