parse_iupac_condensed: Parse IUPAC-condensed Structures

In glyparse: Parsing Glycan Structure Text Representations

Parse IUPAC-condensed Structures

Description

This function parses IUPAC-condensed strings into a glyrepr::glycan_structure(). For more information about IUPAC-condensed notation, see \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1351/pac199668101919")}.

Usage

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

Arguments

x	A character vector of IUPAC-condensed 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-condensed notation is a compact form of IUPAC-extended notation. It is used by the GlyConnect database. It contains the following information:

• Monosaccharide name, e.g. "Gal", "GlcNAc", "Neu5Ac".

• Substituent, e.g. "9Ac", "4Ac", "3Me", "?S".

• Linkage, e.g. "b1-3", "a1-2", "a1-?".

An example of IUPAC-condensed string is "Gal(b1-3)GlcNAc(b1-4)Glc(a1-".

The reducing-end monosaccharide can be with or without anomer information. For example, the two strings below are all valid:

• "Neu5Ac(a2-"

• "Neu5Ac"

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_short(), parse_iupac_extended()

Examples

iupac <- "Gal(b1-3)GlcNAc(b1-4)Glc(a1-"
parse_iupac_condensed(iupac)

glyparse documentation built on Oct. 30, 2026, 9:10 a.m.