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Parse IUPAC-extended Structures

Source: R/parse-iupac-extended.R
parse_iupac_extended.Rd

Parse IUPAC-extended-style structure characters into a glyrepr::glycan_structure(). For more information about IUPAC-extended format, see doi:10.1351/pac199668101919 .

Usage

parse_iupac_extended(x)

Arguments

x

A character vector of IUPAC-extended strings. NA values are allowed and will be returned as NA structures.

Value

A glyrepr::glycan_structure() object.

Details

The function accepts both a Unicode format (using the Greek letters alpha/beta and the arrow symbol ->) and a plain-text format (using the strings "alpha", "beta", and "->"). For example, both "\u03b2-D-Galp-(1\u21923)-\u03b1-D-GalpNAc-(1\u2192" and "beta-D-Galp-(1->3)-alpha-D-GalpNAc-(1->" are valid inputs.

See also

parse_iupac_condensed(), parse_iupac_short()

Examples

iupac <- "\u03b2-D-Galp-(1\u21923)-\u03b1-D-GalpNAc-(1\u2192"
parse_iupac_extended(iupac)
#> <glycan_structure[1]>
#> [1] Gal(b1-3)GalNAc(a1-
#> # Unique structures: 1
parse_iupac_extended("beta-D-Galp-(1->3)-alpha-D-GalpNAc-(1->")
#> <glycan_structure[1]>
#> [1] Gal(b1-3)GalNAc(a1-
#> # Unique structures: 1