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revert #372 (#380)
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* Revert "Merge pull request #372 from HossFir/update-reportEnzymeUsage"

This reverts commit cc8e449, reversing
changes made to 883b40d.

* fix: reportEnzymeUsage gives total protein usage
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@edkerk
edkerk authored May 27, 2024
1 parent cb54747 commit 10cfd74
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Showing 4 changed files with 45 additions and 78 deletions.
53 changes: 25 additions & 28 deletions doc/src/geckomat/utilities/enzymeUsage.html
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Expand Up @@ -54,7 +54,6 @@ <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 @@ -100,33 +99,31 @@ <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">% 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>
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>
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50 changes: 18 additions & 32 deletions doc/src/geckomat/utilities/reportEnzymeUsage.html
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Expand Up @@ -123,38 +123,24 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0061 topUsage.rxnNames = {};
0062 topUsage.grRules = {};
0063
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>
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 usageReport.totalUsageFlux = protPool;
0081 <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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2 changes: 0 additions & 2 deletions src/geckomat/utilities/enzymeUsage.m
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,6 @@
% 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)
Expand All @@ -43,7 +42,6 @@
usageData.LB = ecModel.lb(rxnIdx);
usageData.absUsage = abs(fluxes(rxnIdx));
usageData.capUsage = abs(usageData.absUsage./usageData.LB);
usageData.fluxes = fluxes;

if ~zero
nonzero = usageData.absUsage<0;
Expand Down
18 changes: 2 additions & 16 deletions src/geckomat/utilities/reportEnzymeUsage.m
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Original file line number Diff line number Diff line change
Expand Up @@ -61,20 +61,7 @@
topUsage.rxnNames = {};
topUsage.grRules = {};

% Calculate the protein pool flux from the 'prot_pool_exchange' reaction
protPoolExchangeFlux = -ecModel.lb(strcmp(ecModel.rxns,'prot_pool_exchange'));

fluxValues = usageData.fluxes;

% Sum fluxes for all 'usage_prot_' reactions, excluding the 'usage_prot_standard'
usageProtIndices = startsWith(ecModel.rxns, 'usage_prot_') & ...
~contains(ecModel.rxns, 'standard');

% Sum the absolute values of the usage fluxes
totalUsageProtFlux = sum(abs(fluxValues(usageProtIndices)));

% Define the new protein pool as the sum of prot_pool_exchange flux and total usage_prot fluxes
protPool = (protPoolExchangeFlux + totalUsageProtFlux)/100;
protPool = -ecModel.lb(strcmp(ecModel.rxns,'prot_pool_exchange'))/100;

for i=1:numel(topEnzyme)
[rxns, kcat, idx, rxnNames, grRules] = getReactionsFromEnzyme(ecModel,topEnzyme{i});
Expand All @@ -90,6 +77,5 @@
topUsage.grRules(end+1:end+rxnNumber,1) = grRules;
end
usageReport.topAbsUsage = struct2table(topUsage);
usageReport.totalProtPool = protPoolExchangeFlux;
usageReport.totalUsageFlux = totalUsageProtFlux;
usageReport.totalUsageFlux = protPool;
end

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