From fa8748950f555e728b2cdbc3892ff89348428e4a Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Fri, 12 Jan 2024 18:22:45 +0100 Subject: [PATCH 1/2] fix: saveEcModel without appending xml if already xml --- src/geckomat/utilities/saveEcModel.m | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/geckomat/utilities/saveEcModel.m b/src/geckomat/utilities/saveEcModel.m index 69f4bf953..9c0e5badc 100644 --- a/src/geckomat/utilities/saveEcModel.m +++ b/src/geckomat/utilities/saveEcModel.m @@ -40,12 +40,12 @@ function saveEcModel(ecModel,filename,modelAdapter) switch filename(end-3:end) case {'.xml','sbml'} - exportModel(ecModel,[filename '.xml']); + exportModel(ecModel, filename); %Convert notation "e-005" to "e-05 " in stoich. coeffs. to avoid %inconsistencies between Windows and MAC: - copyfile([filename '.xml'],'backup.xml') + copyfile(filename,'backup.xml') fin = fopen('backup.xml', 'r'); - fout = fopen([filename '.xml'], 'w'); + fout = fopen(filename, 'w'); still_reading = true; while still_reading inline = fgets(fin); From 83412ed34a2d7aa33b2bae83df79d6b0ccb9dc15 Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Fri, 12 Jan 2024 18:23:32 +0100 Subject: [PATCH 2/2] chore: typo in tutorial light protocol --- tutorials/light_ecModel/protocol.m | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tutorials/light_ecModel/protocol.m b/tutorials/light_ecModel/protocol.m index 008125e08..f64671312 100644 --- a/tutorials/light_ecModel/protocol.m +++ b/tutorials/light_ecModel/protocol.m @@ -74,7 +74,7 @@ % STEP 26 Merge BRENDA and DLKcat derived values kcatList_merged = mergeDLKcatAndFuzzyKcats(kcatList_DLKcat, kcatList_fuzzy); -% STEP 27 Implement kcat avlues into model.ec.kcat +% STEP 27 Implement kcat values into model.ec.kcat ecModel = selectKcatValue(ecModel,kcatList_merged); % STEP 28 @@ -96,7 +96,7 @@ % -standardMW/standardKcat as the stoiciometric coefficient. [ecModel, rxnsMissingGPR, standardMW, standardKcat] = getStandardKcat(ecModel); -% STEP 31 Apply kcat avlues to S-matrix +% STEP 31 Apply kcat values to S-matrix % In light ecModels the kcat values are also kept in ecModels.ec.kcat, and % only after running applyKcatConstraints are these introduced in the % ecModel.S matrix. In constrast to full ecModels, the applyKcatConstraints