Construct a Glycan Structure Vector from Trusted Data

Assemble a glycan structure vector from IUPAC-condensed values and a graph lookup table without graph validation, canonicalization, IUPAC generation, vector-level compatibility checks, or graph deduplication.

Usage

new_glycan_structure(iupac = character(), graphs = list())

Arguments

iupac: A character vector of canonical IUPAC-condensed strings. Missing values are allowed, and names are preserved exactly.
graphs: A named list of valid, canonical, mutually compatible igraph glycan graphs keyed by IUPAC-condensed strings.

Value

A glyrepr_structure vector.

Details

graphs must be a named list containing one graph for every distinct, non-missing value in iupac. Additional named graphs are allowed so that vctrs prototypes can retain their graph lookup tables. Graph names must be unique and non-missing. This function checks these inexpensive representation invariants but trusts that each graph matches its key.

Low-level API warning

These functions are low-level, developer-facing APIs. Calling them directly is usually not a good idea unless you understand and can guarantee all glycan graph and glyrepr_structure invariants. Prefer as_glycan_structure() for ordinary construction. Incorrect use of these functions can create invalid structure vectors that fail in later operations.

Name-preserving manual construction

The five low-level functions can reproduce strict graph-based construction while preserving the names of the input graph list:

input_names <- names(graphs)
graphs <- unname(graphs)

graphs <- purrr::map(graphs, validate_glycan_graph)
graphs <- purrr::map(graphs, canonicalize_glycan_graph)
validate_glycan_graph_vector(graphs)

iupacs <- purrr::map_chr(graphs, graph_to_iupac)
names(iupacs) <- input_names

unique <- !duplicated(unname(iupacs))
unique_graphs <- graphs[unique]
names(unique_graphs) <- unname(iupacs[unique])

new_glycan_structure(iupacs, unique_graphs)

Unlike as_glycan_structure(graphs, on_failure = "na"), this strict pipeline stops at the first invalid graph.