fix: checkModelStruct skip metSmiles (SysBioChalmers#503)

qqlaoxia · Jul 15, 2023 · 0e3d007 · 0e3d007
1 parent cd8ee29
commit 0e3d007
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Showing 2 changed files with 11 additions and 77 deletions.
diff --git a/core/checkModelStruct.m b/core/checkModelStruct.m
@@ -363,39 +363,6 @@ function checkModelStruct(model,throwErrors,trimWarnings)
     EM='The following InChI strings are associated to more than one unique metabolite name:';
     dispEM(EM,false,allInchis(hasMultiple),trimWarnings);
 end
-
-%Check if there are metabolites with different names but the same SMILES
-if isfield(model,'metSmiles')
-    metSmiles=containers.Map();
-    for i=1:numel(model.mets)
-        if ~isempty(model.metSmiles{i})
-            %Get existing metabolite indexes
-            if isKey(metSmiles,model.metSmiles{i})
-                existing=metSmiles(model.metSmiles{i});
-            else
-                existing=[];
-            end
-            metSmiles(model.metSmiles{i})=[existing;i];
-        end
-    end
-
-    %Get all keys
-    allmetSmiles=keys(metSmiles);
-
-    hasMultiple=false(numel(metSmiles),1);
-    for i=1:numel(metSmiles)
-        if numel(metSmiles(metSmiles{i}))>1
-            %Check if they all have the same name
-            if numel(unique(model.metNames(metSmiles(allmetSmiles{i}))))>1
-                hasMultiple(i)=true;
-            end
-        end
-    end
-
-    %Print output
-    EM='The following metSmiles strings are associated to more than one unique metabolite name:';
-    dispEM(EM,false,allmetSmiles(hasMultiple),trimWarnings);
-end
 end
 
 function I=duplicates(strings)

diff --git a/doc/core/checkModelStruct.html b/doc/core/checkModelStruct.html
@@ -422,50 +422,17 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0363     EM=<span class="string">'The following InChI strings are associated to more than one unique metabolite name:'</span>;
 0364     <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false,allInchis(hasMultiple),trimWarnings);
 0365 <span class="keyword">end</span>
-0366 
-0367 <span class="comment">%Check if there are metabolites with different names but the same SMILES</span>
-0368 <span class="keyword">if</span> isfield(model,<span class="string">'metSmiles'</span>)
-0369     metSmiles=containers.Map();
-0370     <span class="keyword">for</span> i=1:numel(model.mets)
-0371         <span class="keyword">if</span> ~isempty(model.metSmiles{i})
-0372             <span class="comment">%Get existing metabolite indexes</span>
-0373             <span class="keyword">if</span> isKey(metSmiles,model.metSmiles{i})
-0374                 existing=metSmiles(model.metSmiles{i});
-0375             <span class="keyword">else</span>
-0376                 existing=[];
-0377             <span class="keyword">end</span>
-0378             metSmiles(model.metSmiles{i})=[existing;i];
-0379         <span class="keyword">end</span>
-0380     <span class="keyword">end</span>
-0381     
-0382     <span class="comment">%Get all keys</span>
-0383     allmetSmiles=keys(metSmiles);
-0384     
-0385     hasMultiple=false(numel(metSmiles),1);
-0386     <span class="keyword">for</span> i=1:numel(metSmiles)
-0387         <span class="keyword">if</span> numel(metSmiles(metSmiles{i}))&gt;1
-0388             <span class="comment">%Check if they all have the same name</span>
-0389             <span class="keyword">if</span> numel(unique(model.metNames(metSmiles(allmetSmiles{i}))))&gt;1
-0390                 hasMultiple(i)=true;
-0391             <span class="keyword">end</span>
-0392         <span class="keyword">end</span>
-0393     <span class="keyword">end</span>
-0394     
-0395     <span class="comment">%Print output</span>
-0396     EM=<span class="string">'The following metSmiles strings are associated to more than one unique metabolite name:'</span>;
-0397     <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false,allmetSmiles(hasMultiple),trimWarnings);
-0398 <span class="keyword">end</span>
-0399 <span class="keyword">end</span>
-0400 
-0401 <a name="_sub1" href="#_subfunctions" class="code">function I=duplicates(strings)</a>
-0402 I=false(numel(strings),1);
-0403 [J, K]=unique(strings);
-0404 <span class="keyword">if</span> numel(J)~=numel(strings)
-0405     L=1:numel(strings);
-0406     L(K)=[];
-0407     I(L)=true;
-0408 <span class="keyword">end</span>
-0409 <span class="keyword">end</span></pre></div>
+0366 <span class="keyword">end</span>
+0367 
+0368 <a name="_sub1" href="#_subfunctions" class="code">function I=duplicates(strings)</a>
+0369 I=false(numel(strings),1);
+0370 [J, K]=unique(strings);
+0371 <span class="keyword">if</span> numel(J)~=numel(strings)
+0372     L=1:numel(strings);
+0373     L(K)=[];
+0374     I(L)=true;
+0375 <span class="keyword">end</span>
+0376 <span class="keyword">end</span></pre></div>
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