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Reactions are unaware of groups (and subsystems) #938
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I think the main implementation concern is being careful with circular references as much as possible so that deletion and addition of objects doesn't mangle group membership. This is probably why _associate_gene and _dissociate_gene are written as "private" methods. I think this would be a welcome feature but would require a lot of work on the API (and might seem weird if functions for associating genes with reactions are still private). Implementing it in |
I'm a bit confused. |
It's true that It would be pretty easy though to do the same thing for |
Quick input:
Groups are much more powerful then the |
Problem description
The model has groups that contain members (list of reactions).
However, the reactions do not have a groups field, and the subsystems is always an empty string.
I think it should behave like genes, where reaction has a set of groups and relevant functions _associate_group(self, cobra_group) _dissociate_group(self, cobra_group)
If that's approved, models that include groups should associate them with reactions when loaded.
This is similar, but different from #543 and #473 - I understand this should be encoded as groups, but I think reactions should know their groups.
I would suggest having subsystems either be
If the key developers can comment on this.
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