Unverified Commit e20ba0ec authored by Miroslav Kratochvil's avatar Miroslav Kratochvil Committed by GitHub
Browse files

Merge pull request #606 from LCSB-BioCore/mo-small-fixes

Small fixes
parents 418186b1 f406440e
Pipeline #55697 passed with stages
in 24 minutes and 30 seconds
......@@ -7,7 +7,6 @@ id :: String
name :: Maybe{String}
notes :: Dict{String, Vector{String}}
annotation :: Dict{String, Union{Vector{String}, String}}
molar_mass :: Maybe{Float64}
````
"""
mutable struct Gene
......@@ -15,13 +14,7 @@ mutable struct Gene
name::Maybe{String}
notes::Notes
annotations::Annotations
molar_mass::Maybe{Float64}
Gene(
id::String = "";
name = nothing,
notes = Notes(),
annotations = Annotations(),
molar_mass = nothing,
) = new(id, name, notes, annotations, molar_mass)
Gene(id::String = ""; name = nothing, notes = Notes(), annotations = Annotations()) =
new(id, name, notes, annotations)
end
......@@ -55,10 +55,10 @@ The structure contains fields `columns` that describe the contents of the
coupling columns, `coupling_row_reaction`, `coupling_row_gene_product` and
`coupling_row_mass_group` that describe correspondence of the coupling rows to
original model and determine the coupling bounds, and `inner`, which is the
original wrapped model. Note, `objective` is the objective vector of the model,
special care needs to be taken to ensure that its length is `n_reactions(model)
+ n_genes(model)` when the user modifies it, where `model` is the GeckoModel in
question.
original wrapped model. Note, `objective` is the objective vector of the model.
Special care needs to be taken to ensure that its length is the sum of
`n_reactions(model)` and `n_genes(model)` when the user modifies it, where
`model` is the GeckoModel in question.
Implementation exposes the split reactions (available as `reactions(model)`),
but retains the original "simple" reactions accessible by [`fluxes`](@ref). All
......
......@@ -46,8 +46,10 @@
)
prot_mass = sum(ecoli_core_gene_product_masses[gid] * c for (gid, c) in prot_concens)
mass_groups = gene_product_mass_group_dict(gm, opt_model)
@test isapprox(prot_mass, total_gene_product_mass, atol = TEST_TOLERANCE)
@test isapprox(prot_mass, mass_groups["uncategorized"], atol = TEST_TOLERANCE)
end
@testset "GECKO small model" begin
......
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