fix/feat: various, including ecFVA, enzymeUsage, constrainEnzConcs, c…

…onstrainFluxData (#382)

* fix: getECfromDatabase correct input parameter doc

* feat: makeEcModel error if none of proteins match

* fix: getStandardKcat not remove if real enzyme

* style: various

* todo: refactor fuzzyKcatMatching to use regexprep

* fix: calculateFfactor handle protData multi conds

* fix getStandardKcat

* feat: setKcatForReactions allows multiple kcat as input

* feat: reportEnzymeUsage if enzyme cat. more rxns

* chore: updateGECKOdoc

* fix: reportEnzymeUsage correct percUsage

* fix: constrainFluxData (-)1000 constraints

* fix: ecFVA correct swapped rev fluxes

* fix: reportEnzymeUsage highUsage split isozymes

* refactor: fuzzyKcatMatching use regexprep

* fix: plotEcFVA cdfplot and only plot non-zero rxns

* feat: constrainEnzConcs can remove enzConstraints

* chore: rerun tutorials

* fix: getStandardKcat for light ecModels

* fix: constrainEnzConcs remove enz constraints

doc/src/geckomat/change_model/setKcatForReactions.html

@@ -88,26 +88,33 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0022 <span class="comment">%               changed reactions will read 'from setKcatForReactions'</span>
 0023 <span class="comment">%</span>
 0024 <span class="comment">% Usage: ecModel = setKcatForReactions(ecModel,rxnIds,kcat)</span>
-0025 <span class="keyword">if</span> numel(kcat)&gt;1
-0026     error(<span class="string">'Provide one kcat'</span>)
-0027 <span class="keyword">end</span>
-0028 rxnIds = convertCharArray(rxnIds);
-0029 
-0030 hasExp       = ~cellfun(@isempty,regexp(rxnIds,<span class="string">'_EXP_\d+$'</span>));
-0031 nonExpRxns   = regexprep(ecModel.ec.rxns,<span class="string">'_EXP_\d+$'</span>,<span class="string">''</span>);
-0032 rxnsToChange = [];
-0033 <span class="keyword">for</span> i=1:numel(hasExp)
-0034     <span class="keyword">if</span> hasExp(i) == 1
-0035         rxnsToChange = [rxnsToChange; find(strcmpi(ecModel.ec.rxns,rxnIds{i}))];
-0036     <span class="keyword">else</span>
-0037         nonExpRxn    = regexprep(rxnIds(i),<span class="string">'_EXP_\d+$'</span>,<span class="string">''</span>);
-0038         rxnsToChange = [rxnsToChange; find(strcmpi(nonExpRxns,nonExpRxn))];
-0039     <span class="keyword">end</span>
-0040 <span class="keyword">end</span>
-0041 
-0042 ecModel.ec.kcat(rxnsToChange)   = kcat;
-0043 ecModel.ec.source(rxnsToChange) = {<span class="string">'from setKcatForReactions'</span>};
-0044 <span class="keyword">end</span></pre></div>
+0025 rxnIds = convertCharArray(rxnIds);
+0026 
+0027 hasExp       = ~cellfun(@isempty,regexp(rxnIds,<span class="string">'_EXP_\d+$'</span>));
+0028 nonExpRxns   = regexprep(ecModel.ec.rxns,<span class="string">'_EXP_\d+$'</span>,<span class="string">''</span>);
+0029 rxnsToChange = [];
+0030 <span class="keyword">for</span> i=1:numel(hasExp)
+0031     <span class="keyword">if</span> hasExp(i) == 1
+0032         rxnsToChange = [rxnsToChange; find(strcmpi(ecModel.ec.rxns,rxnIds{i}))];
+0033     <span class="keyword">else</span>
+0034         nonExpRxn    = regexprep(rxnIds(i),<span class="string">'_EXP_\d+$'</span>,<span class="string">''</span>);
+0035         rxnsToChange = [rxnsToChange; find(strcmpi(nonExpRxns,nonExpRxn))];
+0036     <span class="keyword">end</span>
+0037 <span class="keyword">end</span>
+0038 <span class="keyword">if</span> isscalar(rxnsToChange)
+0039     <span class="keyword">if</span> length(kcat) ~= 1
+0040         error(<span class="string">'Found one reaction whose kcat should change, you should provide one kcat value only.'</span>)
+0041     <span class="keyword">end</span>
+0042 <span class="keyword">else</span>
+0043     <span class="keyword">if</span> isscalar(kcat)
+0044         <span class="comment">% Is fine, all reactions get the same kcat</span>
+0045     <span class="keyword">elseif</span> length(kcat) ~= length(rxnsToChange)
+0046         error(<span class="string">'Found %d reactions whose kcat should change, the new kcat should be either a single value, or a vector of length %d.'</span>, length(rxnsToChange), length(rxnsToChange))
+0047     <span class="keyword">end</span>
+0048 <span class="keyword">end</span>
+0049 ecModel.ec.kcat(rxnsToChange)   = kcat;
+0050 ecModel.ec.source(rxnsToChange) = {<span class="string">'from setKcatForReactions'</span>};
+0051 <span class="keyword">end</span></pre></div>
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doc/src/geckomat/gather_kcats/mergeDLKcatAndFuzzyKcats.html

@@ -52,7 +52,7 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
                        BRENDA matches (Optional, default 3)
 
  Output:
-   mergedKcatList  The merged list of kcats
+   mergedKcatList      merged list of kcats
 
  The origin parameter:
    1: correct organism, correct substrate, kcat
@@ -111,7 +111,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0024 <span class="comment">%                       BRENDA matches (Optional, default 3)</span>
 0025 <span class="comment">%</span>
 0026 <span class="comment">% Output:</span>
-0027 <span class="comment">%   mergedKcatList  The merged list of kcats</span>
+0027 <span class="comment">%   mergedKcatList      merged list of kcats</span>
 0028 <span class="comment">%</span>
 0029 <span class="comment">% The origin parameter:</span>
 0030 <span class="comment">%   1: correct organism, correct substrate, kcat</span>