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Return enzyme concentrations in useful units #757

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merged 4 commits into from
Feb 17, 2023
Merged

Return enzyme concentrations in useful units #757

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0acdf62
rather map through molar masses
stelmo Feb 16, 2023
6346ac7
Update docstring for clarity
stelmo Feb 17, 2023
50f6171
more docstrings
stelmo Feb 17, 2023
f515349
fix docstrings
stelmo Feb 17, 2023
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10 changes: 5 additions & 5 deletions src/types/wrappers/EnzymeConstrainedModel.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -176,7 +176,7 @@ end
$(TYPEDSIGNATURES)

Get the mapping of the reaction rates in [`EnzymeConstrainedModel`](@ref) to
the original fluxes in the wrapped model
the original fluxes in the wrapped model.
"""
Accessors.reaction_variables(model::EnzymeConstrainedModel) =
Accessors.Internal.make_mapping_dict(
Expand All @@ -188,16 +188,16 @@ Accessors.reaction_variables(model::EnzymeConstrainedModel) =
"""
$(TYPEDSIGNATURES)

Get a mapping of enzyme variables to variables -- for enzyme constrained models,
this is just a direct mapping.
Get a mapping of enzyme concentration (on a mass basis, i.e. mass enzyme/mass
cell) variables to inner variables.
"""
Accessors.enzyme_variables(model::EnzymeConstrainedModel) =
Dict(gid => Dict(gid => 1.0) for gid in genes(model)) # this is enough for all the semantics to work
Dict(gid => Dict(gid => gene_product_molar_mass(model, gid)) for gid in genes(model)) # this is enough for all the semantics to work

"""
$(TYPEDSIGNATURES)

Get a mapping of enzyme groups to variables.
Get a mapping of enzyme groups to variables. See [`enzyme_variables`](@ref).
"""
function Accessors.enzyme_group_variables(model::EnzymeConstrainedModel)
enz_ids = genes(model)
Expand Down
15 changes: 11 additions & 4 deletions test/reconstruction/enzyme_constrained.jl
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Expand Up @@ -60,11 +60,18 @@
atol = TEST_TOLERANCE,
)

prot_mass = sum(ecoli_core_gene_product_masses[gid] * c for (gid, c) in prot_concens)
mass_groups = values_dict(:enzyme_group, gm, opt_model)

@test isapprox(prot_mass, total_gene_product_mass, atol = TEST_TOLERANCE)
@test isapprox(prot_mass, mass_groups["uncategorized"], atol = TEST_TOLERANCE)
@test isapprox(
sum(values(prot_concens)),
total_gene_product_mass,
atol = TEST_TOLERANCE,
)
@test isapprox(
sum(values(prot_concens)),
mass_groups["uncategorized"],
atol = TEST_TOLERANCE,
)

# test enzyme objective
growth_lb = rxn_fluxes["BIOMASS_Ecoli_core_w_GAM"] * 0.9
Expand Down Expand Up @@ -147,7 +154,7 @@ end
mass_groups = values_dict(:enzyme_group, gm, opt_model)

@test isapprox(rxn_fluxes["r6"], 1.1688888886502442, atol = TEST_TOLERANCE)
@test isapprox(gene_products["g4"], 0.02666666666304931, atol = TEST_TOLERANCE)
@test isapprox(gene_products["g4"], 0.02666666666304931 * 4.0, atol = TEST_TOLERANCE)
@test isapprox(mass_groups["uncategorized"], 0.5, atol = TEST_TOLERANCE)
@test isapprox(mass_groups["bound2"], 0.04, atol = TEST_TOLERANCE)
@test length(genes(gm)) == 4
Expand Down