RAVEN 2.10.5

Author: edkerk

core/checkModelStruct.m

@@ -124,6 +124,10 @@ function checkModelStruct(model,throwErrors,trimWarnings)
         EM='If "grRules" field exists, the model should also contain a "genes" field';
         dispEM(EM,throwErrors);
     else
+        %Erroneous grRules that start/end with OR/AND
+        EM='The following reaction(s) have grRules that start or end with ''OR'' or ''AND'':';
+        dispEM(EM,throwErrors,model.rxns(startsWith(model.grRules,{'or ','and '}) | endsWith(model.grRules,{' or',' and'})),trimWarnings);
+        %grRules that are not in genes field
         geneList = getGenesFromGrRules(model.grRules);
         geneList = setdiff(unique(geneList),model.genes);
         if ~isempty(geneList)

core/getExchangeRxns.m

@@ -26,8 +26,8 @@
 %                                 positive flux value would imply uptake,
 %                                 but reaction bounds are not considered
 %                       'out'     reactions where the boundary metabolite
-%                                 is the substrate of the reaction, a
-%                                 positive flux value would imply uptake,
+%                                 is the product of the reaction, a
+%                                 negative flux value would imply uptake,
 %                                 but reaction bounds are not considered.
 %
 % Output:

core/setParam.m

@@ -39,6 +39,9 @@
 else
     rxnList=convertCharArray(rxnList);
 end
+if isempty(rxnList)
+    return;
+end
 
 %Allow to set several parameters to the same value
 if numel(rxnList)~=numel(params) && numel(params)~=1
@@ -59,23 +62,16 @@
 %as we do not want to throw errors if matches fail
 indexes=zeros(numel(rxnList),1);
 
-for i=1:numel(rxnList)
-    index=find(strcmp(rxnList{i},model.rxns),1);
-    if ~isempty(index)
-        indexes(i)=index;
-    else
-        indexes(i)=-1;
-        EM=['Reaction ' rxnList{i} ' is not present in the reaction list'];
-        dispEM(EM,false);
-    end
+[Lia,Locb] = ismember(rxnList,model.rxns);
+indexes(Lia) = Locb;
+if any(~Lia)
+    params(~Lia)=[];
+    indexes(~Lia)=[];
+    paramType(~Lia)=[];
+    dispEM('Reactions not present in model, will be ignored:',false,rxnLise(~Lia));
 end
 
-%Remove the reactions that were not found
-params(indexes==-1)=[];
-indexes(indexes==-1)=[];
-paramType(indexes==-1)=[];
 %Change the parameters
-
 if ~isempty(indexes)
     if contains(paramType,'obj')
         model.c=zeros(numel(model.c),1); % parameter is changed, not added

doc/core/checkModelStruct.html

@@ -54,8 +54,8 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
                                  positive flux value would imply uptake,
                                  but reaction bounds are not considered
                        'out'     reactions where the boundary metabolite
-                                 is the substrate of the reaction, a
-                                 positive flux value would imply uptake,
+                                 is the product of the reaction, a
+                                 negative flux value would imply uptake,
                                  but reaction bounds are not considered.
 
  Output:
@@ -109,8 +109,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0026 <span class="comment">%                                 positive flux value would imply uptake,</span>
 0027 <span class="comment">%                                 but reaction bounds are not considered</span>
 0028 <span class="comment">%                       'out'     reactions where the boundary metabolite</span>
-0029 <span class="comment">%                                 is the substrate of the reaction, a</span>
-0030 <span class="comment">%                                 positive flux value would imply uptake,</span>
+0029 <span class="comment">%                                 is the product of the reaction, a</span>
+0030 <span class="comment">%                                 negative flux value would imply uptake,</span>
 0031 <span class="comment">%                                 but reaction bounds are not considered.</span>
 0032 <span class="comment">%</span>
 0033 <span class="comment">% Output:</span>

