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Parse LINUCS Structures

Source: R/parse-linucs.R
parse_linucs.Rd

Parse LINUCS strings into a glyrepr::glycan_structure(). LINUCS is a tree-oriented glycan format that writes each residue as a linkage token, a residue token, and a braced child list, for example "[][Hexp]{[(4+1)][Hexp]{}}".

Usage

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

Arguments

x

A character vector of LINUCS 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

LINUCS linkages are written as "(parent+child)", where parent is the linkage position on the parent residue and child is the anomeric linkage position on the child residue. Residue labels are normalized to the monosaccharide and substituent vocabulary used by glyrepr::glyrepr. A -ol suffix on the root residue is retained as alditol status.

Examples

linucs <- "[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}"
parse_linucs(linucs)
#> <glycan_structure[1]>
#> [1] Gal(b1-4)Glc(b1-
#> # Unique structures: 1