cobratoolbox
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Should model.rules only be generated on the fly?
Should model.rules only be generated on the fly within a function from model.grRules? It seems like people might get dependent on .rules, like they did with .rev as the former duplicates (although in an abbreviated way, the information in model.grRules.
Id actually advocate it rather the other way around since there are no restrictions on the values of model.genes and thus a grRules field could have unparsable entries. At least to me, grRules is only a visualisation of model.rules and rules should have priority.
Model fields should never be modified manually but always through functions, as otherwise you never know, whether fields get out of sync.