fix: compatibility with RAVEN 2.10.0 (#391)

* fix: compatible with next RAVEN release

* fix: rename anaerobicModel

A yeast-GEM-specific script that ideally should be refactored. For now, just rename to avoid conflict with the function in yeast-GEM repository

doc/index.html

@@ -25,7 +25,7 @@ <h2>Matlab Files found in these Directories</h2>
 				<td><a href="src/geckomat/model_adapter/adapterTemplate.html" title="src\geckomat\model_adapter">adapterTemplate</a></td>		<td><a href="src/geckomat/limit_proteins/fillEnzConcs.html" title="src\geckomat\limit_proteins">fillEnzConcs</a></td>		<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/getrSample.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">getrSample</a></td>		<td><a href="src/geckomat/kcat_sensitivity_analysis/sensitivityTuning.html" title="src\geckomat\kcat_sensitivity_analysis">sensitivityTuning</a></td>	</tr>	<tr>
 				<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/addCarbonNum.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">addCarbonNum</a></td>		<td><a href="src/geckomat/get_enzyme_data/findECInDB.html" title="src\geckomat\get_enzyme_data">findECInDB</a></td>		<td><a href="src/geckomat/get_enzyme_data/loadBRENDAdata.html" title="src\geckomat\get_enzyme_data">loadBRENDAdata</a></td>		<td><a href="src/geckomat/change_model/setKcatForReactions.html" title="src\geckomat\change_model">setKcatForReactions</a></td>	</tr>	<tr>
 				<td><a href="src/geckomat/utilities/addNewRxnsToEC.html" title="src\geckomat\utilities">addNewRxnsToEC</a></td>		<td><a href="src/geckomat/utilities/findGECKOroot.html" title="src\geckomat\utilities">findGECKOroot</a></td>		<td><a href="src/geckomat/utilities/loadConventionalGEM.html" title="src\geckomat\utilities">loadConventionalGEM</a></td>		<td><a href="src/geckomat/change_model/setProtPoolSize.html" title="src\geckomat\change_model">setProtPoolSize</a></td>	</tr>	<tr>
-				<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">anaerobicModel</a></td>		<td><a href="src/geckomat/kcat_sensitivity_analysis/findMaxValue.html" title="src\geckomat\kcat_sensitivity_analysis">findMaxValue</a></td>		<td><a href="src/geckomat/get_enzyme_data/loadDatabases.html" title="src\geckomat\get_enzyme_data">loadDatabases</a></td>		<td><a href="src/geckomat/kcat_sensitivity_analysis/sigmaFitter.html" title="src\geckomat\kcat_sensitivity_analysis">sigmaFitter</a></td>	</tr>	<tr>
+				<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel_GECKO.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">anaerobicModel_GECKO</a></td>		<td><a href="src/geckomat/kcat_sensitivity_analysis/findMaxValue.html" title="src\geckomat\kcat_sensitivity_analysis">findMaxValue</a></td>		<td><a href="src/geckomat/get_enzyme_data/loadDatabases.html" title="src\geckomat\get_enzyme_data">loadDatabases</a></td>		<td><a href="src/geckomat/kcat_sensitivity_analysis/sigmaFitter.html" title="src\geckomat\kcat_sensitivity_analysis">sigmaFitter</a></td>	</tr>	<tr>
 				<td><a href="src/geckomat/change_model/applyComplexData.html" title="src\geckomat\change_model">applyComplexData</a></td>		<td><a href="src/geckomat/change_model/findMetSmiles.html" title="src\geckomat\change_model">findMetSmiles</a></td>		<td><a href="src/geckomat/utilities/loadEcModel.html" title="src\geckomat\utilities">loadEcModel</a></td>		<td><a href="src/geckomat/utilities/startGECKOproject.html" title="src\geckomat\utilities">startGECKOproject</a></td>	</tr>	<tr>
 				<td><a href="src/geckomat/change_model/applyCustomKcats.html" title="src\geckomat\change_model">applyCustomKcats</a></td>		<td><a href="src/geckomat/limit_proteins/flexibilizeEnzConcs.html" title="src\geckomat\limit_proteins">flexibilizeEnzConcs</a></td>		<td><a href="src/geckomat/utilities/loadFluxData.html" title="src\geckomat\utilities">loadFluxData</a></td>		<td><a href="src/geckomat/kcat_sensitivity_analysis/truncateValues.html" title="src\geckomat\kcat_sensitivity_analysis">truncateValues</a></td>	</tr>	<tr>
 				<td><a href="src/geckomat/change_model/applyKcatConstraints.html" title="src\geckomat\change_model">applyKcatConstraints</a></td>		<td><a href="src/geckomat/gather_kcats/fuzzyKcatMatching.html" title="src\geckomat\gather_kcats">fuzzyKcatMatching</a></td>		<td><a href="src/geckomat/utilities/loadProtData.html" title="src\geckomat\utilities">loadProtData</a></td>		<td><a href="src/geckomat/utilities/updateGECKOdoc.html" title="src\geckomat\utilities">updateGECKOdoc</a></td>	</tr>	<tr>

doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.html

@@ -54,7 +54,7 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
 <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
 This function calls:
 <ul style="list-style-image:url(../../../../matlabicon.gif)">
-<li><a href="addCarbonNum.html" class="code" title="function model = addCarbonNum(model)">addCarbonNum</a>	addCarbonNum</li><li><a href="anaerobicModel.html" class="code" title="function model = anaerobicModel(model)">anaerobicModel</a>	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</li><li><a href="changeMedia.html" class="code" title="function [model,pos] = changeMedia(model,c_source,media,anox,flux)">changeMedia</a>	changeMedia</li></ul>
+<li><a href="addCarbonNum.html" class="code" title="function model = addCarbonNum(model)">addCarbonNum</a>	addCarbonNum</li><li><a href="anaerobicModel_GECKO.html" class="code" title="function model = anaerobicModel_GECKO(model)">anaerobicModel_GECKO</a>	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</li><li><a href="changeMedia.html" class="code" title="function [model,pos] = changeMedia(model,c_source,media,anox,flux)">changeMedia</a>	changeMedia</li></ul>
 This function is called by:
 <ul style="list-style-image:url(../../../../matlabicon.gif)">
 <li><a href="bayesianSensitivityTuning.html" class="code" title="function ecModel = bayesianSensitivityTuning(ecModel,modelAdapter,maxIterations)">bayesianSensitivityTuning</a>	bayesianSensitivityTuning</li></ul>
@@ -152,7 +152,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0085         model_tmp = changeRxnBounds(model_tmp,<span class="string">'r_1631'</span>,0,<span class="string">'b'</span>);
 0086 
 0087         <span class="keyword">if</span> strcmp(data(i,14),<span class="string">'anaerobic'</span>) ||strcmp(data(i,14),<span class="string">'limited'</span>) 
-0088             model_tmp = <a href="anaerobicModel.html" class="code" title="function model = anaerobicModel(model)">anaerobicModel</a>(model_tmp);
+0088             model_tmp = <a href="anaerobicModel_GECKO.html" class="code" title="function model = anaerobicModel_GECKO(model)">anaerobicModel_GECKO</a>(model_tmp);
 0089         <span class="keyword">end</span>
 0090         <span class="keyword">if</span> strcmp(data(i,14),<span class="string">'limited'</span>) 
 0091              model_tmp.lb(strcmp(model_tmp.rxnNames,<span class="string">'oxygen exchange'</span>)) = -5;<span class="comment">%TODO: Currently hard-coded for yeast</span>

doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.html → doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel_GECKO.html

@@ -2,8 +2,8 @@
                 "http://www.w3.org/TR/REC-html40/loose.dtd">
 <html>
 <head>
-  <title>Description of anaerobicModel</title>
-  <meta name="keywords" content="anaerobicModel">
+  <title>Description of anaerobicModel_GECKO</title>
+  <meta name="keywords" content="anaerobicModel_GECKO">
   <meta name="description" content="%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%">
   <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
   <meta name="generator" content="m2html v1.5 &copy; 2003-2005 Guillaume Flandin">
@@ -12,23 +12,23 @@
 </head>
 <body>
 <a name="_top"></a>
-<div><a href="../../../../index.html">Home</a> &gt;  <a href="#">src</a> &gt; <a href="#">geckomat</a> &gt; <a href="../index.html">kcat_sensitivity_analysis</a> &gt; <a href="index.html">Bayesian</a> &gt; anaerobicModel.m</div>
+<div><a href="../../../../index.html">Home</a> &gt;  <a href="#">src</a> &gt; <a href="#">geckomat</a> &gt; <a href="../index.html">kcat_sensitivity_analysis</a> &gt; <a href="index.html">Bayesian</a> &gt; anaerobicModel_GECKO.m</div>
 
