Skip to content

Commit

Permalink
chore: updateGECKOdoc
Browse files Browse the repository at this point in the history
  • Loading branch information
@edkerk
edkerk committed May 8, 2024
1 parent 9a1e7e8 commit 2f2194a
Show file tree
Hide file tree
Showing 3 changed files with 65 additions and 47 deletions.
2 changes: 1 addition & 1 deletion doc/src/geckomat/limit_proteins/calculateFfactor.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0046 <span class="keyword">if</span> ischar(protData) &amp;&amp; endsWith(protData,<span class="string">'paxDB.tsv'</span>)
0047 fID = fopen(fullfile(protData),<span class="string">'r'</span>);
0048 fileContent = textscan(fID,<span class="string">'%s'</span>,<span class="string">'delimiter'</span>,<span class="string">'\n'</span>);
0049 headerLines = sum(startsWith(fileContent{1},<span class="string">'#'</span>));
0049 headerLines = find(startsWith(fileContent{1},<span class="string">'#'</span>),1,<span class="string">'last'</span>);
0050 fclose(fID);
0051
0052 <span class="comment">%Read data file, excluding headerlines</span>
Expand Down
53 changes: 28 additions & 25 deletions doc/src/geckomat/utilities/enzymeUsage.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,7 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
absUsage vector of absolute enzyme usages
UB vector of enzyme exchange reaction upper bounds
protID string array of matching protein IDs
fluxes vector of fluxes, copy of input fluxes

Usage:
usageData = enzymeUsage(ecModel,fluxes,zero)</pre></div>
Expand Down Expand Up @@ -99,31 +100,33 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0026 <span class="comment">% absUsage vector of absolute enzyme usages</span>
0027 <span class="comment">% UB vector of enzyme exchange reaction upper bounds</span>
0028 <span class="comment">% protID string array of matching protein IDs</span>
0029 <span class="comment">%</span>
0030 <span class="comment">% Usage:</span>
0031 <span class="comment">% usageData = enzymeUsage(ecModel,fluxes,zero)</span>
0032
0033 <span class="keyword">if</span> nargin&lt;3
0034 zero=true;
0035 <span class="keyword">end</span>
0036 <span class="keyword">if</span> ecModel.ec.geckoLight
0037 error(<span class="string">'This function does not work on GECKO light models.'</span>)
0038 <span class="keyword">end</span>
0039 usageData.protID = ecModel.ec.enzymes;
0040 [~,rxnIdx] = ismember(strcat(<span class="string">'usage_prot_'</span>,ecModel.ec.enzymes),ecModel.rxns);
0041
0042 usageData.LB = ecModel.lb(rxnIdx);
0043 usageData.absUsage = abs(fluxes(rxnIdx));
0044 usageData.capUsage = abs(usageData.absUsage./usageData.LB);
0045
0046 <span class="keyword">if</span> ~zero
0047 nonzero = usageData.absUsage&lt;0;
0048 usageData.absUsage = usageData.absUsage(nonzero);
0049 usageData.capUsage = usageData.capUsage(nonzero);
0050 usageData.LB = usageData.LB(nonzero);
0051 usageData.protID = usageData.protID(nonzero);
0052 <span class="keyword">end</span>
0053 <span class="keyword">end</span></pre></div>
0029 <span class="comment">% fluxes vector of fluxes, copy of input fluxes</span>
0030 <span class="comment">%</span>
0031 <span class="comment">% Usage:</span>
0032 <span class="comment">% usageData = enzymeUsage(ecModel,fluxes,zero)</span>
0033
0034 <span class="keyword">if</span> nargin&lt;3
0035 zero=true;
0036 <span class="keyword">end</span>
0037 <span class="keyword">if</span> ecModel.ec.geckoLight
0038 error(<span class="string">'This function does not work on GECKO light models.'</span>)
0039 <span class="keyword">end</span>
0040 usageData.protID = ecModel.ec.enzymes;
0041 [~,rxnIdx] = ismember(strcat(<span class="string">'usage_prot_'</span>,ecModel.ec.enzymes),ecModel.rxns);
0042
0043 usageData.LB = ecModel.lb(rxnIdx);
0044 usageData.absUsage = abs(fluxes(rxnIdx));
0045 usageData.capUsage = abs(usageData.absUsage./usageData.LB);
0046 usageData.fluxes = fluxes;
0047
0048 <span class="keyword">if</span> ~zero
0049 nonzero = usageData.absUsage&lt;0;
0050 usageData.absUsage = usageData.absUsage(nonzero);
0051 usageData.capUsage = usageData.capUsage(nonzero);
0052 usageData.LB = usageData.LB(nonzero);
0053 usageData.protID = usageData.protID(nonzero);
0054 <span class="keyword">end</span>
0055 <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>
</body>
</html>
57 changes: 36 additions & 21 deletions doc/src/geckomat/utilities/reportEnzymeUsage.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,15 +24,15 @@ <h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../
<div class="box"><strong>reportEnzymeUsage</strong></div>

<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../../../up.png"></a></h2>
<div class="box"><strong>function usageReport = topEnzymeUsage(ecModel, usageData, highCapUsage, topAbsUsage) </strong></div>
<div class="box"><strong>function usageReport = reportEnzymeUsage(ecModel, usageData, highCapUsage, topAbsUsage) </strong></div>

<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../../../up.png"></a></h2>
<div class="fragment"><pre class="comment"> reportEnzymeUsage
Summarizes the results from enzymeUsage.

