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parseRxnFormula error

Anonymous
2013-02-19
2013-05-30

  • Anonymous
    2013-02-19

    I cannot get parseRxnFormula to work. Could someone please help, here is the problem:

    rname=model.rxns{i,1}

    rname =

    AKGDH

    >> formula = printRxnFormula(model,rname,false)

    formula =

        'akg + coa + nad  -> co2 + nadh + succoa '
    >>  = parseRxnFormula(formula)
    ??? Operands to the || and && operators must be convertible to logical scalar
    values.

    Error in ==> parseRxnFormula at 61
        elseif strcmp(t,'->') || strcmp(t,'->')

     
  • Daniel Hyduke
    Daniel Hyduke
    2013-02-19

    I'm not able to repeat your problem.  What version of the CoBRA Toolbox are you using?  What model are you using?

    This is what happens when I copy & paste your formula string:
    >> formula= 'akg + coa + nad  -> co2 + nadh + succoa'

    formula =

    akg + coa + nad  -> co2 + nadh + succoa

    >>  = parseRxnFormula(formula)

    metaboliteList =

        'akg'    'coa'    'nad'    'co2'    'nadh'    'succoa'

    stoichCoeffList =

        -1    -1    -1     1     1     1

    revFlag =

         0

     

  • Anonymous
    2013-02-20

    I am using cobra 2 on linux, the model is E coli core with a few reactions modified, AKGDH is not among them

     

  • Anonymous
    2013-02-20

    Very interesting. The same: when I copy - paste the formula, I get it to work. But when I repeat assigning formula through printRxnFormula, it does not:

    formula =

    akg + coa + nad  -> co2 + nadh + succoa

    >>  = parseRxnFormula(formula)

    metaboliteList =

        'akg'    'coa'    'nad'    'co2'    'nadh'    'succoa'

    stoichCoeffList =

        -1    -1    -1     1     1     1

    revFlag =

         0

    >> formula = printRxnFormula(model,rname,false)

    formula =

        'akg + coa + nad  -> co2 + nadh + succoa '

    >>  = parseRxnFormula(formula)
    ??? Operands to the || and && operators must be convertible to logical scalar
    values.

    Error in ==> parseRxnFormula at 61
        elseif strcmp(t,'->') || strcmp(t,'->')

     

  • Anonymous
    2013-02-20

    I got it!!
    formula1=formula{1,1}

    formula1 =

    akg + coa + nad  -> co2 + nadh + succoa

    >>  = parseRxnFormula(formula1)

    metaboliteList =

        'akg'    'coa'    'nad'    'co2'    'nadh'    'succoa'

    stoichCoeffList =

        -1    -1    -1     1     1     1

    revFlag =

         0