refactor: speed up writing model fields

code/io/importYaml.m

@@ -164,13 +164,13 @@
                 model = readFieldValue(model, 'rxnNames', tline_value);
 
             case 'lower_bound'
-                model.lb = [model.lb; tline_value];
-                leftEqns  = [leftEqns; leftEquation];
-                rightEqns = [rightEqns; rightEquation];
+                model.lb(end+1,1)  = {tline_value};
+                leftEqns(end+1,1)  = {leftEquation};
+                rightEqns(end+1,1) = {rightEquation};
                 readEquation = false;
 
             case 'upper_bound'
-                model.ub = [model.ub; tline_value];
+                model.ub(end+1,1)  = {tline_value};
 
             case 'gene_reaction_rule'
                 model = readFieldValue(model, 'grRules', tline_value);
@@ -182,7 +182,7 @@
                 model = readFieldValue(model, 'rxnFrom', tline_value);
 
             case 'objective_coefficient'
-                objRxns = [objRxns; rxnId];
+                objRxns(end+1,1) = {rxnId};
 
             case 'eccodes'
                 model = readFieldValue(model, 'eccodes', tline_value);
@@ -196,33 +196,33 @@
 
             case 'confidence_score'
                 model = readFieldValue(model, 'rxnConfidenceScores', tline_value);
-                model.subSystems = [model.subSystems; {subSystems}];
+                model.subSystems(end+1,1) = {subSystems};
                 readSubsystems = false;
 
             case 'metabolites'
                 readEquation = true;
-                leftEquation  = {''};
-                rightEquation = {''};
+                leftEquation  = '';
+                rightEquation = '';
 
             otherwise
                 if readSubsystems
-                    subSystems = [subSystems; regexprep(tline_key, '"', '')];
+                    subSystems(end+1,1) = {regexprep(tline_key, '"', '')};
 
                 % resolve the equation
                 elseif readEquation
                     metCoeffi = regexp(regexprep(tline, ' +- ', ''), ': ', 'split');
-                    coeffi = str2num(metCoeffi{2});
-                    if coeffi < 0
+                    coeffi = metCoeffi{2};
+                    if str2double(coeffi) < 0
                         if strcmp(leftEquation, '')
-                            leftEquation = strcat(num2str(abs(coeffi), 12),32,metCoeffi{1});
+                            leftEquation = [coeffi(2:end),' ',metCoeffi{1}]; %Remove minus sign from coefficient
                         else
-                            leftEquation = strcat(leftEquation,' +',32,num2str(abs(coeffi), 12),32,metCoeffi{1});
+                            leftEquation = [leftEquation,' + ',coeffi(2:end),' ',metCoeffi{1}];
                         end
                     else
                         if strcmp(rightEquation, '')
-                            rightEquation = strcat(32,num2str(coeffi, 12),32,metCoeffi{1});
+                            rightEquation = [' ',coeffi,' ',metCoeffi{1}];
                         else
-                            rightEquation = strcat(rightEquation,' +',32,num2str(coeffi, 12),32,metCoeffi{1});
+                            rightEquation = [rightEquation,' + ',coeffi,' ',metCoeffi{1}];
                         end
                     end
                 end
@@ -238,8 +238,8 @@
     % import compartments:
     if section == 5
         [tline_key, tline_value] = tokenizeYamlLine(tline);
-        model.comps = [model.comps; tline_key];
-        model.compNames = [model.compNames; tline_value];
+        model.comps(end+1,1) = {tline_key};
+        model.compNames(end+1,1) = {tline_value};
     end
 
 end
@@ -286,7 +286,7 @@
 end
 
 function model = readFieldValue(model, fieldName, value)
-    model.(fieldName) = [model.(fieldName); {value}];
+    model.(fieldName)(end+1,1) = {value};
 end
 
 function [line_key, line_value]= tokenizeYamlLine(line)

model/Human-GEM.yml

@@ -4,7 +4,7 @@
     short_name: "Human-GEM"
     full_name: "Generic genome-scale metabolic model of Homo sapiens"
     version: ""
-    date: "2021-12-18"
+    date: "2022-06-14"
     authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas"
     email: "[email protected]"
     organization: "Chalmers University of Technology"
@@ -292964,7 +292964,7 @@
       - rxnNotes: "DOI:10.1007/978-1-4419-0840-7"
       - rxnFrom: "Recon3D"
       - eccodes: ""
-      - references: PMID:17655371"
+      - references: "PMID:17655371"
       - subsystem:
           - "Drug metabolism"
       - confidence_score: 0
@@ -305769,8 +305769,8 @@
       - id: "MAR13086"
       - name: ""
       - metabolites: !!omap
-          - MAM02847n: -1
           - MAM02847c: 1
+          - MAM02847n: -1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000030066 and ENSG00000047410 and ENSG00000058804 and ENSG00000069248 and ENSG00000075188 and ENSG00000085415 and ENSG00000093000 and ENSG00000094914 and ENSG00000095319 and ENSG00000101146 and ENSG00000102900 and ENSG00000108559 and ENSG00000110713 and ENSG00000111581 and ENSG00000113569 and ENSG00000119392 and ENSG00000120253 and ENSG00000124789 and ENSG00000125450 and ENSG00000126883 and ENSG00000132182 and ENSG00000136243 and ENSG00000138750 and ENSG00000139496 and ENSG00000153201 and ENSG00000153207 and ENSG00000155561 and ENSG00000157020 and ENSG00000157349 and ENSG00000163002 and ENSG00000196313 and ENSG00000213024"