feat: getStandardKcat use custom list of non-enzyme reactions to ignore

[edkerk]

Main improvements in this PR:

• feat:
  • getStandardKcat can use data/pseudoRxns.tsv (if it exists) to define custom non-enzyme reactions that should be ignored when assigning standard kcats. (solves getStandardKcat assigns protein costs to pseudo-reactions #280)
  • getStandardKcat removes previous standard kcat assignments, so that the function can be run repeatedly on the same model.
• fix:
  • getStandardKcat also specifies model.ec.source{i} = 'standard' if a standard kcat is assigned to a zero-kcat reaction. (solves ec.source in getStandardKcat #286)
  • remaining corrections for prot_pool_exchange minimization (solves Error in minimizing protein pool usage #287)

I hereby confirm that I have:

• Selected develop as a target branch (top left drop-down menu)

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 
Running geckoCoreFunctionTests
================================================================================
Verification failed in geckoCoreFunctionTests/testsaveECModel_tc0009.
    ---------------------
    Framework Diagnostic:
    ---------------------
    verifyEqual failed.
    --> Path to failure: .rev
        --> The numeric values are not equal using "isequaln".
        --> Failure table:
                Index    Actual    Expected    Error    RelativeError
                _____    ______    ________    _____    _____________
            
                 12        1          0          1           Inf     
                 13        1          0          1           Inf     
                 14        1          0          1           Inf     
                 15        1          0          1           Inf     
                 16        1          0          1           Inf     
                 17        1          0          1           Inf     
        
        Actual double:
            17x1 double
        Expected double:
            17x1 double
    
    Actual Value:
      struct with fields:
    
               name: 'testModel'
                 id: 'testModel'
         annotation: [1x1 struct]
               date: '2023-03-20'
        description: ''
            version: ''
               rxns: {17x1 cell}
                  S: [10x17 double]
                rev: [17x1 double]
           metNames: {10x1 cell}
              comps: {2x1 cell}
          compNames: {2x1 cell}
           metComps: [10x1 double]
               mets: {10x1 cell}
            grRules: {17x1 cell}
         rxnGeneMat: [17x5 double]
              genes: {5x1 cell}
                 ub: [17x1 double]
                 lb: [17x1 double]
                  c: [17x1 double]
           rxnNames: {17x1 cell}
                  b: [10x1 double]
            eccodes: {17x1 cell}
           metNotes: {10x1 cell}
                 ec: [1x1 struct]
    Expected Value:
      struct with fields:
    
                 id: 'testModel'
               name: 'testModel'
        description: ''
            version: ''
               date: '2023-03-20'
         annotation: [1x1 struct]
               rxns: {17x1 cell}
           rxnNames: {17x1 cell}
               mets: {10x1 cell}
           metNames: {10x1 cell}
                  S: [10x17 double]
                 lb: [17x1 double]
                 ub: [17x1 double]
                rev: [17x1 double]
                  c: [17x1 double]
                  b: [10x1 double]
              genes: {5x1 cell}
            grRules: {17x1 cell}
         rxnGeneMat: [17x5 double]
            eccodes: {17x1 cell}
           metComps: [10x1 double]
           metNotes: {10x1 cell}
              comps: {2x1 cell}
          compNames: {2x1 cell}
                 ec: [1x1 struct]
    ------------------
    Stack Information:
    ------------------
    In /home/m/actions-runner/_work/GECKO/GECKO/test/unit_tests/geckoCoreFunctionTests.m (testsaveECModel_tc0009) at 232
================================================================================
Model-specific DLKcat input stored at /home/m/actions-runner/_work/GECKO/GECKO/test/unit_tests/ecTestGEM/data/DLKcat_input_test.tsv
Limit has been reached. Protein P5 seems to be problematic. Consider changing the kcat.
Done geckoCoreFunctionTests
__________

Failure Summary:

     Name                                           Failed  Incomplete  Reason(s)
    ============================================================================================
     geckoCoreFunctionTests/testsaveECModel_tc0009    X                 Failed by verification.

Note: In the case of multiple test runs, this post will be edited.

[ae-tafur]

Looks good!

[Yu-sysbio]

Looks good!