opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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Refactor: gam_in_biomass should return the GAM value #592

Open ChristianLieven opened 5 years ago

ChristianLieven commented 5 years ago

Problem description

Currently the function biomass.gam_in_model only returns a Boolean. It should return the actual GAM value to be even more useful, users then don't have to look it up/ calculate it themselves.

For the value to be correct, gam_in_biomass will have to differentiate between lumped and split biomass reactions because in lumped biomass reactions the stoichiometric coefficient of ATP will be a sum of the maintenance value and the stoichiometry of ATP contributing to DNA. In a split reaction, the coefficient will just account for GAM.