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edkerk merged 2 commits into from
May 9, 2025
Merged

GECKO 3.2.3 #399

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5e2ef53
fix: flexibilizeEnzConcs mix up flexibilized proteins (#398)
edkerk Apr 7, 2025
3aa5af0
fix: getStandardKcat use modelAdapter enzyme_comp (#402)
edkerk May 9, 2025
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6 changes: 1 addition & 5 deletions GECKOInstaller.m
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Original file line number Diff line number Diff line change
Expand Up @@ -72,15 +72,11 @@ function checkRAVENversion(minmVer)
minmVerNum = str2double(strsplit(minmVer,'.'));
if currVerNum(1) < minmVerNum(1)
wrongVersion = true;
elseif currVerNum(1) > minmVerNum(1)
wrongVersion = false;
elseif currVerNum(2) < minmVerNum(2)
wrongVersion = true;
elseif currVerNum(2) > minmVerNum(2)
wrongVersion = false;
elseif currVerNum(3) < minmVerNum(3)
wrongVersion = true;
elseif currVerNum(3) >= minmVerNum(3)
else
wrongVersion = false;
end
end
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259 changes: 133 additions & 126 deletions doc/src/geckomat/gather_kcats/getStandardKcat.html
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Expand Up @@ -279,134 +279,141 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0177 <span class="comment">% Add a new metabolite named prot_standard</span>
0178 proteinStdMets.mets = <span class="string">'prot_standard'</span>;
0179 proteinStdMets.metNames = proteinStdMets.mets;
0180 proteinStdMets.compartments = <span class="string">'c'</span>;
0181 <span class="keyword">if</span> isfield(model,<span class="string">'metNotes'</span>)
0182 proteinStdMets.metNotes = <span class="string">'Standard enzyme-usage pseudometabolite'</span>;
0183 <span class="keyword">end</span>
0184 model = addMets(model, proteinStdMets);
0185
0186 <span class="comment">% Add a protein usage reaction if not a light version</span>
0187 proteinStdUsageRxn.rxns = {<span class="string">'usage_prot_standard'</span>};
0188 proteinStdUsageRxn.rxnNames = proteinStdUsageRxn.rxns;
0189 proteinStdUsageRxn.mets = {proteinStdMets.mets, <span class="string">'prot_pool'</span>};
0190 proteinStdUsageRxn.stoichCoeffs = [-1, 1];
0191 proteinStdUsageRxn.lb = -1000;
0192 proteinStdUsageRxn.ub = 0;
0193 proteinStdUsageRxn.grRules = proteinStdGenes.genes;
0194
0195 model = addRxns(model, proteinStdUsageRxn);
0196 <span class="keyword">end</span>
0197 <span class="comment">% Update .ec structure in model</span>
0198 model.ec.genes(end+1) = {<span class="string">'standard'</span>};
0199 model.ec.enzymes(end+1) = {<span class="string">'standard'</span>};
0200 model.ec.mw(end+1) = standardMW;
0201 model.ec.sequence(end+1) = {<span class="string">''</span>};
0202 <span class="comment">% Additional info</span>
0203 <span class="keyword">if</span> isfield(model.ec,<span class="string">'concs'</span>)
0204 model.ec.concs(end+1) = nan();
0205 <span class="keyword">end</span>
0206
0207 <span class="comment">% Expand the enzyme rxns matrix</span>
0208 model.ec.rxnEnzMat = [model.ec.rxnEnzMat, zeros(length(model.ec.rxns), 1)]; <span class="comment">% 1 new enzyme</span>
0209 model.ec.rxnEnzMat = [model.ec.rxnEnzMat; zeros(length(rxnsMissingGPR), length(model.ec.enzymes))]; <span class="comment">% new rxns</span>
0210 <span class="keyword">end</span>
0211 stdMetIdx = find(strcmpi(model.ec.enzymes, <span class="string">'standard'</span>));
0212
0213 <span class="comment">% Remove previous standard kcat assignment</span>
0214 oldStandardEnz = find(strcmp(model.ec.source,<span class="string">'standard'</span>));
0215 <span class="keyword">if</span> ~isempty(oldStandardEnz)
0216 oldStandardProt = logical(model.ec.rxnEnzMat(oldStandardEnz,stdMetIdx));
0217 <span class="comment">% If annotated with real enzyme =&gt; set kcat to zero</span>
0218 model.ec.kcat(oldStandardEnz(~oldStandardProt)) = 0;
0219 model.ec.source(oldStandardEnz(~oldStandardProt)) = {<span class="string">''</span>};