doc/core/getExchangeRxns.html

@@ -111,96 +111,92 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0039 <span class="keyword">else</span>
 0040     rxnList=<a href="convertCharArray.html" class="code" title="function inputConverted = convertCharArray(funcInput)">convertCharArray</a>(rxnList);
 0041 <span class="keyword">end</span>
-0042 
-0043 <span class="comment">%Allow to set several parameters to the same value</span>
-0044 <span class="keyword">if</span> numel(rxnList)~=numel(params) &amp;&amp; numel(params)~=1
-0045     EM=<span class="string">'The number of parameter values and the number of reactions must be the same'</span>;
-0046     <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM);
-0047 <span class="keyword">end</span>
-0048 
-0049 <span class="keyword">if</span> length(rxnList)&gt;1
-0050     <span class="keyword">if</span> length(paramType)==1
-0051         paramType(1:length(rxnList))=paramType;
-0052     <span class="keyword">end</span>
-0053     <span class="keyword">if</span> length(params)==1
-0054         params(1:length(rxnList))=params;
+0042 <span class="keyword">if</span> isempty(rxnList)
+0043     <span class="keyword">return</span>;
+0044 <span class="keyword">end</span>
+0045 
+0046 <span class="comment">%Allow to set several parameters to the same value</span>
+0047 <span class="keyword">if</span> numel(rxnList)~=numel(params) &amp;&amp; numel(params)~=1
+0048     EM=<span class="string">'The number of parameter values and the number of reactions must be the same'</span>;
+0049     <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM);
+0050 <span class="keyword">end</span>
+0051 
+0052 <span class="keyword">if</span> length(rxnList)&gt;1
+0053     <span class="keyword">if</span> length(paramType)==1
+0054         paramType(1:length(rxnList))=paramType;
 0055     <span class="keyword">end</span>
-0056 <span class="keyword">end</span>
-0057 
-0058 <span class="comment">%Find the indexes for the reactions in rxnList. Do not use getIndexes</span>
-0059 <span class="comment">%as we do not want to throw errors if matches fail</span>
-0060 indexes=zeros(numel(rxnList),1);
-0061 
-0062 <span class="keyword">for</span> i=1:numel(rxnList)
-0063     index=find(strcmp(rxnList{i},model.rxns),1);
-0064     <span class="keyword">if</span> ~isempty(index)
-0065         indexes(i)=index;
-0066     <span class="keyword">else</span>
-0067         indexes(i)=-1;
-0068         EM=[<span class="string">'Reaction '</span> rxnList{i} <span class="string">' is not present in the reaction list'</span>];
-0069         <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false);
-0070     <span class="keyword">end</span>
-0071 <span class="keyword">end</span>
-0072 
-0073 <span class="comment">%Remove the reactions that were not found</span>
-0074 params(indexes==-1)=[];
-0075 indexes(indexes==-1)=[];
-0076 paramType(indexes==-1)=[];
-0077 <span class="comment">%Change the parameters</span>
-0078 
-0079 <span class="keyword">if</span> ~isempty(indexes)
-0080     <span class="keyword">if</span> contains(paramType,<span class="string">'obj'</span>)
-0081         model.c=zeros(numel(model.c),1); <span class="comment">% parameter is changed, not added</span>
-0082     <span class="keyword">end</span>
-0083     <span class="keyword">for</span> j=1:length(paramType)
-0084         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'eq'</span>)
+0056     <span class="keyword">if</span> length(params)==1
+0057         params(1:length(rxnList))=params;
+0058     <span class="keyword">end</span>
+0059 <span class="keyword">end</span>
+0060 
+0061 <span class="comment">%Find the indexes for the reactions in rxnList. Do not use getIndexes</span>
+0062 <span class="comment">%as we do not want to throw errors if matches fail</span>
+0063 indexes=zeros(numel(rxnList),1);
+0064 
+0065 [Lia,Locb] = ismember(rxnList,model.rxns);
+0066 indexes(Lia) = Locb;
+0067 <span class="keyword">if</span> any(~Lia)
+0068     params(~Lia)=[];
+0069     indexes(~Lia)=[];
+0070     paramType(~Lia)=[];
+0071     <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(<span class="string">'Reactions not present in model, will be ignored:'</span>,false,rxnLise(~Lia));
+0072 <span class="keyword">end</span>
+0073 
+0074 <span class="comment">%Change the parameters</span>
+0075 <span class="keyword">if</span> ~isempty(indexes)
+0076     <span class="keyword">if</span> contains(paramType,<span class="string">'obj'</span>)
+0077         model.c=zeros(numel(model.c),1); <span class="comment">% parameter is changed, not added</span>
+0078     <span class="keyword">end</span>
+0079     <span class="keyword">for</span> j=1:length(paramType)
+0080         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'eq'</span>)
+0081             model.lb(indexes(j))=params(j);
+0082             model.ub(indexes(j))=params(j);
+0083         <span class="keyword">end</span>
+0084         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'lb'</span>)
 0085             model.lb(indexes(j))=params(j);
-0086             model.ub(indexes(j))=params(j);
-0087         <span class="keyword">end</span>
-0088         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'lb'</span>)
-0089             model.lb(indexes(j))=params(j);
-0090         <span class="keyword">end</span>
-0091         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'ub'</span>)
