Reversible (_r) reactions in pFBA

[sowmyamanojna]

This is regarding the reactions that are completely reversible and tagged with _r by convertToIrreversible.
Once the reaction classes are returned, the assignment to the different classes only consider _[f|b], neglecting the _r reactions. I am not sure if it is meant to be implemented this way, but, when I read through the pFBA paper, I didn't find anything related to discarding the _r reactions.

How to reproduce:

model = readCbModel('e_coli_core.xml');
[~, RxnClasses, ~] = pFBA(model, 'geneoption', 0);

The model performs the classification, but also prints out this:

The reaction "FORt_r" is not in your model!

The .xml model is taken from BiGG. In case, _r can be considered, I can open a PR for the same.

Any clarification would be of great help. Thanks!

I hereby confirm that I have:

• [X] Tried to solve the issue on my own
• [X] Retried to run my code with the latest version of The COBRA Toolbox
• [X] Checked that a similar issue has not already been opened

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