Merge pull request #757 from LCSB-BioCore/mo-sensible-enzyme-map

Return enzyme concentrations in useful units
LCSB-BioCore · Feb 17, 2023 · 979d57c · 979d57c
2 parents c5ac155 + f515349
commit 979d57c
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Showing 2 changed files with 16 additions and 9 deletions.
diff --git a/src/types/wrappers/EnzymeConstrainedModel.jl b/src/types/wrappers/EnzymeConstrainedModel.jl
@@ -146,7 +146,7 @@ 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(
@@ -158,16 +158,16 @@ 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)

diff --git a/test/reconstruction/enzyme_constrained.jl b/test/reconstruction/enzyme_constrained.jl
@@ -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
@@ -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