-0092             model.ub(indexes(j))=params(j);
-0093         <span class="keyword">end</span>
-0094         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'obj'</span>)
-0095             model.c(indexes(j))=params(j);
+0086         <span class="keyword">end</span>
+0087         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'ub'</span>)
+0088             model.ub(indexes(j))=params(j);
+0089         <span class="keyword">end</span>
+0090         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'obj'</span>)
+0091             model.c(indexes(j))=params(j);
+0092         <span class="keyword">end</span>
+0093         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'rev'</span>)
+0094             <span class="comment">%Non-zero values are interpreted as reversible</span>
+0095             model.rev(indexes(j))=params(j)~=0;
 0096         <span class="keyword">end</span>
-0097         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'rev'</span>)
-0098             <span class="comment">%Non-zero values are interpreted as reversible</span>
-0099             model.rev(indexes(j))=params(j)~=0;
-0100         <span class="keyword">end</span>
-0101         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'var'</span>)
-0102             <span class="keyword">if</span> params(j) &lt; 0
-0103                 model.lb(indexes(j)) = params(j) * (1+var/200);
-0104                 model.ub(indexes(j)) = params(j) * (1-var/200);
-0105             <span class="keyword">else</span>
-0106                 model.lb(indexes(j)) = params(j) * (1-var/200);
-0107                 model.ub(indexes(j)) = params(j) * (1+var/200);
-0108             <span class="keyword">end</span>
-0109         <span class="keyword">end</span>
-0110         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'unc'</span>)
-0111             <span class="keyword">if</span> isfield(model.annotation,<span class="string">'defaultLB'</span>)
-0112                 lb = model.annotation.defaultLB;
-0113             <span class="keyword">else</span>
-0114                 lb = -1000;
-0115             <span class="keyword">end</span>
-0116             <span class="keyword">if</span> isfield(model.annotation,<span class="string">'defaultUB'</span>)
-0117                 ub = model.annotation.defaultUB;
-0118             <span class="keyword">else</span>
-0119                 ub = 1000;
-0120             <span class="keyword">end</span>
-0121             model.lb(indexes(j)) = lb;
-0122             model.ub(indexes(j)) = ub;
-0123         <span class="keyword">end</span>
-0124     <span class="keyword">end</span>
-0125 <span class="keyword">end</span>
-0126 <span class="keyword">if</span> any(ismember(paramType,{<span class="string">'lb'</span>,<span class="string">'ub'</span>,<span class="string">'unc'</span>}))
-0127     invalidBound = model.lb(indexes) &gt; model.ub(indexes);
-0128     <span class="keyword">if</span> any(invalidBound)
-0129         error([<span class="string">'Invalid set of bounds for reaction(s): '</span>, strjoin(model.rxns(indexes(invalidBound)),<span class="string">', '</span>), <span class="string">'.'</span>])
-0130     <span class="keyword">end</span>
-0131 <span class="keyword">end</span></pre></div>
+0097         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'var'</span>)
+0098             <span class="keyword">if</span> params(j) &lt; 0
+0099                 model.lb(indexes(j)) = params(j) * (1+var/200);
+0100                 model.ub(indexes(j)) = params(j) * (1-var/200);
+0101             <span class="keyword">else</span>
+0102                 model.lb(indexes(j)) = params(j) * (1-var/200);
+0103                 model.ub(indexes(j)) = params(j) * (1+var/200);
+0104             <span class="keyword">end</span>
+0105         <span class="keyword">end</span>
+0106         <span class="keyword">if</span> strcmpi(paramType{j},<span class="string">'unc'</span>)
+0107             <span class="keyword">if</span> isfield(model.annotation,<span class="string">'defaultLB'</span>)
+0108                 lb = model.annotation.defaultLB;
+0109             <span class="keyword">else</span>
+0110                 lb = -1000;
+0111             <span class="keyword">end</span>
+0112             <span class="keyword">if</span> isfield(model.annotation,<span class="string">'defaultUB'</span>)
+0113                 ub = model.annotation.defaultUB;
+0114             <span class="keyword">else</span>
+0115                 ub = 1000;
+0116             <span class="keyword">end</span>
+0117             model.lb(indexes(j)) = lb;
+0118             model.ub(indexes(j)) = ub;
+0119         <span class="keyword">end</span>
+0120     <span class="keyword">end</span>
+0121 <span class="keyword">end</span>
+0122 <span class="keyword">if</span> any(ismember(paramType,{<span class="string">'lb'</span>,<span class="string">'ub'</span>,<span class="string">'unc'</span>}))
+0123     invalidBound = model.lb(indexes) &gt; model.ub(indexes);
+0124     <span class="keyword">if</span> any(invalidBound)
+0125         error([<span class="string">'Invalid set of bounds for reaction(s): '</span>, strjoin(model.rxns(indexes(invalidBound)),<span class="string">', '</span>), <span class="string">'.'</span>])
+0126     <span class="keyword">end</span>
+0127 <span class="keyword">end</span></pre></div>
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