0220 <span class="comment">% If annotated with standard protein =&gt; remove entry</span>
0221 model.ec.rxns(oldStandardEnz(oldStandardProt)) = [];
0222 model.ec.kcat(oldStandardEnz(oldStandardProt)) = [];
0223 model.ec.source(oldStandardEnz(oldStandardProt)) = [];
0224 model.ec.notes(oldStandardEnz(oldStandardProt)) = [];
0225 model.ec.eccodes(oldStandardEnz(oldStandardProt)) = [];
0226 model.ec.rxnEnzMat(oldStandardEnz(oldStandardProt),:) = [];
0227 <span class="keyword">end</span>
0228
0229 numRxns = length(model.ec.rxns);
0230 <span class="keyword">for</span> i = 1:numel(rxnsMissingGPR)
0231 rxnIdx = rxnsMissingGPR(i);
0232
0233 <span class="comment">% Update .ec structure in model</span>
0234 <span class="keyword">if</span> ~model.ec.geckoLight
0235 model.ec.rxns(end+1) = model.rxns(rxnIdx);
0236 <span class="comment">% Add prefix in case is light version</span>
0237 <span class="keyword">else</span>
0238 model.ec.rxns{end+1} = [<span class="string">'001_'</span> model.rxns{rxnIdx}];
0239 <span class="keyword">end</span>
0240
0241 <span class="keyword">if</span> ~standard
0242 kcatSubSystemIdx = strcmpi(enzSubSystem_names, model.subSystems{rxnIdx}(1));
0243 <span class="keyword">if</span> all(kcatSubSystemIdx)
0244 model.ec.kcat(end+1) = kcatSubSystem(kcatSubSystemIdx);
0245 <span class="keyword">else</span>
0246 model.ec.kcat(end+1) = standardKcat;
0247 <span class="keyword">end</span>
0248 <span class="keyword">else</span>
0249 model.ec.kcat(end+1) = standardKcat;
0250 <span class="keyword">end</span>
0251
0252 model.ec.source(end+1) = {<span class="string">'standard'</span>};
0253 model.ec.notes(end+1) = {<span class="string">''</span>};
0254 model.ec.eccodes(end+1) = {<span class="string">''</span>};
0255
0256 <span class="comment">% Update the enzyme rxns matrix</span>
0257 model.ec.rxnEnzMat(numRxns+i, stdMetIdx) = 1;
0258 <span class="keyword">end</span>
0259 <span class="comment">% Get the rxns identifiers of the updated rxns</span>
0260 rxnsMissingGPR = model.rxns(rxnsMissingGPR);
0261
0262 <span class="keyword">if</span> fillZeroKcat
0263 zeroKcat = model.ec.kcat == 0 | isnan(model.ec.kcat);
0264 model.ec.kcat(zeroKcat) = standardKcat;
0265 model.ec.source(zeroKcat) = {<span class="string">'standard'</span>};
0266 rxnsNoKcat = model.ec.rxns(zeroKcat);
0267 <span class="keyword">else</span>
0268 rxnsNoKcat = [];
0269 <span class="keyword">end</span>
0270 <span class="keyword">end</span>
0271
0272 <a name="_sub1" href="#_subfunctions" class="code">function Cflat = flattenCell(C,strFlag)</a>
0273 <span class="comment">%FLATTENCELL Flatten a nested column cell array into a matrix cell array.</span>
0274 <span class="comment">%</span>
0275 <span class="comment">% CFLAT = FLATTENCELL(C) takes a column cell array in which one or more</span>
0276 <span class="comment">% entries is a nested cell array, and flattens it into a 2D matrix cell</span>
0277 <span class="comment">% array, where the nested entries are spread across new columns.</span>
0278 <span class="comment">%</span>
0279 <span class="comment">% CFLAT = FLATTENCELL(C,STRFLAG) if STRFLAG is TRUE, empty entries in the</span>
0280 <span class="comment">% resulting CFLAT will be replaced with empty strings {''}. Default = FALSE</span>
0281 <span class="keyword">if</span> nargin &lt; 2
0282 strFlag = false;
0283 <span class="keyword">end</span>
0284
0285 <span class="comment">% determine which entries are cells</span>
0286 cells = cellfun(@iscell,C);
0287
0288 <span class="comment">% determine number of elements in each nested cell</span>
0289 cellsizes = cellfun(@numel,C);
0290 cellsizes(~cells) = 1; <span class="comment">% ignore non-cell entries</span>
0180 <span class="comment">% Validate compartment</span>
0181 proteinStdMets.compartments = strcmp(model.compNames,params.enzyme_comp);
0182 <span class="keyword">if</span> ~any(proteinStdMets.compartments)
0183 error([<span class="string">'Compartment '</span> params.enzyme_comp <span class="string">' (specified in params.enzyme_comp) '</span><span class="keyword">...</span>
