auto_parse: Automatic Structure Parsing

In glyparse: Parsing Glycan Structure Text Representations

Automatic Structure Parsing

Description

Detect the structure string type and use the appropriate parser to parse automatically. Mixed types are supported.

Supported types:

1. GlycoCT

2. IUPAC-condensed

3. IUPAC-extended

4. IUPAC-short

5. GlyCAM IUPAC

6. IUPAC-compact

7. WURCS

8. Linear Code

9. pGlyco

10. StrucGP

11. KCF

12. LINUCS

13. GlycoWorkbench

Usage

auto_parse(x, on_failure = "error", progress = FALSE)

Arguments

x	A character vector of structure strings. NA values are allowed and will be returned as NA structures.
on_failure	How to handle parsing failures. "error" aborts when a structure cannot be parsed. "na" returns NA at invalid positions.
progress	Whether to show a progress bar while parsing.

Value

A glyrepr::glycan_structure() object.

Examples

# Single structure
x <- "Gal(b1-3)GlcNAc(b1-4)Glc(a1-"  # IUPAC-condensed
auto_parse(x)

# Mixed types
x <- c(
  "Gal(b1-3)GlcNAc(b1-4)Glc(a1-",  # IUPAC-condensed
  "Neu5Aca3Gala3(Fuca6)GlcNAcb-"  # IUPAC-short
)
auto_parse(x)

glyparse documentation built on Oct. 30, 2026, 9:10 a.m.