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.
Installation
You can install the development version of glyparse from GitHub with:
# install.packages("pak")
pak::pak("glycoverse/glyparse")Documentation
- 📚 Reference: Here
Role in glycoverse
While 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.
Example
# 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")
#> <glycan_structure[1]>
#> [1] Gal(b1-3)GlcNAc(b1-4)Glc(?1-
#> # 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