Merge pull request #295 from SysBioChalmers/fix/standardKcat

fix: minor issues raised

protocol.m

@@ -130,7 +130,7 @@
 ecModel = getKcatAcrossIsoenzymes(ecModel);
 
 % STEP 12 Get standard kcat
-% Assign an enzyme cost to reactions without gene assocation. These
+% Assign a protein cost to reactions without gene assocation. These
 % reactions are identified as those with empty entry in ecModel.grRules.
 % The following reactions are exempted:
 % A Exchange reactions: exchanging a metabolite across the model boundary,
@@ -141,13 +141,13 @@
 %   are mostly representing diffusion or pseudotransport processes such as
 %   vesicles moving from ER to Golgi. While proteins are involved in such
 %   processes, they are not catalyzed by enzymes.
-% C Pseudoreactions: any other reaction that should be considered to be
+% C Pseudoreactions: any other reaction that should not be considered to be
 %   catalyzed by an enzyme. getStandardKcat recognizes these from the
 %   reaction name contaning "pseudoreaction".
 % D Custom list of non-enzyme reactions: if the above approaches does not
 %   correctly identify all non-enzyme reactions that should be ignored by
-%   getStandardKcat, /data/pseudoRxns.tsv can be specified in adapter
-%   folder.
+%   getStandardKcat, /data/pseudoRxns.tsv can be specified in the adapter
+%   folder, containing the relevant reaction identifiers.
 
 [ecModel, rxnsMissingGPR, standardMW, standardKcat] = getStandardKcat(ecModel);
 

src/geckomat/gather_kcats/fuzzyKcatMatching.m

@@ -2,9 +2,13 @@
 % fuzzyKcatMatching
 %   Matchs the model EC numbers and substrates to the BRENDA database, to
 %   return the corresponding kcats for each reaction. If no exact match is
-%   found, less specific kcat values are found from (a) closely related
-%   organism; (b) different substrate; (c) calculated from specific
-%   activities; (d) wildcards in the EC number.
+%   found, less specific kcat values are found from (a) evolutionary
+%   closely related organism; (b) different substrate; (c) calculated from
+%   specific activities; (d) wildcards in the EC number. The model organism
+%   is provided in the model adapter as obj.params.org_name, and
+%   evolutionary distance to other organisms is determined via KEGG
+%   phylogeny. If an organism name occurs multiple times in KEGG, the first
+%   instance will be used when determining evolutionary distance.
 %
 % Input:
 %   model        an ecModel in GECKO 3 format (with ecModel.ec structure)

src/geckomat/gather_kcats/getStandardKcat.m

@@ -141,7 +141,7 @@
     fileData   = textscan(fID,'%s %s','delimiter','\t');
     fclose(fID);
     customRxns = fileData{1};
-    customRxns = find(strcmp(customRxns,model.rxns));
+    customRxns = find(ismember(model.rxns,customRxns));
 else
     customRxns = [];
 end