0184 <span class="string">'cannot be found in model.compNames'</span>])
0185 <span class="keyword">end</span>
0186 proteinStdMets.compartments = model.comps(compartmentID);
0187
0188 <span class="keyword">if</span> isfield(model,<span class="string">'metNotes'</span>)
0189 proteinStdMets.metNotes = <span class="string">'Standard enzyme-usage pseudometabolite'</span>;
0190 <span class="keyword">end</span>
0191 model = addMets(model, proteinStdMets);
0192
0193 <span class="comment">% Add a protein usage reaction if not a light version</span>
0194 proteinStdUsageRxn.rxns = {<span class="string">'usage_prot_standard'</span>};
0195 proteinStdUsageRxn.rxnNames = proteinStdUsageRxn.rxns;
0196 proteinStdUsageRxn.mets = {proteinStdMets.mets, <span class="string">'prot_pool'</span>};
0197 proteinStdUsageRxn.stoichCoeffs = [-1, 1];
0198 proteinStdUsageRxn.lb = -1000;
0199 proteinStdUsageRxn.ub = 0;
0200 proteinStdUsageRxn.grRules = proteinStdGenes.genes;
0201
0202 model = addRxns(model, proteinStdUsageRxn);
0203 <span class="keyword">end</span>
0204 <span class="comment">% Update .ec structure in model</span>
0205 model.ec.genes(end+1) = {<span class="string">'standard'</span>};
0206 model.ec.enzymes(end+1) = {<span class="string">'standard'</span>};
0207 model.ec.mw(end+1) = standardMW;
0208 model.ec.sequence(end+1) = {<span class="string">''</span>};
0209 <span class="comment">% Additional info</span>
0210 <span class="keyword">if</span> isfield(model.ec,<span class="string">'concs'</span>)
0211 model.ec.concs(end+1) = nan();
0212 <span class="keyword">end</span>
0213
0214 <span class="comment">% Expand the enzyme rxns matrix</span>
0215 model.ec.rxnEnzMat = [model.ec.rxnEnzMat, zeros(length(model.ec.rxns), 1)]; <span class="comment">% 1 new enzyme</span>
0216 model.ec.rxnEnzMat = [model.ec.rxnEnzMat; zeros(length(rxnsMissingGPR), length(model.ec.enzymes))]; <span class="comment">% new rxns</span>
0217 <span class="keyword">end</span>
0218 stdMetIdx = find(strcmpi(model.ec.enzymes, <span class="string">'standard'</span>));
0219
0220 <span class="comment">% Remove previous standard kcat assignment</span>
0221 oldStandardEnz = find(strcmp(model.ec.source,<span class="string">'standard'</span>));
0222 <span class="keyword">if</span> ~isempty(oldStandardEnz)
0223 oldStandardProt = logical(model.ec.rxnEnzMat(oldStandardEnz,stdMetIdx));
0224 <span class="comment">% If annotated with real enzyme =&gt; set kcat to zero</span>
0225 model.ec.kcat(oldStandardEnz(~oldStandardProt)) = 0;
0226 model.ec.source(oldStandardEnz(~oldStandardProt)) = {<span class="string">''</span>};
0227 <span class="comment">% If annotated with standard protein =&gt; remove entry</span>
0228 model.ec.rxns(oldStandardEnz(oldStandardProt)) = [];
0229 model.ec.kcat(oldStandardEnz(oldStandardProt)) = [];
0230 model.ec.source(oldStandardEnz(oldStandardProt)) = [];
0231 model.ec.notes(oldStandardEnz(oldStandardProt)) = [];
0232 model.ec.eccodes(oldStandardEnz(oldStandardProt)) = [];
0233 model.ec.rxnEnzMat(oldStandardEnz(oldStandardProt),:) = [];
0234 <span class="keyword">end</span>
0235
0236 numRxns = length(model.ec.rxns);
0237 <span class="keyword">for</span> i = 1:numel(rxnsMissingGPR)
0238 rxnIdx = rxnsMissingGPR(i);
0239
0240 <span class="comment">% Update .ec structure in model</span>
0241 <span class="keyword">if</span> ~model.ec.geckoLight
0242 model.ec.rxns(end+1) = model.rxns(rxnIdx);
0243 <span class="comment">% Add prefix in case is light version</span>
0244 <span class="keyword">else</span>
0245 model.ec.rxns{end+1} = [<span class="string">'001_'</span> model.rxns{rxnIdx}];
0246 <span class="keyword">end</span>
0247
0248 <span class="keyword">if</span> ~standard
0249 kcatSubSystemIdx = strcmpi(enzSubSystem_names, model.subSystems{rxnIdx}(1));
0250 <span class="keyword">if</span> all(kcatSubSystemIdx)
0251 model.ec.kcat(end+1) = kcatSubSystem(kcatSubSystemIdx);
0252 <span class="keyword">else</span>
0253 model.ec.kcat(end+1) = standardKcat;
0254 <span class="keyword">end</span>
