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feat: removeStandardKcat new function
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edkerk committed May 21, 2024
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33 changes: 17 additions & 16 deletions doc/index.html
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Expand Up @@ -19,22 +19,23 @@ <h2>Matlab Directories</h2>
<h2>Matlab Files found in these Directories</h2>
<table width="100%">
<tr>
<td><a href="src/geckomat/model_adapter/ModelAdapter.html" title="src\geckomat\model_adapter">ModelAdapter</a></td> <td><a href="src/geckomat/get_enzyme_data/copyECtoGEM.html" title="src\geckomat\get_enzyme_data">copyECtoGEM</a></td> <td><a href="src/geckomat/change_model/getKcatAcrossIsozymes.html" title="src\geckomat\change_model">getKcatAcrossIsozymes</a></td> <td><a href="src/geckomat/gather_kcats/readDLKcatOutput.html" title="src\geckomat\gather_kcats">readDLKcatOutput</a></td> </tr> <tr>
<td><a href="src/geckomat/model_adapter/ModelAdapterManager.html" title="src\geckomat\model_adapter">ModelAdapterManager</a></td> <td><a href="src/geckomat/utilities/ecFSEOF.html" title="src\geckomat\utilities">ecFSEOF</a></td> <td><a href="src/geckomat/change_model/getReactionsFromEnzyme.html" title="src\geckomat\change_model">getReactionsFromEnzyme</a></td> <td><a href="src/geckomat/utilities/reportEnzymeUsage.html" title="src\geckomat\utilities">reportEnzymeUsage</a></td> </tr> <tr>
<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">abc_max</a></td> <td><a href="src/geckomat/utilities/ecFVA.html" title="src\geckomat\utilities">ecFVA</a></td> <td><a href="src/geckomat/gather_kcats/getStandardKcat.html" title="src\geckomat\gather_kcats">getStandardKcat</a></td> <td><a href="src/geckomat/gather_kcats/runDLKcat.html" title="src\geckomat\gather_kcats">runDLKcat</a></td> </tr> <tr>
<td><a href="src/geckomat/model_adapter/adapterTemplate.html" title="src\geckomat\model_adapter">adapterTemplate</a></td> <td><a href="src/geckomat/utilities/enzymeUsage.html" title="src\geckomat\utilities">enzymeUsage</a></td> <td><a href="src/geckomat/utilities/getSubsetEcModel.html" title="src\geckomat\utilities">getSubsetEcModel</a></td> <td><a href="src/geckomat/utilities/saveEcModel.html" title="src\geckomat\utilities">saveEcModel</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/limit_proteins/fillEnzConcs.html" title="src\geckomat\limit_proteins">fillEnzConcs</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/getcarbonnum.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">getcarbonnum</a></td> <td><a href="src/geckomat/gather_kcats/selectKcatValue.html" title="src\geckomat\gather_kcats">selectKcatValue</a></td> </tr> <tr>
<td><a href="src/geckomat/utilities/addNewRxnsToEC.html" title="src\geckomat\utilities">addNewRxnsToEC</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/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/anaerobicModel.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">anaerobicModel</a></td> <td><a href="src/geckomat/utilities/findGECKOroot.html" title="src\geckomat\utilities">findGECKOroot</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/change_model/applyComplexData.html" title="src\geckomat\change_model">applyComplexData</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/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/change_model/applyCustomKcats.html" title="src\geckomat\change_model">applyCustomKcats</a></td> <td><a href="src/geckomat/change_model/findMetSmiles.html" title="src\geckomat\change_model">findMetSmiles</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/applyKcatConstraints.html" title="src\geckomat\change_model">applyKcatConstraints</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/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/kcat_sensitivity_analysis/Bayesian/bayesianSensitivityTuning.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">bayesianSensitivityTuning</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/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/limit_proteins/calculateFfactor.html" title="src\geckomat\limit_proteins">calculateFfactor</a></td> <td><a href="src/geckomat/change_model/getComplexData.html" title="src\geckomat\change_model">getComplexData</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>
<td><a href="src/geckomat/get_enzyme_data/calculateMW.html" title="src\geckomat\get_enzyme_data">calculateMW</a></td> <td><a href="src/geckomat/limit_proteins/getConcControlCoeffs.html" title="src\geckomat\limit_proteins">getConcControlCoeffs</a></td> <td><a href="src/geckomat/change_model/makeEcModel.html" title="src\geckomat\change_model">makeEcModel</a></td> <td><a href="src/geckomat/limit_proteins/updateProtPool.html" title="src\geckomat\limit_proteins">updateProtPool</a></td> </tr> <tr>
<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">changeMedia</a></td> <td><a href="src/geckomat/get_enzyme_data/getECfromDatabase.html" title="src\geckomat\get_enzyme_data">getECfromDatabase</a></td> <td><a href="src/geckomat/utilities/mapRxnsToConv.html" title="src\geckomat\utilities">mapRxnsToConv</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/updateprior.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">updateprior</a></td> </tr> <tr>
