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Parse KCF Structures

Source: R/parse-kcf.R
parse_kcf.Rd

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)

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.

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)
#> <glycan_structure[1]>
#> [1] GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)Glc(b1-
#> # Unique structures: 1