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fix: getStandardKcat no standard gene in light-ec
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edkerk committed Jun 26, 2023
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265 changes: 132 additions & 133 deletions doc/src/geckomat/gather_kcats/getStandardKcat.html
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Expand Up @@ -247,140 +247,139 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0150
0151 <span class="comment">% Only add if not geckoLight &amp; getStandardKcat was not run earlier</span>
0152 <span class="keyword">if</span> ~any(strcmp(model.mets,<span class="string">'prot_standard'</span>))
0153 <span class="comment">% Add a new gene to be consistent with ec field named standard</span>
0154 proteinStdGenes.genes = <span class="string">'standard'</span>;
0155 <span class="keyword">if</span> isfield(model,<span class="string">'geneShortNames'</span>)
0156 proteinStdGenes.geneShortNames = <span class="string">'std'</span>;
0157 <span class="keyword">end</span>
0158 model = addGenesRaven(model, proteinStdGenes);
0159
0160 <span class="keyword">if</span> ~model.ec.geckoLight
0161 <span class="comment">% Add a new metabolite named prot_standard</span>
0162 proteinStdMets.mets = <span class="string">'prot_standard'</span>;
0163 proteinStdMets.metNames = proteinStdMets.mets;
0164 proteinStdMets.compartments = <span class="string">'c'</span>;
0165 <span class="keyword">if</span> isfield(model,<span class="string">'metNotes'</span>)
0166 proteinStdMets.metNotes = <span class="string">'Standard enzyme-usage pseudometabolite'</span>;
0167 <span class="keyword">end</span>
0168 model = addMets(model, proteinStdMets);
0169
0170 <span class="comment">% Add a protein usage reaction if not a light version</span>
0171 proteinStdUsageRxn.rxns = {<span class="string">'usage_prot_standard'</span>};
0172 proteinStdUsageRxn.rxnNames = proteinStdUsageRxn.rxns;
0173 proteinStdUsageRxn.mets = {proteinStdMets.mets, <span class="string">'prot_pool'</span>};
0174 proteinStdUsageRxn.stoichCoeffs = [-1, 1];
0175 proteinStdUsageRxn.lb = -1000;
0176 proteinStdUsageRxn.ub = 0;
0177 proteinStdUsageRxn.grRules = proteinStdGenes.genes;
0178
0179 model = addRxns(model, proteinStdUsageRxn);
0180 <span class="keyword">end</span>
0181 <span class="comment">% Update .ec structure in model</span>
0182 model.ec.genes(end+1) = {<span class="string">'standard'</span>};
0183 model.ec.enzymes(end+1) = {<span class="string">'standard'</span>};
0184 model.ec.mw(end+1) = standardMW;
0185 model.ec.sequence(end+1) = {<span class="string">''</span>};
0186 <span class="comment">% Additional info</span>
0187 <span class="keyword">if</span> isfield(model.ec,<span class="string">'concs'</span>)
0188 model.ec.concs(end+1) = nan();
0189 <span class="keyword">end</span>
0190
0191 <span class="comment">% Expand the enzyme rxns matrix</span>
0192 model.ec.rxnEnzMat = [model.ec.rxnEnzMat, zeros(length(model.ec.rxns), 1)]; <span class="comment">% 1 new enzyme</span>
0193 model.ec.rxnEnzMat = [model.ec.rxnEnzMat; zeros(length(rxnsMissingGPR), length(model.ec.enzymes))]; <span class="comment">% new rxns</span>
0194 <span class="keyword">end</span>
0195 numRxns = length(model.ec.rxns);
0196 stdMetIdx = find(strcmpi(model.ec.enzymes, <span class="string">'standard'</span>));
0197
0198 <span class="comment">% Remove previous standard kcat assignment</span>
0199 oldStandardEnz = find(strcmp(model.ec.source,<span class="string">'standard'</span>));
0200 <span class="keyword">if</span> ~isempty(oldStandardEnz)
0201 model.ec.rxns(oldStandardEnz) = [];
0202 model.ec.kcat(oldStandardEnz) = [];
0203 model.ec.source(oldStandardEnz) = [];
0204 model.ec.notes(oldStandardEnz) = [];
0205 model.ec.eccodes(oldStandardEnz) = [];
0206 model.ec.rxnEnzMat(oldStandardEnz,:) = [];
0207 <span class="keyword">end</span>
0208
0209 <span class="keyword">for</span> i = 1:numel(rxnsMissingGPR)
0210 rxnIdx = rxnsMissingGPR(i);
0211
