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Parse IUPAC-condensed Structures

parse_iupac_condensed.Rd

This function parses IUPAC-condensed strings into a glycan graph. For more information about IUPAC-condensed notation, see https://doi.org/10.1351/pac199668101919.

Usage

parse_iupac_condensed(x)

Arguments

x

A character vector of IUPAC-condensed strings.

Value

A glycan graph if x is a single character, or a list of glycan graphs if x is a character vector.

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".

See also

parse_iupac_short(), parse_iupac_extended()

Examples

iupac <- "Gal(b1-3)GlcNAc(b1-4)Glc(a1-"
parse_iupac_condensed(iupac)
#> <glycan_structure[1]>
#> [1] Gal(b1-3)GlcNAc(b1-4)Glc(a1-
#> # Unique structures: 1