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Merged
edkerk merged 4 commits into from
Oct 24, 2025
Merged

RAVEN 2.10.5 #592

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33bbcb5
fix: readYAMLmodel if entries are broken over multiple lines (#588)
edkerk Oct 24, 2025
d76bd38
fix: getExchangeRxns correct 'out' flag definition (#589)
edkerk Oct 24, 2025
3c92bf2
refactor: speed-up setParam, solveLP and optimizeProb (#590)
edkerk Oct 24, 2025
820cc5c
feat: checkModelStruct grRules start/end w/ and/or (#591)
edkerk Oct 24, 2025
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4 changes: 4 additions & 0 deletions core/checkModelStruct.m
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Expand Up @@ -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)
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4 changes: 2 additions & 2 deletions core/getExchangeRxns.m
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Expand Up @@ -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:
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24 changes: 10 additions & 14 deletions core/setParam.m
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Expand Up @@ -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
Expand All @@ -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
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642 changes: 323 additions & 319 deletions doc/core/checkModelStruct.html
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8 changes: 4 additions & 4 deletions doc/core/getExchangeRxns.html
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Expand Up @@ -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:
Expand Down Expand Up @@ -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>
Expand Down
170 changes: 83 additions & 87 deletions doc/core/setParam.html
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Expand Up @@ -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>
<hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
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