parse_kcf: Parse KCF Structures

In glyparse: Parsing Glycan Structure Text Representations

Parse KCF Structures

Description

This function parses KCF strings into a glyrepr::glycan_structure(). KCF is a graph-oriented format used by KEGG GLYCAN.

Usage

parse_kcf(
  x,
  on_failure = "error",
  progress = FALSE,
  validate = lifecycle::deprecated()
)

Arguments

x	A character vector of KCF 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.
validate	Deprecated and ignored. Array records are always validated by glyrepr::structure_from_arrays().

Value

A glyrepr::glycan_structure() object.

Examples

kcf <- paste0(
  "ENTRY       G00066                      Glycan\n",
  "NODE        6\n",
  "            1   Cer        18     0\n",
  "            2   Glc        12     0\n",
  "            3   Gal         6     0\n",
  "            4   GlcNAc     -2     0\n",
  "            5   Gal       -10     0\n",
  "            6   GlcNAc    -18     0\n",
  "EDGE        5\n",
  "            1     2:b1    1:1\n",
  "            2     3:b1    2:4\n",
  "            3     4:b1    3:3\n",
  "            4     5:b1    4:4\n",
  "            5     6:b1    5:3\n",
  "///"
)
parse_kcf(kcf)

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