parse_iupac_short: Parse IUPAC-short Structures

In glyparse: Parsing Glycan Structure Text Representations

Parse IUPAC-short Structures

Description

Parse IUPAC-short-style structure characters into a glyrepr::glycan_structure(). For more information about IUPAC-short format, see \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1351/pac199668101919")}.

Usage

parse_iupac_short(x, on_failure = "error", progress = FALSE)

Arguments

x	A character vector of IUPAC-short strings. NA values are allowed and will be returned as NA structures.
on_failure	How to handle parsing failures. "error" aborts when a structure cannot be parsed. "na" returns NA at invalid positions.
progress	Whether to show a progress bar while parsing.

Details

The IUPAC-short notation is a compact form of IUPAC-condensed notation. It is rarely used in database, but appears a lot in literature for its conciseness. Compared with IUPAC-condensed notation, IUPAC-short notation ignore the anomer positions, assuming they are known for common monosaccharides. For example, "Neu5Aca3Gala-" assumes the anomer of Neu5Ac is C2 (a2-3 linked). Also, the parentheses around linkages are omitted, and parentheses are used to indicate branching, e.g. "Neu5Aca3Gala3(Fuca3)GlcNAcb-".

In the first case, the anomer is "a2". In the second case, the anomer is "?2".

Value

A glyrepr::glycan_structure() object.

See Also

parse_iupac_condensed(), parse_iupac_extended()

Examples

iupac <- "Neu5Aca3Gala3(Fuca6)GlcNAcb-"
parse_iupac_short(iupac)

glyparse documentation built on Oct. 31, 2026, 9:06 a.m.