| Title: | Parsing Glycan Structure Text Representations |
| Version: | 0.5.3 |
| Description: | 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, WURCS, Linear Code, and GlycoCT format. It also provides an automatic parser to detect the format and parse the structure string. |
| License: | MIT + file LICENSE |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.3 |
| URL: | https://glycoverse.github.io/glyparse/, https://github.com/glycoverse/glyparse |
| Imports: | checkmate, cli, dplyr, glyrepr (≥ 0.7.0), igraph, purrr, rlang, rstackdeque, stringr |
| Depends: | R (≥ 4.1) |
| VignetteBuilder: | knitr |
| BugReports: | https://github.com/glycoverse/glyparse/issues |
| NeedsCompilation: | no |
| Packaged: | 2025-11-01 07:09:21 UTC; fubin |
| Author: | Bin Fu  [aut, cre,
cph] |
| Maintainer: | Bin Fu <23110220018@m.fudan.edu.cn> |
| Repository: | CRAN |
| Date/Publication: | 2025-11-04 19:30:02 UTC |
Automatic Structure Parsing
Description
Detect the structure string type and use the appropriate parser to parse automatically. Mixed types are supported.
Supported types:
GlycoCT
IUPAC-condensed
IUPAC-extended
IUPAC-short
WURCS
Linear Code
pGlyco
StrucGP
Usage
auto_parse(x)
Arguments
x |
A character vector of structure strings. |
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)
Parse GlycoCT Structures
Description
This function parses GlycoCT strings into a glyrepr::glycan_structure().
GlycoCT is a format used by databases like GlyTouCan and GlyGen.
Usage
parse_glycoct(x)
Arguments
x |
A character vector of GlycoCT strings. |
Details
GlycoCT format consists of two parts:
RES: Contains monosaccharides (lines starting with 'b:') and substituents (lines starting with 's:')
LIN: Contains linkage information between residues
For more information about GlycoCT format, see the glycoct.md documentation.
Value
A glyrepr::glycan_structure() object.
Examples
glycoct <- paste0(
"RES\n",
"1b:a-dgal-HEX-1:5\n",
"2s:n-acetyl\n",
"3b:b-dgal-HEX-1:5\n",
"LIN\n",
"1:1d(2+1)2n\n",
"2:1o(3+1)3d"
)
parse_glycoct(glycoct)
Parse IUPAC-condensed Structures
Description
This function parses IUPAC-condensed strings into a glyrepr::glycan_structure().
For more information about IUPAC-condensed notation, see doi:10.1351/pac199668101919.
Usage
parse_iupac_condensed(x)
Arguments
x |
A character vector of IUPAC-condensed strings. |
Details
The IUPAC-condensed notation is a compact form of IUPAC-extended notation. It is used by the GlyConnect database. It contains the following information:
Monosaccharide name, e.g. "Gal", "GlcNAc", "Neu5Ac".
Substituent, e.g. "9Ac", "4Ac", "3Me", "?S".
Linkage, e.g. "b1-3", "a1-2", "a1-?".
An example of IUPAC-condensed string is "Gal(b1-3)GlcNAc(b1-4)Glc(a1-".
The reducing-end monosaccharide can be with or without anomer information. For example, the two strings below are all valid:
"Neu5Ac(a2-"
"Neu5Ac"
In the first case, the anomer is "a2". In the second case, the anomer is "?2".
Value
A glyrepr::glycan_structure() object.
See Also
parse_iupac_short(), parse_iupac_extended()
Examples
iupac <- "Gal(b1-3)GlcNAc(b1-4)Glc(a1-"
parse_iupac_condensed(iupac)
Parse IUPAC-extended Structures
Description
Parse IUPAC-extended-style structure characters into a glyrepr::glycan_structure().
For more information about IUPAC-extended format, see doi:10.1351/pac199668101919.
Usage
parse_iupac_extended(x)
Arguments
x |
A character vector of IUPAC-extended strings. |
Value
A glyrepr::glycan_structure() object.
See Also
parse_iupac_condensed(), parse_iupac_short()
Examples
iupac <- "\u03b2-D-Galp-(1\u21923)-\u03b1-D-GalpNAc-(1\u2192"
parse_iupac_extended(iupac)
Parse IUPAC-short Structures
Description
Parse IUPAC-short-style structure characters into a glyrepr::glycan_structure().
For more information about IUPAC-short format, see doi:10.1351/pac199668101919.
Usage
parse_iupac_short(x)
Arguments
x |
A character vector of IUPAC-short strings. |
Details
The IUPAC-short notation is a compact form of IUPAC-condensed notation. It is rarely used in database, but appears a lot in literature for its conciseness. Compared with IUPAC-condensed notation, IUPAC-short notation ignore the anomer positions, assuming they are known for common monosaccharides. For example, "Neu5Aca3Gala-" assumes the anomer of Neu5Ac is C2 (a2-3 linked). Also, the parentheses around linkages are omitted, and parentheses are used to indicate branching, e.g. "Neu5Aca3Gala3(Fuca3)GlcNAcb-".
In the first case, the anomer is "a2". In the second case, the anomer is "?2".
Value
A glyrepr::glycan_structure() object.
See Also
parse_iupac_condensed(), parse_iupac_extended()
Examples
iupac <- "Neu5Aca3Gala3(Fuca6)GlcNAcb-"
parse_iupac_short(iupac)
Parse Linear Code Structures
Description
Parse Linear Code structures into a glyrepr::glycan_structure().
To know more about Linear Code, see this article.
Usage
parse_linear_code(x)
Arguments
x |
A character vector of Linear Code strings. |
Value
A glyrepr::glycan_structure() object.
Examples
linear_code <- "Ma3(Ma6)Mb4GNb4GNb"
parse_linear_code(linear_code)
Parse pGlyco Structures
Description
Parse pGlyco-style structure characters into a glyrepr::glycan_structure().
See example below for the structure format.
Usage
parse_pglyco_struc(x)
Arguments
x |
A character vector of pGlyco-style structure strings. |
Value
A glyrepr::glycan_structure() object.
Examples
glycan <- parse_pglyco_struc("(N(F)(N(H(H(N))(H(N(H))))))")
print(glycan, verbose = TRUE)
Parse StrucGP Structures
Description
Parse StrucGP-style structure characters into a glyrepr::glycan_structure().
See example below for the structure format.
Usage
parse_strucgp_struc(x)
Arguments
x |
A character vector of StrucGP-style structure strings. |
Value
A glyrepr::glycan_structure() object.
Examples
glycan <- parse_strucgp_struc("A2B2C1D1E2F1fedD1E2edcbB5ba")
print(glycan, verbose = TRUE)
Parse WURCS Structures
Description
This function parses WURCS strings into a glyrepr::glycan_structure().
Currently, only WURCS 2.0 is supported.
For more information about WURCS, see WURCS.
Usage
parse_wurcs(x)
Arguments
x |
A character vector of WURCS strings. |
Value
A glyrepr::glycan_structure() object.
Examples
wurcs <- paste0(
"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"
)
parse_wurcs(wurcs)