torchcell.metabolism.yeast_GEM.YeastGEM
- class YeastGEM(root: str = 'data/torchcell/yeast-GEM', version: str = '9.0.2', induced_gene_set: GeneSet | None = None)[source]
Bases:
objectDownload, load, and expose the yeast-GEM genome-scale model.
- property model: Model
Return the lazily loaded cobra SBML model.
- property reaction_map: Hypergraph
Create a hypergraph where edges represent reactions with gene combinations.
- Raises:
MemberlessReactionError – if any reaction has no metabolites.
- property bipartite_graph: DiGraph
Returns a directed bipartite graph representation of the metabolic network.
The graph has two types of nodes: - Reactions (node_type=”reaction”) - Metabolites (node_type=”metabolite”)
Edges connect reactions to metabolites with a directed structure: - Reaction → Metabolite with edge_type=”product” (metabolite is produced) - Reaction → Metabolite with edge_type=”reactant” (metabolite is consumed)
The edge direction is always from reaction to metabolite, with the edge_type indicating whether the metabolite is a reactant or product.
- Returns:
A directed bipartite graph
- Return type:
nx.DiGraph
- Raises:
MemberlessReactionError – if any reaction has no metabolites.