Parsing Glycan Structure Text Representations

Provides functions to parse glycan structure text representations into 'glyrepr' glycan structures. Currently, it supports StrucGP-style, pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, IUPAC-compact, WURCS, LINUCS, Linear Code, GlycoCT, KCF, and GlycoWorkbench formats. It also provides an automatic parser to detect the format and parse the structure string.

glyparse

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 latest release of glyparse from CRAN:

pak::pkg_install("glyparse")

Or from r-universe:

pak::repo_add(glycoverse = "https://glycoverse.r-universe.dev")
pak::pkg_install("glyparse")

Or install the latest GitHub release:

pak::pkg_install("glycoverse/glyparse@*release")

Or install the development version from GitHub:

pak::pkg_install("glycoverse/glyparse")

Documentation

• 🚀 Get started: Here
• 📚 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

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