diff --git a/doc/index.html b/doc/index.html index f332bb806..63add7002 100644 --- a/doc/index.html +++ b/doc/index.html @@ -25,7 +25,7 @@

Matlab Files found in these Directories

adapterTemplate fillEnzConcs getrSample sensitivityTuning addCarbonNum findECInDB loadBRENDAdata setKcatForReactions addNewRxnsToEC findGECKOroot loadConventionalGEM setProtPoolSize - anaerobicModel findMaxValue loadDatabases sigmaFitter + anaerobicModel_GECKO findMaxValue loadDatabases sigmaFitter applyComplexData findMetSmiles loadEcModel startGECKOproject applyCustomKcats flexibilizeEnzConcs loadFluxData truncateValues applyKcatConstraints fuzzyKcatMatching loadProtData updateGECKOdoc diff --git a/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.html b/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.html index b077b3f2f..8b53eca43 100644 --- a/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.html +++ b/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.html @@ -54,7 +54,7 @@

DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

This function calls: +
  • addCarbonNum addCarbonNum
  • anaerobicModel_GECKO %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  • changeMedia changeMedia
    • This function is called by: @@ -152,7 +152,7 @@

    SOURCE CODE ^'r_1631',0,'b'); 0086 0087 if strcmp(data(i,14),'anaerobic') ||strcmp(data(i,14),'limited') -0088 model_tmp = anaerobicModel(model_tmp); +0088 model_tmp = anaerobicModel_GECKO(model_tmp); 0089 end 0090 if strcmp(data(i,14),'limited') 0091 model_tmp.lb(strcmp(model_tmp.rxnNames,'oxygen exchange')) = -5;%TODO: Currently hard-coded for yeast diff --git a/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.html b/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel_GECKO.html similarity index 98% rename from doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.html rename to doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel_GECKO.html index 77886c37d..897661008 100644 --- a/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.html +++ b/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel_GECKO.html @@ -2,8 +2,8 @@ "http://www.w3.org/TR/REC-html40/loose.dtd"> - Description of anaerobicModel - + Description of anaerobicModel_GECKO + @@ -12,23 +12,23 @@ -
    Home > src > geckomat > kcat_sensitivity_analysis > Bayesian > anaerobicModel.m
    +
    Home > src > geckomat > kcat_sensitivity_analysis > Bayesian > anaerobicModel_GECKO.m
    -

    anaerobicModel +

    anaerobicModel_GECKO

    PURPOSE ^

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    SYNOPSIS ^

    -
    function model = anaerobicModel(model)
    +
    function model = anaerobicModel_GECKO(model)

    DESCRIPTION ^

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- anaerobicModel.m
+ anaerobicModel_GECKO.m
  Converts model to anaerobic
 
  Benjamin J. Sanchez
@@ -52,14 +52,14 @@ 
    SUBFUNCTIONS ^SOURCE CODE ^
    
 
    0001 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-0002 % anaerobicModel.m
+0002 % anaerobicModel_GECKO.m
 0003 % Converts model to anaerobic
 0004 %
 0005 % Benjamin J. Sanchez
 0006 % Feiran Li - 2019-09-24
 0007 % Feiran Li - Last update: 2019-10-02 modify the order of changes
 0008 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-0009 function model = anaerobicModel(model)
+0009 function model = anaerobicModel_GECKO(model)
 0010 
 0011 %1th change: Refit GAM and NGAM to exp. data, change biomass composition
 0012 GAM   = 58.1988;  %Data from Nissen et al. 1997
diff --git a/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.html b/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.html
index f6d673531..f4202b402 100644
--- a/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.html
+++ b/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.html
@@ -54,7 +54,7 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
      
-
    • anaerobicModel	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    
+
  • anaerobicModel_GECKO	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    • 
 This function is called by:
 
@@ -180,7 +180,7 @@ 
    SOURCE CODE ^% change aeerobic or anaerobic
 0114 if strcmp(anox,'anaerobic')
 0115     1
-0116     model = anaerobicModel(model);
+0116     model = anaerobicModel_GECKO(model);
 0117 end
 0118 end
 0119 
diff --git a/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/index.html b/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/index.html
index c6a86815b..5cade9575 100644
--- a/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/index.html
+++ b/doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/index.html
@@ -19,7 +19,7 @@ 
    Index for src\geckomat\kcat_sensitivity_analysis\Bayesian
    
 
 
    Matlab files in this directory:
    
 
-
     abc_maxsetProtPoolSize 
     addCarbonNumaddCarbonNum 
     anaerobicModel%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
     bayesianSensitivityTuningbayesianSensitivityTuning 
     changeMediachangeMedia 
     getcarbonnumgetcarbonnum 
     getrSamplegetrSample 
     updatepriorupdateprior 
    
+ abc_maxsetProtPoolSize  addCarbonNumaddCarbonNum  anaerobicModel_GECKO%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  bayesianSensitivityTuningbayesianSensitivityTuning  changeMediachangeMedia  getcarbonnumgetcarbonnum  getrSamplegetrSample  updatepriorupdateprior 
 
 
 
diff --git a/src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.m b/src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.m
index f2e2e1ca9..c9bf54254 100644
--- a/src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.m
+++ b/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
diff --git a/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.m b/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel_GECKO.m
similarity index 99%
rename from src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.m
rename to src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel_GECKO.m
index d1e205b80..9cba35819 100644
--- a/src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.m
+++ b/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
diff --git a/src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.m b/src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.m
index ba493911d..67b25b8fa 100644
--- a/src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.m
+++ b/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