Parse different glycan structure text nomenclature into
glyrepr::glycan_structure.
Currently, the following formats are supported: IUPAC-extended, IUPAC-condensed, IUPAC-short, WURCS, GlycoCT, StrucGP-style, pGlyco-style.
You can install the latest release of glyparse from CRAN with:
install.packages("glyparse")Or install the development version from GitHub:
remotes::install_github("glycoverse/glyparse")glycoverseWhile glyrepr natively supports parsing IUPAC-condensed
format through as_glycan_structure(), the glycan community
has developed numerous other nomenclature formats that remain widely
adopted in different contexts. glyparse serves as a
comprehensive extension to glyrepr, providing robust
parsing capabilities for these diverse formats. The package can be
utilized directly by researchers to parse glycan structure text strings,
or integrated with other packages such as glyread to
seamlessly handle structure parsing when processing results from glycan
and glycopeptide analysis software.
library(glyparse)# Parse a StrucGP-style structure string
parse_strucgp_struc("A2B2C1D1E2F1fedD1E2edcbB5ba")
#> <glycan_structure[1]>
#> [1] Hex(??-?)HexNAc(??-?)Hex(??-?)[HexNAc(??-?)Hex(??-?)]Hex(??-?)HexNAc(??-?)[dHex(??-?)]HexNAc(??-
#> # Unique structures: 1# Parse a pGlyco-style structure string
parse_pglyco_struc("(N(F)(N(H(H(N))(H(N(H))))))")
#> <glycan_structure[1]>
#> [1] Hex(??-?)HexNAc(??-?)Hex(??-?)[HexNAc(??-?)Hex(??-?)]Hex(??-?)HexNAc(??-?)[dHex(??-?)]HexNAc(??-
#> # Unique structures: 1# Parse a condensed IUPAC structure string
parse_iupac_condensed("Gal(b1-3)GlcNAc(b1-4)Glc(a1-")
#> <glycan_structure[1]>
#> [1] Gal(b1-3)GlcNAc(b1-4)Glc(a1-
#> # Unique structures: 1# Parse a WURCS structure string
parse_wurcs("WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1")
#> <glycan_structure[1]>
#> [1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> # Unique structures: 1