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Convert Glycan Structure to IUPAC-like Sequence

structure_to_iupac.Rd

Convert a glycan structure to a sequence representation in the form of mono(linkage)mono, with branches represented by square brackets []. The backbone is chosen as the longest path, and for branches, linkages are ordered lexicographically with smaller linkages on the backbone.

Usage

structure_to_iupac(glycan)

Arguments

glycan

A glyrepr_structure vector.

Value

A character vector representing the IUPAC sequences.

Sequence Format

The sequence follows the format mono(linkage)mono, where:

  • mono: monosaccharide name with optional substituents (e.g., Glc, GlcNAc, Glc3Me)

  • linkage: glycosidic linkage (e.g., b1-4, a1-3)

  • Branches are enclosed in square brackets []

  • Substituents are appended directly to monosaccharide names (e.g., Glc3Me for Glc with 3Me substituent)

Backbone Selection

The backbone is selected as the longest path in the tree. For branches, the same rule applies recursively.

Linkage Comparison

Linkages are compared lexicographically:

  1. First by anomeric configuration: ? > b > a

  2. Then by first position: ? > numbers (numerically)

  3. Finally by second position: ? > numbers (numerically)

Smaller linkages are placed on the backbone, larger ones in branches.

Examples

# Simple linear structure
structure_to_iupac(o_glycan_core_1())
#> [1] "Gal(b1-3)GalNAc(a1-"

# Branched structure  
structure_to_iupac(n_glycan_core())
#> [1] "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(?1-"

# Structure with substituents
graph <- igraph::make_graph(~ 1-+2)
igraph::V(graph)$mono <- c("Glc", "GlcNAc")
igraph::V(graph)$sub <- c("3Me", "6Ac")
igraph::E(graph)$linkage <- "b1-4"
graph$anomer <- "a1"
graph$alditol <- FALSE
glycan <- glycan_structure(graph)
structure_to_iupac(glycan)  # Returns "GlcNAc6Ac(b1-4)Glc3Me(a1-"
#> [1] "GlcNAc6Ac(b1-4)Glc3Me(a1-"

# Vectorized structures
structs <- glycan_structure(o_glycan_core_1(), n_glycan_core())
structure_to_iupac(structs)
#> [1] "Gal(b1-3)GalNAc(a1-"                                
#> [2] "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(?1-"