Input:
ecModel a GECKO3 ecModel
usageData output from reportEnzymeUsage
usageData output from enzymeUsage
highCapUsage minimum ratio of enzyme capacity usage to be considered
as high usage (Optional, default 0.9, refering to a
minimum of 90% capacity usage)
Expand Down Expand Up @@ -60,13 +60,13 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^


<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../../../up.png"></a></h2>
<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function usageReport = topEnzymeUsage(ecModel, usageData, highCapUsage, topAbsUsage)</a>
<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function usageReport = reportEnzymeUsage(ecModel, usageData, highCapUsage, topAbsUsage)</a>
0002 <span class="comment">% reportEnzymeUsage</span>
0003 <span class="comment">% Summarizes the results from enzymeUsage.</span>
0004 <span class="comment">%</span>
0005 <span class="comment">% Input:</span>
0006 <span class="comment">% ecModel a GECKO3 ecModel</span>
0007 <span class="comment">% usageData output from reportEnzymeUsage</span>
0007 <span class="comment">% usageData output from enzymeUsage</span>
0008 <span class="comment">% highCapUsage minimum ratio of enzyme capacity usage to be considered</span>
0009 <span class="comment">% as high usage (Optional, default 0.9, refering to a</span>
0010 <span class="comment">% minimum of 90% capacity usage)</span>
Expand Down Expand Up @@ -123,23 +123,38 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0061 topUsage.rxnNames = {};
0062 topUsage.grRules = {};
0063
0064 protPool = -ecModel.lb(strcmp(ecModel.rxns,<span class="string">'prot_pool_exchange'</span>))/100;
0065
0066 <span class="keyword">for</span> i=1:numel(topEnzyme)
0067 [rxns, kcat, idx, rxnNames, grRules] = getReactionsFromEnzyme(ecModel,topEnzyme{i});
0068 rxnNumber = numel(rxns);
0069 topUsage.protID(end+1:end+rxnNumber,1) = topEnzyme(i);
0070 topUsage.geneID(end+1:end+rxnNumber,1) = geneIDs(i);
0071 topUsage.absUsage(end+1:end+rxnNumber,1) = usageData.absUsage(topUse(i));
0072 topUsage.percUsage(end+1:end+rxnNumber,1) = topUsage.absUsage(end-(rxnNumber-1):<span class="keyword">end</span>,1)/protPool;
0073 topUsage.kcat(end+1:end+rxnNumber,1) = kcat;
0074 topUsage.source(end+1:end+rxnNumber,1) = ecModel.ec.source(idx);
0075 topUsage.rxnID(end+1:end+rxnNumber,1) = rxns;
0076 topUsage.rxnNames(end+1:end+rxnNumber,1) = rxnNames;
0077 topUsage.grRules(end+1:end+rxnNumber,1) = grRules;
0078 <span class="keyword">end</span>
0079 usageReport.topAbsUsage = struct2table(topUsage);
0080 <span class="keyword">end</span></pre></div>
0064 <span class="comment">% Calculate the protein pool flux from the 'prot_pool_exchange' reaction</span>
0065 protPoolExchangeFlux = -ecModel.lb(strcmp(ecModel.rxns,<span class="string">'prot_pool_exchange'</span>));
0066
0067 fluxValues = usageData.fluxes;
0068
0069 <span class="comment">% Sum fluxes for all 'usage_prot_' reactions, excluding the 'usage_prot_standard'</span>
0070 usageProtIndices = startsWith(ecModel.rxns, <span class="string">'usage_prot_'</span>) &amp; <span class="keyword">...</span>
0071 ~contains(ecModel.rxns, <span class="string">'standard'</span>);
0072
0073 <span class="comment">% Sum the absolute values of the usage fluxes</span>
0074 totalUsageProtFlux = sum(abs(fluxValues(usageProtIndices)));
0075
0076 <span class="comment">% Define the new protein pool as the sum of prot_pool_exchange flux and total usage_prot fluxes</span>
0077 protPool = (protPoolExchangeFlux + totalUsageProtFlux)/100;
0078
0079 <span class="keyword">for</span> i=1:numel(topEnzyme)
0080 [rxns, kcat, idx, rxnNames, grRules] = getReactionsFromEnzyme(ecModel,topEnzyme{i});
0081 rxnNumber = numel(rxns);
0082 topUsage.protID(end+1:end+rxnNumber,1) = topEnzyme(i);
0083 topUsage.geneID(end+1:end+rxnNumber,1) = geneIDs(i);
0084 topUsage.absUsage(end+1:end+rxnNumber,1) = usageData.absUsage(topUse(i));
0085 topUsage.percUsage(end+1:end+rxnNumber,1) = topUsage.absUsage(end-(rxnNumber-1):<span class="keyword">end</span>,1)/protPool;
0086 topUsage.kcat(end+1:end+rxnNumber,1) = kcat;
0087 topUsage.source(end+1:end+rxnNumber,1) = ecModel.ec.source(idx);
0088 topUsage.rxnID(end+1:end+rxnNumber,1) = rxns;
0089 topUsage.rxnNames(end+1:end+rxnNumber,1) = rxnNames;
0090 topUsage.grRules(end+1:end+rxnNumber,1) = grRules;
0091 <span class="keyword">end</span>
0092 usageReport.topAbsUsage = struct2table(topUsage);
0093 usageReport.totalProtPool = protPoolExchangeFlux;
0094 usageReport.totalUsageFlux = totalUsageProtFlux;
0095 <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>
</body>
</html>

0 comments on commit 2f2194a

Please sign in to comment.