Parse GlycoCT Structures — parse

This function parses GlycoCT strings into a glyrepr::glycan_structure(). GlycoCT is a format used by databases like GlyTouCan and GlyGen.

Usage

parse_glycoct(x, on_failure = "error", progress = FALSE, validate = TRUE)

Arguments

x: A character vector of GlycoCT 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.
validate: Whether to validate parsed glycan graphs before constructing the result.

Value

A glyrepr::glycan_structure() object.

Details

GlycoCT format consists of:

RES: Contains monosaccharides (lines starting with 'b:') and substituents (lines starting with 's:')
LIN: Contains linkage information between residues
UND: Contains floating substructures or substituents whose attachment to the main glycan is unresolved

Main reducing-end alditol residues retain their alditol status and use an unknown anomer configuration.

For more information about GlycoCT format, see the glycoct.md documentation.

Examples

glycoct <- paste0(
  "RES\n",
  "1b:a-dgal-HEX-1:5\n",
  "2s:n-acetyl\n",
  "3b:b-dgal-HEX-1:5\n",
  "LIN\n",
  "1:1d(2+1)2n\n",
  "2:1o(3+1)3d"
)
parse_glycoct(glycoct)
#> <glycan_structure[1]>
#> [1] Gal(b1-3)GalNAc(a1-
#> # Unique structures: 1