<td><a href="src/geckomat/limit_proteins/constrainEnzConcs.html" title="src\geckomat\limit_proteins">constrainEnzConcs</a></td> <td><a href="src/geckomat/get_enzyme_data/getECfromGEM.html" title="src\geckomat\get_enzyme_data">getECfromGEM</a></td> <td><a href="src/geckomat/gather_kcats/mergeDLKcatAndFuzzyKcats.html" title="src\geckomat\gather_kcats">mergeDLKcatAndFuzzyKcats</a></td> <td><a href="src/geckomat/gather_kcats/writeDLKcatInput.html" title="src\geckomat\gather_kcats">writeDLKcatInput</a></td> </tr> <tr>
<td><a href="src/geckomat/limit_proteins/constrainFluxData.html" title="src\geckomat\limit_proteins">constrainFluxData</a></td> <td><a href="src/geckomat/get_enzyme_data/getECstring.html" title="src\geckomat\get_enzyme_data">getECstring</a></td> <td><a href="src/geckomat/utilities/plotEcFVA.html" title="src\geckomat\utilities">plotEcFVA</a></td> <td><a href="" title=""></a></td> </tr></table>
<td><a href="src/geckomat/model_adapter/ModelAdapter.html" title="src\geckomat\model_adapter">ModelAdapter</a></td> <td><a href="src/geckomat/utilities/ecFSEOF.html" title="src\geckomat\utilities">ecFSEOF</a></td> <td><a href="src/geckomat/gather_kcats/getStandardKcat.html" title="src\geckomat\gather_kcats">getStandardKcat</a></td> <td><a href="src/geckomat/gather_kcats/runDLKcat.html" title="src\geckomat\gather_kcats">runDLKcat</a></td> </tr> <tr>
<td><a href="src/geckomat/model_adapter/ModelAdapterManager.html" title="src\geckomat\model_adapter">ModelAdapterManager</a></td> <td><a href="src/geckomat/utilities/ecFVA.html" title="src\geckomat\utilities">ecFVA</a></td> <td><a href="src/geckomat/utilities/getSubsetEcModel.html" title="src\geckomat\utilities">getSubsetEcModel</a></td> <td><a href="src/geckomat/utilities/saveEcModel.html" title="src\geckomat\utilities">saveEcModel</a></td> </tr> <tr>
<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">abc_max</a></td> <td><a href="src/geckomat/utilities/enzymeUsage.html" title="src\geckomat\utilities">enzymeUsage</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/getcarbonnum.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">getcarbonnum</a></td> <td><a href="src/geckomat/gather_kcats/selectKcatValue.html" title="src\geckomat\gather_kcats">selectKcatValue</a></td> </tr> <tr>
<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/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>
<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/bayesianSensitivityTuning.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">bayesianSensitivityTuning</a></td> <td><a href="src/geckomat/change_model/getComplexData.html" title="src\geckomat\change_model">getComplexData</a></td> <td><a href="src/geckomat/change_model/makeEcModel.html" title="src\geckomat\change_model">makeEcModel</a></td> <td><a href="src/geckomat/limit_proteins/updateProtPool.html" title="src\geckomat\limit_proteins">updateProtPool</a></td> </tr> <tr>
<td><a href="src/geckomat/limit_proteins/calculateFfactor.html" title="src\geckomat\limit_proteins">calculateFfactor</a></td> <td><a href="src/geckomat/limit_proteins/getConcControlCoeffs.html" title="src\geckomat\limit_proteins">getConcControlCoeffs</a></td> <td><a href="src/geckomat/utilities/mapRxnsToConv.html" title="src\geckomat\utilities">mapRxnsToConv</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/updateprior.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">updateprior</a></td> </tr> <tr>
<td><a href="src/geckomat/get_enzyme_data/calculateMW.html" title="src\geckomat\get_enzyme_data">calculateMW</a></td> <td><a href="src/geckomat/get_enzyme_data/getECfromDatabase.html" title="src\geckomat\get_enzyme_data">getECfromDatabase</a></td> <td><a href="src/geckomat/gather_kcats/mergeDLKcatAndFuzzyKcats.html" title="src\geckomat\gather_kcats">mergeDLKcatAndFuzzyKcats</a></td> <td><a href="src/geckomat/gather_kcats/writeDLKcatInput.html" title="src\geckomat\gather_kcats">writeDLKcatInput</a></td> </tr> <tr>
<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">changeMedia</a></td> <td><a href="src/geckomat/get_enzyme_data/getECfromGEM.html" title="src\geckomat\get_enzyme_data">getECfromGEM</a></td> <td><a href="src/geckomat/utilities/plotEcFVA.html" title="src\geckomat\utilities">plotEcFVA</a></td> <td><a href="" title=""></a></td> </tr> <tr>
<td><a href="src/geckomat/limit_proteins/constrainEnzConcs.html" title="src\geckomat\limit_proteins">constrainEnzConcs</a></td> <td><a href="src/geckomat/get_enzyme_data/getECstring.html" title="src\geckomat\get_enzyme_data">getECstring</a></td> <td><a href="src/geckomat/gather_kcats/readDLKcatOutput.html" title="src\geckomat\gather_kcats">readDLKcatOutput</a></td> <td><a href="" title=""></a></td> </tr> <tr>
<td><a href="src/geckomat/limit_proteins/constrainFluxData.html" title="src\geckomat\limit_proteins">constrainFluxData</a></td> <td><a href="src/geckomat/change_model/getKcatAcrossIsozymes.html" title="src\geckomat\change_model">getKcatAcrossIsozymes</a></td> <td><a href="src/geckomat/gather_kcats/removeStandardKcat.html" title="src\geckomat\gather_kcats">removeStandardKcat</a></td> <td><a href="" title=""></a></td> </tr> <tr>
<td><a href="src/geckomat/get_enzyme_data/copyECtoGEM.html" title="src\geckomat\get_enzyme_data">copyECtoGEM</a></td> <td><a href="src/geckomat/change_model/getReactionsFromEnzyme.html" title="src\geckomat\change_model">getReactionsFromEnzyme</a></td> <td><a href="src/geckomat/utilities/reportEnzymeUsage.html" title="src\geckomat\utilities">reportEnzymeUsage</a></td> <td><a href="" title=""></a></td> </tr></table>


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