structure_tables: Convert Glycan Structures to Graph Tables

In glyrepr: Representation for Glycan Compositions and Structures

Convert Glycan Structures to Graph Tables

Description

structure_nodes(), structure_edges(), structure_floating_parts(), and structure_floating_substituents() convert a glycan structure vector or one glycan igraph to normalized graph tables. structure_from_tibbles() rebuilds a glyrepr_structure vector from those tables, a vector of reducing-end anomers, and optional alditol status.

The glycan_id column is the integer position of each glycan in the input vector. Duplicate structures are expanded to their original vector positions. Missing structures have no node or edge rows and are reconstructed from missing values in anomers. If x is named, all four tibbles also contain a glycan_name column. structure_from_tibbles() uses glycan_name as output names when that column is present.

For structure-vector input, structure_nodes()$node_id follows residue order in the complete canonical IUPAC-condensed string. For graph input, it follows the graph's current numeric vertex positions without canonicalizing or renumbering them. A graph is represented with glycan_id = 1L and no glycan_name column.

In structure_floating_parts(), root_node and every integer in the nodes and parents list-columns refer to structure_nodes()$node_id for the same glycan. nodes contains every node in the floating component. An empty parents vector means all feasible nodes outside that component are candidates. The linkage column describes the virtual attachment to an unresolved parent; this attachment is intentionally absent from structure_edges(). During reconstruction, a row with exactly one effective candidate parent is normalized to an ordinary edge and is therefore absent from the resulting structure_floating_parts() table.

Parent indices written after | in an IUPAC-condensed floating part are complete-sequence node IDs, identical to structure_nodes()$node_id for a canonical structure. Residues in floating blocks precede the main tree, and substituent blocks contribute no nodes. structure_from_tibbles() expects these same global node IDs and preserves cross-component domains.

In structure_floating_substituents(), each row describes one unresolved substituent. substituent is its canonical position-and-name token, and the parents list-column contains candidate global node IDs. An empty vector means all feasible residue nodes are candidates. A singleton candidate is normalized into structure_nodes()$sub, so it does not remain in the floating-substituent table.

Usage

structure_nodes(x)

structure_edges(x)

structure_floating_parts(x)

structure_floating_substituents(x)

structure_from_tibbles(
  nodes,
  edges,
  anomers,
  floating_parts = NULL,
  floating_substituents = NULL,
  alditols = FALSE
)

Arguments

x	A glycan structure vector or one glycan igraph.
nodes	A data frame with columns glycan_id, node_id, mono, and sub, and optionally glycan_name.
edges	A data frame with columns glycan_id, edge_id, from_node, to_node, and linkage, and optionally glycan_name.
anomers	A character vector of reducing-end anomers, one per glycan.
floating_parts	A data frame returned by structure_floating_parts(), or NULL when no floating parts are present.
floating_substituents	A data frame returned by structure_floating_substituents(), or NULL when no floating substituents are present.
alditols	A logical vector indicating alditol status, either one value or one per glycan. Missing values are allowed only for missing glycans. Defaults to FALSE for backward compatibility.

Value

• structure_nodes() returns a tibble with columns glycan_id, node_id, mono, and sub.

• structure_edges() returns a tibble with columns glycan_id, edge_id, from_node, to_node, and linkage.

• structure_floating_parts() returns a tibble with columns glycan_id, part_id, root_node, the list-column nodes, linkage, and the list-column parents.

• structure_floating_substituents() returns a tibble with columns glycan_id, substituent_id, substituent, and the list-column parents.

• structure_from_tibbles() returns a glyrepr_structure vector.

Examples

glycans <- c(o_glycan_core_1(), o_glycan_core_1())
nodes <- structure_nodes(glycans)
edges <- structure_edges(glycans)
structure_from_tibbles(nodes, edges, get_anomer(glycans))

floating <- as_glycan_structure(
  "{6S|1,2}{Neu5Ac(a2-6)|2,3}Gal(b1-3)GalNAc(a1-"
)
floating_parts <- structure_floating_parts(floating)
floating_substituents <- structure_floating_substituents(floating)
structure_from_tibbles(
  structure_nodes(floating),
  structure_edges(floating),
  get_anomer(floating),
  floating_parts,
  floating_substituents
)

glyrepr documentation built on Sept. 22, 2026, 5:09 p.m.