Merge pull request #1631 from BenjaSanchez/feat/bound-sbo-terms

feat: SBO terms for reaction bounds
opencobra · Oct 15, 2020 · 942be7d · 942be7d
2 parents a30fe49 + 9c811fb
commit 942be7d
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diff --git a/src/base/io/utilities/writeSBML.m b/src/base/io/utilities/writeSBML.m
@@ -387,6 +387,11 @@
 
         fbc_parameter.id=listUniqueNames{i,1};
         fbc_parameter.value=listUniqueValues(i);
+        if fbc_parameter.value == -1000 || fbc_parameter.value == +1000 || fbc_parameter.value == 0 || isinf(fbc_parameter.value)
+            fbc_parameter.sboTerm=626;
+        else
+            fbc_parameter.sboTerm=625;
+        end
         if i==1
             sbmlModel.parameter=fbc_parameter;
         else

diff --git a/test/verifiedTests/base/testIO/testWriteSBML.m b/test/verifiedTests/base/testIO/testWriteSBML.m
@@ -38,6 +38,19 @@
 % assess any potential differences
 assert(~any(numDiff))
 
+% obtain SBML structure
+testSBMLstruct = writeSBML(testModelSBML,'testModelSBML.sbml');
+
+% asses if lower/upper bounds have proper SBO terms assigned
+for i = 1:length(testSBMLstruct.parameter)
+    value = testSBMLstruct.parameter(i).value;
+    if abs(value) == 1000 || isinf(value) || value == 0
+        assert(testSBMLstruct.parameter(i).sboTerm == 626)
+    else
+        assert(testSBMLstruct.parameter(i).sboTerm == 625)
+    end
+end
+
 % remove the written file to clean up
 delete 'testModelSBML.sbml.xml';