0212 <span class="comment">% Update .ec structure in model</span>
0213 <span class="keyword">if</span> ~model.ec.geckoLight
0214 model.ec.rxns(end+1) = model.rxns(rxnIdx);
0215 <span class="comment">% Add prefix in case is light version</span>
0216 <span class="keyword">else</span>
0217 model.ec.rxns{end+1} = [<span class="string">'001_'</span> model.rxns{rxnIdx}];
0218 <span class="keyword">end</span>
0219
0220 <span class="keyword">if</span> ~standard
0221 kcatSubSystemIdx = strcmpi(enzSubSystem_names, model.subSystems{rxnIdx}(1));
0222 <span class="keyword">if</span> all(kcatSubSystemIdx)
0223 model.ec.kcat(end+1) = kcatSubSystem(kcatSubSystemIdx);
0224 <span class="keyword">else</span>
0225 model.ec.kcat(end+1) = standardKcat;
0226 <span class="keyword">end</span>
0227 <span class="keyword">else</span>
0228 model.ec.kcat(end+1) = standardKcat;
0229 <span class="keyword">end</span>
0230
0231 model.ec.source(end+1) = {<span class="string">'standard'</span>};
0232 model.ec.notes(end+1) = {<span class="string">''</span>};
0233 model.ec.eccodes(end+1) = {<span class="string">''</span>};
0234
0235 <span class="comment">% Update the enzyme rxns matrix</span>
0236 model.ec.rxnEnzMat(numRxns+i, stdMetIdx) = 1;
0237 <span class="keyword">end</span>
0238 <span class="comment">% Get the rxns identifiers of the updated rxns</span>
0239 rxnsMissingGPR = model.rxns(rxnsMissingGPR);
0240
0241 <span class="keyword">if</span> fillZeroKcat
0242 zeroKcat = model.ec.kcat == 0 | isnan(model.ec.kcat);
0243 model.ec.kcat(zeroKcat) = standardKcat;
0244 model.ec.source(zeroKcat) = {<span class="string">'standard'</span>};
0245 rxnsNoKcat = model.ec.rxns(zeroKcat);
0246 <span class="keyword">else</span>
0247 rxnsNoKcat = [];
0153 <span class="keyword">if</span> ~model.ec.geckoLight
0154 <span class="comment">% Add a new gene to be consistent with ec field named standard</span>
0155 proteinStdGenes.genes = <span class="string">'standard'</span>;
0156 <span class="keyword">if</span> isfield(model,<span class="string">'geneShortNames'</span>)
0157 proteinStdGenes.geneShortNames = <span class="string">'std'</span>;
0158 <span class="keyword">end</span>
0159 model = addGenesRaven(model, proteinStdGenes);
0160 <span class="comment">% Add a new metabolite named prot_standard</span>
0161 proteinStdMets.mets = <span class="string">'prot_standard'</span>;
0162 proteinStdMets.metNames = proteinStdMets.mets;
0163 proteinStdMets.compartments = <span class="string">'c'</span>;
0164 <span class="keyword">if</span> isfield(model,<span class="string">'metNotes'</span>)
0165 proteinStdMets.metNotes = <span class="string">'Standard enzyme-usage pseudometabolite'</span>;
0166 <span class="keyword">end</span>
0167 model = addMets(model, proteinStdMets);
0168
0169 <span class="comment">% Add a protein usage reaction if not a light version</span>
0170 proteinStdUsageRxn.rxns = {<span class="string">'usage_prot_standard'</span>};
0171 proteinStdUsageRxn.rxnNames = proteinStdUsageRxn.rxns;
0172 proteinStdUsageRxn.mets = {proteinStdMets.mets, <span class="string">'prot_pool'</span>};
0173 proteinStdUsageRxn.stoichCoeffs = [-1, 1];
0174 proteinStdUsageRxn.lb = -1000;
0175 proteinStdUsageRxn.ub = 0;
0176 proteinStdUsageRxn.grRules = proteinStdGenes.genes;
0177
0178 model = addRxns(model, proteinStdUsageRxn);
0179 <span class="keyword">end</span>
0180 <span class="comment">% Update .ec structure in model</span>
0181 model.ec.genes(end+1) = {<span class="string">'standard'</span>};
0182 model.ec.enzymes(end+1) = {<span class="string">'standard'</span>};
0183 model.ec.mw(end+1) = standardMW;
0184 model.ec.sequence(end+1) = {<span class="string">''</span>};
0185 <span class="comment">% Additional info</span>
0186 <span class="keyword">if</span> isfield(model.ec,<span class="string">'concs'</span>)
0187 model.ec.concs(end+1) = nan();
0188 <span class="keyword">end</span>
0189
0190 <span class="comment">% Expand the enzyme rxns matrix</span>
0191 model.ec.rxnEnzMat = [model.ec.rxnEnzMat, zeros(length(model.ec.rxns), 1)]; <span class="comment">% 1 new enzyme</span>
