Merge pull request #2384 from almut-heinken/demeterFixes

Fix in DEMETER to ensure reaction names are read
opencobra · Feb 6, 2025 · 1d8fe69 · 1d8fe69
2 parents 6a3baa9 + 3a9dd89
commit 1d8fe69
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diff --git a/src/reconstruction/demeter/src/debugging/removeFutileCycles.m b/src/reconstruction/demeter/src/debugging/removeFutileCycles.m
@@ -540,6 +540,7 @@
     'FTMAOR' , [],'FTMAOR','FTMAORi'
     'NTMAOR' , [],'NTMAOR','NTMAORi'
     'D4DGCD',[],'D4DGCD','D4DGCDi'
+    'NDPK7 AND NTP13',[],'NTP13','NTP13i'
     };
 
 

diff --git a/src/reconstruction/demeter/src/debugging/untargetedGapFilling.m b/src/reconstruction/demeter/src/debugging/untargetedGapFilling.m
@@ -193,10 +193,8 @@
             % may result in transporters being added without the exchange
             % reaction-need to add the exchange reaction in this case
             exMets={};
-            for j=1:length(addedRxns)
-                mets=findMetsFromRxns(relaxedModel,addedRxns{j});
-                exMets=union(exMets,mets(find(contains(mets,'[e]'))));
-            end
+            mets=findMetsFromRxns(relaxedModel,addedRxns);
+            exMets=union(exMets,mets(find(contains(mets,'[e]'))));
             exRxns={};
             for j=1:length(exMets)
                 exInd=find(strncmp(database.reactions(:,1),['EX_' strrep(exMets{j},'[e]','(e)')],length(['EX_' strrep(exMets{j},'[e]','(e)')])));

diff --git a/src/reconstruction/demeter/src/refinement/createSBMLFiles.m b/src/reconstruction/demeter/src/refinement/createSBMLFiles.m
@@ -3,7 +3,7 @@ function createSBMLFiles(refinedFolder, sbmlFolder)
 % time-consuming.
 %
 % USAGE
-%   createTestSBMLFiles(refinedFolder, sbmlFolder)
+%   createSBMLFiles(refinedFolder, sbmlFolder)
 %
 % INPUTS
 % refinedFolder            Folder with refined COBRA models generated by