0255 <span class="keyword">else</span>
0256 model.ec.kcat(end+1) = standardKcat;
0257 <span class="keyword">end</span>
0258
0259 model.ec.source(end+1) = {<span class="string">'standard'</span>};
0260 model.ec.notes(end+1) = {<span class="string">''</span>};
0261 model.ec.eccodes(end+1) = {<span class="string">''</span>};
0262
0263 <span class="comment">% Update the enzyme rxns matrix</span>
0264 model.ec.rxnEnzMat(numRxns+i, stdMetIdx) = 1;
0265 <span class="keyword">end</span>
0266 <span class="comment">% Get the rxns identifiers of the updated rxns</span>
0267 rxnsMissingGPR = model.rxns(rxnsMissingGPR);
0268
0269 <span class="keyword">if</span> fillZeroKcat
0270 zeroKcat = model.ec.kcat == 0 | isnan(model.ec.kcat);
0271 model.ec.kcat(zeroKcat) = standardKcat;
0272 model.ec.source(zeroKcat) = {<span class="string">'standard'</span>};
0273 rxnsNoKcat = model.ec.rxns(zeroKcat);
0274 <span class="keyword">else</span>
0275 rxnsNoKcat = [];
0276 <span class="keyword">end</span>
0277 <span class="keyword">end</span>
0278
0279 <a name="_sub1" href="#_subfunctions" class="code">function Cflat = flattenCell(C,strFlag)</a>
0280 <span class="comment">%FLATTENCELL Flatten a nested column cell array into a matrix cell array.</span>
0281 <span class="comment">%</span>
0282 <span class="comment">% CFLAT = FLATTENCELL(C) takes a column cell array in which one or more</span>
0283 <span class="comment">% entries is a nested cell array, and flattens it into a 2D matrix cell</span>
0284 <span class="comment">% array, where the nested entries are spread across new columns.</span>
0285 <span class="comment">%</span>
0286 <span class="comment">% CFLAT = FLATTENCELL(C,STRFLAG) if STRFLAG is TRUE, empty entries in the</span>
0287 <span class="comment">% resulting CFLAT will be replaced with empty strings {''}. Default = FALSE</span>
0288 <span class="keyword">if</span> nargin &lt; 2
0289 strFlag = false;
0290 <span class="keyword">end</span>
0291
0292 <span class="comment">% flatten single-entry cells</span>
0293 Cflat = C;
0294 Cflat(cells &amp; (cellsizes == 1)) = cellfun(@(x) x{1},Cflat(cells &amp; (cellsizes == 1)),<span class="string">'UniformOutput'</span>,false);
0295
0296 <span class="comment">% iterate through multi-entry cells</span>
0297 multiCells = find(cellsizes &gt; 1);
0298 <span class="keyword">for</span> i = 1:length(multiCells)
0299 cellContents = Cflat{multiCells(i)};
0300 Cflat(multiCells(i),1:length(cellContents)) = cellContents;
0301 <span class="keyword">end</span>
0292 <span class="comment">% determine which entries are cells</span>
0293 cells = cellfun(@iscell,C);
0294
0295 <span class="comment">% determine number of elements in each nested cell</span>
0296 cellsizes = cellfun(@numel,C);
0297 cellsizes(~cells) = 1; <span class="comment">% ignore non-cell entries</span>
0298
0299 <span class="comment">% flatten single-entry cells</span>
0300 Cflat = C;
0301 Cflat(cells &amp; (cellsizes == 1)) = cellfun(@(x) x{1},Cflat(cells &amp; (cellsizes == 1)),<span class="string">'UniformOutput'</span>,false);
0302
0303 <span class="comment">% change empty elements to strings, if specified</span>
0304 <span class="keyword">if</span> ( strFlag )
0305 Cflat(cellfun(@isempty,Cflat)) = {<span class="string">''</span>};
0306 <span class="keyword">end</span>
0307 <span class="keyword">end</span></pre></div>
0303 <span class="comment">% iterate through multi-entry cells</span>
0304 multiCells = find(cellsizes &gt; 1);
0305 <span class="keyword">for</span> i = 1:length(multiCells)
0306 cellContents = Cflat{multiCells(i)};
0307 Cflat(multiCells(i),1:length(cellContents)) = cellContents;
0308 <span class="keyword">end</span>
0309
0310 <span class="comment">% change empty elements to strings, if specified</span>
0311 <span class="keyword">if</span> ( strFlag )
0312 Cflat(cellfun(@isempty,Cflat)) = {<span class="string">''</span>};
0313 <span class="keyword">end</span>
0314 <span class="keyword">end</span></pre></div>
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