Fill anomer positions — fill_anomer

Add anomer positions to glycan structures with missing anomer information based on biological knowledge. For example, "Gal(??-?)GalNAc(??-" will be converted to "Gal(?1-?)GalNAc(?1-". For anomer positions that are already specified in the input structures, this function will not modify them.

Usage

fill_anomer_pos(strucs)

Arguments

strucs: A glyrepr::glycan_structure() vector of "concrete" monosaccharides.

Value

A glyrepr::glycan_structure() vector with anomer positions added where missing.

Details

This function is intended to be used by struc_to_glytoucan() to ensure that glycan structures have complete anomer information before attempting to inquire the GlyTouCan database.

For these monosaccharides, the anomer position is "2": "Neu5Ac", "Neu5Gc", "Neu", "Kdn", "Pse", "Leg", "Aci", "4eLeg", "Kdo", "Dha", "Fru", "Tag", "Sor", and "Psi". All other monosaccharides are assumed to have anomer positions on "1".

Examples

library(glyrepr)
glycans <- as_glycan_structure(c(
  "Gal(??-?)GalNAc(??-",
  "Neu5Ac(??-?)Gal(??-?)GalNAc(??-"
))
fill_anomer_pos(glycans)
#> <glycan_structure[2]>
#> [1] Gal(?1-?)GalNAc(?1-
#> [2] Neu5Ac(?2-?)Gal(?1-?)GalNAc(?1-
#> # Unique structures: 2