 <!--<table width="100%"><tr><td align="left"><a href="../../../../index.html"><img alt="<" border="0" src="../../../../left.png">&nbsp;Master index</a></td>
 <td align="right"><a href="index.html">Index for src\geckomat\kcat_sensitivity_analysis\Bayesian&nbsp;<img alt=">" border="0" src="../../../../right.png"></a></td></tr></table>-->
 
-<h1>anaerobicModel
+<h1>anaerobicModel_GECKO
 </h1>
 
 <h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
 <div class="box"><strong>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</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 model = anaerobicModel(model) </strong></div>
+<div class="box"><strong>function model = anaerobicModel_GECKO(model) </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">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- anaerobicModel.m
+ anaerobicModel_GECKO.m
  Converts model to anaerobic
 
  Benjamin J. Sanchez
@@ -52,14 +52,14 @@ <h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border
 
 <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
 <div class="fragment"><pre>0001 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
-0002 <span class="comment">% anaerobicModel.m</span>
+0002 <span class="comment">% anaerobicModel_GECKO.m</span>
 0003 <span class="comment">% Converts model to anaerobic</span>
 0004 <span class="comment">%</span>
 0005 <span class="comment">% Benjamin J. Sanchez</span>
 0006 <span class="comment">% Feiran Li - 2019-09-24</span>
 0007 <span class="comment">% Feiran Li - Last update: 2019-10-02 modify the order of changes</span>
 0008 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
-0009 <a name="_sub0" href="#_subfunctions" class="code">function model = anaerobicModel(model)</a>
+0009 <a name="_sub0" href="#_subfunctions" class="code">function model = anaerobicModel_GECKO(model)</a>
 0010 
 0011 <span class="comment">%1th change: Refit GAM and NGAM to exp. data, change biomass composition</span>
 0012 GAM   = 58.1988;  <span class="comment">%Data from Nissen et al. 1997</span>

doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.html

@@ -54,7 +54,7 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
 <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
 This function calls:
 <ul style="list-style-image:url(../../../../matlabicon.gif)">
-<li><a href="anaerobicModel.html" class="code" title="function model = anaerobicModel(model)">anaerobicModel</a>	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</li></ul>
+<li><a href="anaerobicModel_GECKO.html" class="code" title="function model = anaerobicModel_GECKO(model)">anaerobicModel_GECKO</a>	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</li></ul>
 This function is called by:
 <ul style="list-style-image:url(../../../../matlabicon.gif)">
 <li><a href="abc_max.html" class="code" title="function [rmse_final,exp,simulated,growthdata,max_growth]=abc_max(ecModel,kcat_random_all,growthdata,max_growth,proc,sample_generation,j,rxn2block)">abc_max</a>	setProtPoolSize</li></ul>
@@ -180,7 +180,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0113 <span class="comment">% change aeerobic or anaerobic</span>
 0114 <span class="keyword">if</span> strcmp(anox,<span class="string">'anaerobic'</span>)
 0115     1
-0116     model = <a href="anaerobicModel.html" class="code" title="function model = anaerobicModel(model)">anaerobicModel</a>(model);
+0116     model = <a href="anaerobicModel_GECKO.html" class="code" title="function model = anaerobicModel_GECKO(model)">anaerobicModel_GECKO</a>(model);
 0117 <span class="keyword">end</span>
 0118 <span class="keyword">end</span>
 0119 

doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/index.html

@@ -19,7 +19,7 @@ <h1>Index for src\geckomat\kcat_sensitivity_analysis\Bayesian</h1>
 
 <h2>Matlab files in this directory:</h2>
 <table>
-<tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="abc_max.html">abc_max</a></td><td>setProtPoolSize </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="addCarbonNum.html">addCarbonNum</a></td><td>addCarbonNum </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="anaerobicModel.html">anaerobicModel</a></td><td>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="bayesianSensitivityTuning.html">bayesianSensitivityTuning</a></td><td>bayesianSensitivityTuning </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="changeMedia.html">changeMedia</a></td><td>changeMedia </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getcarbonnum.html">getcarbonnum</a></td><td>getcarbonnum </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getrSample.html">getrSample</a></td><td>getrSample </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="updateprior.html">updateprior</a></td><td>updateprior </td></tr></table>
+<tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="abc_max.html">abc_max</a></td><td>setProtPoolSize </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="addCarbonNum.html">addCarbonNum</a></td><td>addCarbonNum </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="anaerobicModel_GECKO.html">anaerobicModel_GECKO</a></td><td>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="bayesianSensitivityTuning.html">bayesianSensitivityTuning</a></td><td>bayesianSensitivityTuning </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="changeMedia.html">changeMedia</a></td><td>changeMedia </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getcarbonnum.html">getcarbonnum</a></td><td>getcarbonnum </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getrSample.html">getrSample</a></td><td>getrSample </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="updateprior.html">updateprior</a></td><td>updateprior </td></tr></table>
 
