torchcell.metabolism.pathway.apply_pathway

apply_pathway(model: Model, pathway: HeterologousPathway, *, inplace: bool = False) → Model[source]

Add a pathway’s metabolites, reactions and genes to a genome-scale model.

Parameters:

  • model – The base genome-scale model.

  • pathway – The pathway to add.

  • inplace – Edit model rather than a copy. Default copies, because the base model is shared across arms and a mutated copy is an invisible difference between them.

Returns:

The edited model.

Raises:

ValueError – A pathway id already exists, or a reaction cannot be balanced.