0192 model.ec.rxnEnzMat = [model.ec.rxnEnzMat; zeros(length(rxnsMissingGPR), length(model.ec.enzymes))]; <span class="comment">% new rxns</span>
0193 <span class="keyword">end</span>
0194 numRxns = length(model.ec.rxns);
0195 stdMetIdx = find(strcmpi(model.ec.enzymes, <span class="string">'standard'</span>));
0196
0197 <span class="comment">% Remove previous standard kcat assignment</span>
0198 oldStandardEnz = find(strcmp(model.ec.source,<span class="string">'standard'</span>));
0199 <span class="keyword">if</span> ~isempty(oldStandardEnz)
0200 model.ec.rxns(oldStandardEnz) = [];
0201 model.ec.kcat(oldStandardEnz) = [];
0202 model.ec.source(oldStandardEnz) = [];
0203 model.ec.notes(oldStandardEnz) = [];
0204 model.ec.eccodes(oldStandardEnz) = [];
0205 model.ec.rxnEnzMat(oldStandardEnz,:) = [];
0206 <span class="keyword">end</span>
0207
0208 <span class="keyword">for</span> i = 1:numel(rxnsMissingGPR)
0209 rxnIdx = rxnsMissingGPR(i);
0210
0211 <span class="comment">% Update .ec structure in model</span>
0212 <span class="keyword">if</span> ~model.ec.geckoLight
0213 model.ec.rxns(end+1) = model.rxns(rxnIdx);
0214 <span class="comment">% Add prefix in case is light version</span>
0215 <span class="keyword">else</span>
0216 model.ec.rxns{end+1} = [<span class="string">'001_'</span> model.rxns{rxnIdx}];
0217 <span class="keyword">end</span>
0218
0219 <span class="keyword">if</span> ~standard
0220 kcatSubSystemIdx = strcmpi(enzSubSystem_names, model.subSystems{rxnIdx}(1));
0221 <span class="keyword">if</span> all(kcatSubSystemIdx)
0222 model.ec.kcat(end+1) = kcatSubSystem(kcatSubSystemIdx);
0223 <span class="keyword">else</span>
0224 model.ec.kcat(end+1) = standardKcat;
0225 <span class="keyword">end</span>
0226 <span class="keyword">else</span>
0227 model.ec.kcat(end+1) = standardKcat;
0228 <span class="keyword">end</span>
0229
0230 model.ec.source(end+1) = {<span class="string">'standard'</span>};
0231 model.ec.notes(end+1) = {<span class="string">''</span>};
0232 model.ec.eccodes(end+1) = {<span class="string">''</span>};
0233
0234 <span class="comment">% Update the enzyme rxns matrix</span>
0235 model.ec.rxnEnzMat(numRxns+i, stdMetIdx) = 1;
0236 <span class="keyword">end</span>
0237 <span class="comment">% Get the rxns identifiers of the updated rxns</span>
0238 rxnsMissingGPR = model.rxns(rxnsMissingGPR);
0239
0240 <span class="keyword">if</span> fillZeroKcat
0241 zeroKcat = model.ec.kcat == 0 | isnan(model.ec.kcat);
0242 model.ec.kcat(zeroKcat) = standardKcat;
0243 model.ec.source(zeroKcat) = {<span class="string">'standard'</span>};
0244 rxnsNoKcat = model.ec.rxns(zeroKcat);
0245 <span class="keyword">else</span>
0246 rxnsNoKcat = [];
0247 <span class="keyword">end</span>
0248 <span class="keyword">end</span>
0249 <span class="keyword">end</span>
0250
0251 <a name="_sub1" href="#_subfunctions" class="code">function Cflat = flattenCell(C,strFlag)</a>
0252 <span class="comment">%FLATTENCELL Flatten a nested column cell array into a matrix cell array.</span>
0253 <span class="comment">%</span>
0254 <span class="comment">% CFLAT = FLATTENCELL(C) takes a column cell array in which one or more</span>
0255 <span class="comment">% entries is a nested cell array, and flattens it into a 2D matrix cell</span>
0256 <span class="comment">% array, where the nested entries are spread across new columns.</span>
0257 <span class="comment">%</span>
0258 <span class="comment">% CFLAT = FLATTENCELL(C,STRFLAG) if STRFLAG is TRUE, empty entries in the</span>
0259 <span class="comment">% resulting CFLAT will be replaced with empty strings {''}. Default = FALSE</span>
0260 <span class="keyword">if</span> nargin &lt; 2
0261 strFlag = false;
0262 <span class="keyword">end</span>
0263
0264 <span class="comment">% determine which entries are cells</span>
0265 cells = cellfun(@iscell,C);
0266
0267 <span class="comment">% determine number of elements in each nested cell</span>
0268 cellsizes = cellfun(@numel,C);
