doc: clarify params.enzyme_comp in model adapter

SysBioChalmers · Jul 18, 2024 · 3b5a506 · 3b5a506
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diff --git a/src/geckomat/model_adapter/adapterTemplate.m b/src/geckomat/model_adapter/adapterTemplate.m
@@ -62,7 +62,10 @@
 			% Reaction ID for biomass pseudoreaction
 			obj.params.bioRxn = 'r_4041';
 
-			% Compartment name in which the added enzymes should be located
+			% Name of the compartment where the protein pseudometabolites
+            % should be located (all be located in the same compartment,
+            % this does not interfere with them catalyzing reactions in
+            % different compartments). Typically, cytoplasm is chosen.
 			obj.params.enzyme_comp = 'cytoplasm';
         end
 

diff --git a/tutorials/full_ecModel/YeastGEMAdapter.m b/tutorials/full_ecModel/YeastGEMAdapter.m
@@ -33,6 +33,10 @@
 
 			obj.params.bioRxn = 'r_4041';
 
+            % Name of the compartment where the protein pseudometabolites
+            % should be located (all be located in the same compartment,
+            % this does not interfere with them catalyzing reactions in
+            % different compartments). Typically, cytoplasm is chosen.
 			obj.params.enzyme_comp = 'cytoplasm';			
 		end
 

diff --git a/tutorials/light_ecModel/HumanGEMAdapter.m b/tutorials/light_ecModel/HumanGEMAdapter.m
@@ -47,6 +47,10 @@
 
 			obj.params.bioRxn = 'MAR13082';
 
+			% Name of the compartment where the protein pseudometabolites
+            % should be located (all be located in the same compartment,
+            % this does not interfere with them catalyzing reactions in
+            % different compartments). Typically, cytoplasm is chosen.
 			obj.params.enzyme_comp = 'Cytosol';
 
         end