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LCSB-BioCore · Nov 27, 2021 · 043f2aa · 043f2aa
1 parent aaf25b0
commit 043f2aa
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Showing 2 changed files with 27 additions and 15 deletions.
diff --git a/src/analysis/max_min_driving_force.jl b/src/analysis/max_min_driving_force.jl
@@ -176,7 +176,8 @@ function max_min_driving_force(
             rid => value(opt_model[:dgrs][i]) for (i, rid) in enumerate(reactions(model))
         ),
         concentrations = Dict(
-            mid => exp(value(opt_model[:logcs][i])) for (i, mid) in enumerate(metabolites(model))
+            mid => exp(value(opt_model[:logcs][i])) for
+            (i, mid) in enumerate(metabolites(model))
         ),
     )
 end
@@ -227,7 +228,7 @@ function max_min_driving_force_variability(
     model::MetabolicModel,
     reaction_standard_gibbs_free_energies::Dict{String,Float64},
     optimizer;
-    workers =[myid()],
+    workers = [myid()],
     relax_driving_force = 0.9,
     flux_solution::Dict{String,Float64} = Dict{String,Float64}(),
     proton_ids::Vector{String} = ["h_c", "h_e"],
@@ -261,12 +262,21 @@ function max_min_driving_force_variability(
         small_flux_tol,
         modifications,
         ignore_reaction_ids,
-        )
+    )
 
     mmdf = initsol.mmdf
 
-    dgr_variants = [[[_mmdf_add_df_bound(mmdf, relax_driving_force), _mmdf_dgr_objective(ridx, sense)],] for ridx in 1:n_reactions(model), sense in [MOI.MAX_SENSE, MOI.MIN_SENSE]]
-    concen_variants = [[[_mmdf_add_df_bound(mmdf, relax_driving_force), _mmdf_concen_objective(midx, sense)],] for midx in 1:n_metabolites(model), sense in [MOI.MAX_SENSE, MOI.MIN_SENSE]]
+    dgr_variants = [
+        [[_mmdf_add_df_bound(mmdf, relax_driving_force), _mmdf_dgr_objective(ridx, sense)]] for ridx = 1:n_reactions(model), sense in [MOI.MAX_SENSE, MOI.MIN_SENSE]
+    ]
+    concen_variants = [
+        [
+            [
+                _mmdf_add_df_bound(mmdf, relax_driving_force),
+                _mmdf_concen_objective(midx, sense),
+            ],
+        ] for midx = 1:n_metabolites(model), sense in [MOI.MAX_SENSE, MOI.MIN_SENSE]
+    ]
 
     return screen(
         model;
@@ -285,7 +295,7 @@ function max_min_driving_force_variability(
             T,
             R,
             small_flux_tol,
-            modifications=[modifications; args],
+            modifications = [modifications; args],
             ignore_reaction_ids,
         ),
         workers,
@@ -316,7 +326,7 @@ Helper function to add a new constraint on the driving force.
 function _mmdf_add_df_bound(dg_opt, gamma)
     (model, opt_model) -> begin
         if gamma == 1
-            fix(opt_model[:mmdf], dg_opt; force=true)
+            fix(opt_model[:mmdf], dg_opt; force = true)
         else
             @constraint(opt_model, gamma * dg_opt <= opt_model[:mmdf])
         end

diff --git a/test/analysis/max_min_driving_force.jl b/test/analysis/max_min_driving_force.jl
@@ -37,21 +37,23 @@
         flux_solution = flux_solution,
         proton_ids = ["h_c", "h_e"],
         water_ids = ["h2o_c", "h2o_e"],
-        concentration_ratios = Dict{Tuple{String, String}, Float64}(
+        concentration_ratios = Dict{Tuple{String,String},Float64}(
             ("atp_c", "adp_c") => 10.0,
             ("nadh_c", "nad_c") => 0.13,
             ("nadph_c", "nadp_c") => 1.3,
         ),
-        constant_concentrations = Dict{String, Float64}(
-            # "pi_c" => 10e-3
+        constant_concentrations = Dict{String,Float64}(
+        # "pi_c" => 10e-3
         ),
         concentration_lb = 1e-6,
         concentration_ub = 100e-3,
-        ignore_reaction_ids = [
-            "H2Ot",
-        ],
-        modifications = [change_optimizer_attribute("IPM_IterationsLimit", 1000),]
+        ignore_reaction_ids = ["H2Ot"],
+        modifications = [change_optimizer_attribute("IPM_IterationsLimit", 1000)],
     )
     pyk_idx = first(indexin(["PYK"], reactions(model)))
-    @test isapprox(sols[pyk_idx].dg_reactions["PYK"], -1.5895040002691128; atol=TEST_TOLERANCE)
+    @test isapprox(
+        sols[pyk_idx].dg_reactions["PYK"],
+        -1.5895040002691128;
+        atol = TEST_TOLERANCE,
+    )
 end