From 9200be77c3529f880564ee9057840d9621c0c592 Mon Sep 17 00:00:00 2001
From: Eduard Kerkhoven <eduardk@chalmers.se>
Date: Mon, 2 Nov 2026 11:02:38 +0100
Subject: [PATCH] getPfbaEnzymes: fractionOfOptimum for a negative optimum

---
 src/flux_analysis/getPfbaEnzymes.m       | 15 +++++++------
 test/unit_tests/geckoCoreFunctionTests.m | 28 ++++++++++++++++++++++++
 2 files changed, 36 insertions(+), 7 deletions(-)

diff --git a/src/flux_analysis/getPfbaEnzymes.m b/src/flux_analysis/getPfbaEnzymes.m
index 625eddd8..d14bc34e 100644
--- a/src/flux_analysis/getPfbaEnzymes.m
+++ b/src/flux_analysis/getPfbaEnzymes.m
@@ -21,7 +21,10 @@
 %     (default: use model.c as given).
 % fractionOfOptimum : double
 %     fraction of the optimal objective value to fix before minimising
-%     enzyme usage (default 1.0).
+%     enzyme usage (default 1.0). A value below 1.0 lets the objective fall
+%     by (1 - fractionOfOptimum) times the magnitude of its optimum, so it
+%     also applies to a negative optimum (for example the exchange flux of
+%     a nutrient that is maximised).
 %
 % Returns
 % -------
@@ -89,12 +92,10 @@
 
 % Fix the objective as a constraint, same "fake metabolite" technique
 % solveLP's own minFlux=1 option uses (see solveLP.m).
-target = fractionOfOptimum * solOrig.f;
-if target > 0
-    target = target * 0.999999;
-else
-    target = target * 1.000001;
-end
+% The objective may fall by (1 - fractionOfOptimum*0.999999) of the magnitude
+% of its optimum, for a positive and a negative optimum alike (the band that
+% setParam(model, 'var', ...) sets around a value).
+target = solOrig.f - (1 - fractionOfOptimum*0.999999) * abs(solOrig.f);
 fixModel = model;
 fixModel.S(end+1, :) = model.c';
 fixModel.mets{end+1, 1} = 'getPfbaEnzymes_objective';
diff --git a/test/unit_tests/geckoCoreFunctionTests.m b/test/unit_tests/geckoCoreFunctionTests.m
index 09837df6..e133e721 100644
--- a/test/unit_tests/geckoCoreFunctionTests.m
+++ b/test/unit_tests/geckoCoreFunctionTests.m
@@ -1264,6 +1264,34 @@ function testPfbaEnzymesMinimisesEnzymeUsage_tc0025(testCase)
 end
 
 
+function testPfbaEnzymesFractionOfNegativeOptimum_tc0285(testCase)
+    % Verifies that 'fractionOfOptimum' below 1 lets a negative optimum fall
+    % by that fraction of its magnitude. The objective is -R5 with R5 >= 10,
+    % so its optimum is -10; at 0.9 the objective may fall to -11, and the
+    % solution stays feasible with R5 at its lower bound.
+    geckoPath = findGECKOroot;
+    adapter = ModelAdapterManager.getAdapter(fullfile(geckoPath,'test','unit_tests','ecTestGEM', 'TestGEMAdapter.m'));
+    model = getGeckoTestModel();
+    ecModel = makeEcModel(model, false, adapter);
+    ecModel = getECfromGEM(ecModel);
+    ecModel.ec.kcat(:) = 10;
+    ecModel.ec.source(:) = {'manual'};
+    ecModel = applyKcatConstraints(ecModel);
+    ecModel = setProtPoolSize(ecModel, 0.5, 0.5, 0.5, adapter);
+    ecModel = setParam(ecModel, 'lb', 'R5', 10);
+    ecModel = setParam(ecModel, 'obj', 'R5', -1);
+
+    solution = getPfbaEnzymes(ecModel);
+    verifyEqual(testCase, solution.stat, 1)
+    verifyEqual(testCase, solution.objectiveValue, -10, 'RelTol', 1e-5)
+
+    solution = getPfbaEnzymes(ecModel, 'fractionOfOptimum', 0.9);
+    verifyEqual(testCase, solution.stat, 1)
+    verifyEqual(testCase, solution.objectiveValue, -10, 'RelTol', 1e-5)
+    verifyGreaterThanOrEqual(testCase, solution.objectiveValue, -11)
+end
+
+
 function ecModel = fixtureForRelaxProteomicsGreedy()
 % Builds the shared fixture used by the relaxProteomicsGreedy tests below:
 % ecTestGEM with uniform kcat=10 and protein pool sized via