0269 cellsizes(~cells) = 1; <span class="comment">% ignore non-cell entries</span>
0270
0271 <span class="comment">% flatten single-entry cells</span>
0272 Cflat = C;
0273 Cflat(cells &amp; (cellsizes == 1)) = cellfun(@(x) x{1},Cflat(cells &amp; (cellsizes == 1)),<span class="string">'UniformOutput'</span>,false);
0274
0275 <span class="comment">% iterate through multi-entry cells</span>
0276 multiCells = find(cellsizes &gt; 1);
0277 <span class="keyword">for</span> i = 1:length(multiCells)
0278 cellContents = Cflat{multiCells(i)};
0279 Cflat(multiCells(i),1:length(cellContents)) = cellContents;
0280 <span class="keyword">end</span>
0281
0282 <span class="comment">% change empty elements to strings, if specified</span>
0283 <span class="keyword">if</span> ( strFlag )
0284 Cflat(cellfun(@isempty,Cflat)) = {<span class="string">''</span>};
0285 <span class="keyword">end</span>
0286 <span class="keyword">end</span></pre></div>
0249
0250 <a name="_sub1" href="#_subfunctions" class="code">function Cflat = flattenCell(C,strFlag)</a>
0251 <span class="comment">%FLATTENCELL Flatten a nested column cell array into a matrix cell array.</span>
0252 <span class="comment">%</span>
0253 <span class="comment">% CFLAT = FLATTENCELL(C) takes a column cell array in which one or more</span>
0254 <span class="comment">% entries is a nested cell array, and flattens it into a 2D matrix cell</span>
0255 <span class="comment">% array, where the nested entries are spread across new columns.</span>
0256 <span class="comment">%</span>
0257 <span class="comment">% CFLAT = FLATTENCELL(C,STRFLAG) if STRFLAG is TRUE, empty entries in the</span>
0258 <span class="comment">% resulting CFLAT will be replaced with empty strings {''}. Default = FALSE</span>
0259 <span class="keyword">if</span> nargin &lt; 2
0260 strFlag = false;
0261 <span class="keyword">end</span>
0262
0263 <span class="comment">% determine which entries are cells</span>
0264 cells = cellfun(@iscell,C);
0265
0266 <span class="comment">% determine number of elements in each nested cell</span>
0267 cellsizes = cellfun(@numel,C);
0268 cellsizes(~cells) = 1; <span class="comment">% ignore non-cell entries</span>
0269
0270 <span class="comment">% flatten single-entry cells</span>
0271 Cflat = C;
0272 Cflat(cells &amp; (cellsizes == 1)) = cellfun(@(x) x{1},Cflat(cells &amp; (cellsizes == 1)),<span class="string">'UniformOutput'</span>,false);
0273
0274 <span class="comment">% iterate through multi-entry cells</span>
0275 multiCells = find(cellsizes &gt; 1);
0276 <span class="keyword">for</span> i = 1:length(multiCells)
0277 cellContents = Cflat{multiCells(i)};
0278 Cflat(multiCells(i),1:length(cellContents)) = cellContents;
0279 <span class="keyword">end</span>
0280
0281 <span class="comment">% change empty elements to strings, if specified</span>
0282 <span class="keyword">if</span> ( strFlag )
0283 Cflat(cellfun(@isempty,Cflat)) = {<span class="string">''</span>};
0284 <span class="keyword">end</span>
0285 <span class="keyword">end</span></pre></div>
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13 changes: 6 additions & 7 deletions src/geckomat/gather_kcats/getStandardKcat.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -150,14 +150,13 @@

% Only add if not geckoLight & getStandardKcat was not run earlier
if ~any(strcmp(model.mets,'prot_standard'))
% Add a new gene to be consistent with ec field named standard
proteinStdGenes.genes = 'standard';
if isfield(model,'geneShortNames')
proteinStdGenes.geneShortNames = 'std';
end
model = addGenesRaven(model, proteinStdGenes);

if ~model.ec.geckoLight
% Add a new gene to be consistent with ec field named standard
proteinStdGenes.genes = 'standard';
if isfield(model,'geneShortNames')
proteinStdGenes.geneShortNames = 'std';
end
model = addGenesRaven(model, proteinStdGenes);
% Add a new metabolite named prot_standard
proteinStdMets.mets = 'prot_standard';
proteinStdMets.metNames = proteinStdMets.mets;
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