 
 

doc/src/geckomat/model_adapter/adapterTemplate.html

@@ -108,18 +108,21 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0062             <span class="comment">% Reaction ID for biomass pseudoreaction</span>
 0063             obj.params.bioRxn = <span class="string">'r_4041'</span>;
 0064 
-0065             <span class="comment">% Compartment name in which the added enzymes should be located</span>
-0066             obj.params.enzyme_comp = <span class="string">'cytoplasm'</span>;
-0067         <span class="keyword">end</span>
-0068         
-0069         <a name="_sub1" href="#_subfunctions" class="code">function [spont,spontRxnNames] = getSpontaneousReactions(obj,model)</a>
-0070             <span class="comment">% Indicates how spontaneous reactions are identified. Here it</span>
-0071             <span class="comment">% is done by the reaction have 'spontaneous' in its name.</span>
-0072             spont = contains(model.rxnNames,<span class="string">'spontaneous'</span>);
-0073             spontRxnNames = model.rxnNames(spont);
-0074         <span class="keyword">end</span>
-0075     <span class="keyword">end</span>
-0076 <span class="keyword">end</span></pre></div>
+0065             <span class="comment">% Name of the compartment where the protein pseudometabolites</span>
+0066             <span class="comment">% should be located (all be located in the same compartment,</span>
+0067             <span class="comment">% this does not interfere with them catalyzing reactions in</span>
+0068             <span class="comment">% different compartments). Typically, cytoplasm is chosen.</span>
+0069             obj.params.enzyme_comp = <span class="string">'cytoplasm'</span>;
+0070         <span class="keyword">end</span>
+0071         
+0072         <a name="_sub1" href="#_subfunctions" class="code">function [spont,spontRxnNames] = getSpontaneousReactions(obj,model)</a>
+0073             <span class="comment">% Indicates how spontaneous reactions are identified. Here it</span>
+0074             <span class="comment">% is done by the reaction have 'spontaneous' in its name.</span>
+0075             spont = contains(model.rxnNames,<span class="string">'spontaneous'</span>);
+0076             spontRxnNames = model.rxnNames(spont);
+0077         <span class="keyword">end</span>
+0078     <span class="keyword">end</span>
+0079 <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>

src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.m

@@ -85,7 +85,7 @@
         model_tmp = changeRxnBounds(model_tmp,'r_1631',0,'b');
 
         if strcmp(data(i,14),'anaerobic') ||strcmp(data(i,14),'limited') 
-            model_tmp = anaerobicModel(model_tmp);
+            model_tmp = anaerobicModel_GECKO(model_tmp);
         end
         if strcmp(data(i,14),'limited') 
              model_tmp.lb(strcmp(model_tmp.rxnNames,'oxygen exchange')) = -5;%TODO: Currently hard-coded for yeast

src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.m → src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel_GECKO.m

@@ -1,12 +1,12 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% anaerobicModel.m
+% anaerobicModel_GECKO.m
 % Converts model to anaerobic
 %
 % Benjamin J. Sanchez
 % Feiran Li - 2019-09-24
 % Feiran Li - Last update: 2019-10-02 modify the order of changes
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-function model = anaerobicModel(model)
+function model = anaerobicModel_GECKO(model)
 
 %1th change: Refit GAM and NGAM to exp. data, change biomass composition
 GAM   = 58.1988;  %Data from Nissen et al. 1997

src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.m

@@ -113,7 +113,7 @@
 % change aeerobic or anaerobic
 if strcmp(anox,'anaerobic')
     1
-    model = anaerobicModel(model);
+    model = anaerobicModel_GECKO(model);
 end
 end
 

test/unit_tests/ecTestGEM/data/smilesDB.tsv

@@ -2,3 +2,4 @@ e1	C(C1C)O
 e2	C1C(=NC2)
 m1	C(C1C)O
 m2	C1C(=NC2)
+