Update solveWBMmethod

opencobra · Jan 30, 2025 · 46120e3 · 46120e3
1 parent 891a9b4
commit 46120e3
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Showing 21 changed files with 9 additions and 9 deletions.
diff --git a/papers b/papers
diff --git a/src/analysis/FBA/optimizeCbModel.m b/src/analysis/FBA/optimizeCbModel.m
@@ -425,11 +425,7 @@
         model.c(:)=0;
         doLinearOptimisationFirst = 0;
         minNorm = param.minNorm;
-    else
-        param.solveWBMmethod = [];
     end
-else
-    param.solveWBMmethod = [];
 end
 
 

diff --git a/test/verifiedTests/analysis/testBiomassPrecursorCheck/testBiomassPrecursorCheck.txt b/test/verifiedTests/analysis/testBiomassPrecursorCheck/testBiomassPrecursorCheck.txt
diff --git a/...estCalculateFluxShifts/resultsPostOptimization/fluxShifts/SRR8994378_S47D_flux_shifts.xls b/...estCalculateFluxShifts/resultsPostOptimization/fluxShifts/SRR8994378_S47D_flux_shifts.xls
diff --git a/...testFilterNonFluxReactions/resultsPostOptimization/nonFluxReactionsnonFluxReactionsWT.xls b/...testFilterNonFluxReactions/resultsPostOptimization/nonFluxReactionsnonFluxReactionsWT.xls
diff --git a/...gReactions/resultsPostOptimization/rateLimittingReactions/_rate_limitting_reactionsWT.xls b/...gReactions/resultsPostOptimization/rateLimittingReactions/_rate_limitting_reactionsWT.xls
diff --git a/test/verifiedTests/analysis/testMultiSpeciesModelling/TestResults/ATP_fluxes.csv b/test/verifiedTests/analysis/testMultiSpeciesModelling/TestResults/ATP_fluxes.csv
@@ -0,0 +1,4 @@
+,"Aerobic, Refined","Anaerobic, Refined"
+panAbiotrophia,59.9999999999999,50
+panAcidaminococcus,36.7083333333334,28.1944444444443
+panAcinetobacter,92.7500000000035,48.7916666666679
diff --git a/test/verifiedTests/analysis/testMultiSpeciesModelling/TestResults/Biomass_fluxes.csv b/test/verifiedTests/analysis/testMultiSpeciesModelling/TestResults/Biomass_fluxes.csv
@@ -0,0 +1,4 @@
+,"Unlimited aerobic, Refined","Unlimited anaerobic, Refined","Complex medium aerobic, Refined","Complex medium anaerobic, Refined"
+panAbiotrophia,65.6621686926088,65.6621686926088,1.11844958464248,0.989475300899007
+panAcidaminococcus,112.138835088734,112.138835088734,0.713785512649269,0.576695430546887
+panAcinetobacter,134.213817477338,134.082106174613,1.78726183164546,0.977338632266025
diff --git a/test/verifiedTests/analysis/testMultiSpeciesModelling/panGenusModels/panAbiotrophia.mat b/test/verifiedTests/analysis/testMultiSpeciesModelling/panGenusModels/panAbiotrophia.mat
diff --git a/test/verifiedTests/analysis/testMultiSpeciesModelling/panGenusModels/panAcidaminococcus.mat b/test/verifiedTests/analysis/testMultiSpeciesModelling/panGenusModels/panAcidaminococcus.mat
diff --git a/test/verifiedTests/analysis/testMultiSpeciesModelling/panGenusModels/panAcinetobacter.mat b/test/verifiedTests/analysis/testMultiSpeciesModelling/panGenusModels/panAcinetobacter.mat
diff --git a/...iedTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAbiotrophia_defectiva.mat b/...iedTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAbiotrophia_defectiva.mat
diff --git a/...sts/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcidaminococcus_fermentans.mat b/...sts/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcidaminococcus_fermentans.mat
diff --git a/...ests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcidaminococcus_intestini.mat b/...ests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcidaminococcus_intestini.mat
diff --git a/...edTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcidaminococcus_sp_D21.mat b/...edTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcidaminococcus_sp_D21.mat
diff --git a/...sts/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_haemolyticus.mat b/...sts/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_haemolyticus.mat
diff --git a/...dTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_johnsonii.mat b/...dTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_johnsonii.mat
diff --git a/...ifiedTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_junii.mat b/...ifiedTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_junii.mat
diff --git a/...iedTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_lwoffii.mat b/...iedTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_lwoffii.mat
diff --git a/...fiedTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_pittii.mat b/...fiedTests/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_pittii.mat
diff --git a/...s/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_radioresistens.mat b/...s/analysis/testMultiSpeciesModelling/panSpeciesModels/panAcinetobacter_radioresistens.mat
+161 −2		2021_demeter/input/ReactionDatabase.txt
+0 −0		2023_BarrierRound/3isotropic/PolytopeSamplerMatlab-develop/coverage/problems/basic/polytope_box.m