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Parse GlyCAM IUPAC Structures

Source: R/parse-glycam-iupac.R
parse_glycam_iupac.Rd

Parse GlyCAM IUPAC-style structure strings into a glyrepr::glycan_structure().

Usage

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

Arguments

x

A character vector of GlyCAM IUPAC 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.

Value

A glyrepr::glycan_structure() object.

Details

GlyCAM IUPAC is similar to IUPAC-condensed notation, but monosaccharides include configuration and ring markers such as "DGlcp" and "LFucp", terminal reducing-end residues end in "-OH", and residue modifiers are written in brackets, such as "DGalp[6S]b1-4".

The parser normalizes GlyCAM IUPAC into IUPAC-condensed notation, then uses the IUPAC-condensed parser to construct the glycan structure. Explicit reducing-end moieties, such as "-OH" or "-OME", are normalized to the regular reducing-end IUPAC-condensed form because glyrepr does not represent the terminal moiety separately.

See also

parse_iupac_condensed()

Examples

glycam <- "DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-OH"
parse_glycam_iupac(glycam)
#> <glycan_structure[1]>
#> [1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-
#> # Unique structures: 1