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Only declared output and input anchors create graph edges. Internal reaction metabolites are not stored in the anchor table and therefore cannot create implicit connections.

Usage

gift_graph(db = NULL, quality = NULL)

Arguments

db

Optional open gifter database connection.

quality

Optional filter, `"exact"` or `"compartment_inexact"`.

Value

A tibble with `from_gift`, `shared_anchor`, `to_anchor`, `shared_molecule`, `edge_quality`, and `to_gift`.

Details

`edge_quality` is `exact` when both GIFTs declare the same anchor, and `compartment_inexact` when they declare the same molecule but one side leaves the compartment unresolved. An inexact edge is a real composition step whose location was not evidenced well enough to split; a chain assembled only from exact edges is the stronger claim. Two anchors whose compartments are both specified and different are never connected, so a transport GIFT is required to cross that boundary.