---
title: "Getting Started with glyparse"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Getting Started with glyparse}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  error = FALSE
)
```

## Parsing glycan text

Glycan structures appear in several text formats. If you work with data from
different sources, you may find that each database, software tool, or research
group uses its own conventions for representing structures as text.

`glyparse` provides a parser for each supported format and converts the
results to a common `glyrepr::glycan_structure` representation.

This gives you a consistent starting point for structure comparison and
downstream analysis, without rewriting every input by hand.

All public parsers return `glyrepr::glycan_structure` objects. If you are
unfamiliar with `glyrepr`, see the
[`glyrepr` vignette](https://glycoverse.github.io/glyrepr/articles/glyrepr.html).

```{r setup}
library(glyparse)
```

## Supported formats

Here is a quick overview of the formats supported by the package:

| Format | Parser | Common sources |
|--------|---------|-------------------|
| **IUPAC-condensed** | `parse_iupac_condensed()` | Literature, UniCarbKB |
| **IUPAC-short** | `parse_iupac_short()` | Literature, UniCarbKB |
| **IUPAC-extended** | `parse_iupac_extended()` | Literature, UniCarbKB |
| **IUPAC-compact** | `parse_iupac_compact()` | Compact database and literature notation |
| **GlyCAM IUPAC** | `parse_glycam_iupac()` | GlyCAM workflows |
| **GlycoCT** | `parse_glycoct()` | Literature, GlycomeDB |
| **WURCS** | `parse_wurcs()` | Literature, GlyTouCan |
| **Linear Code** | `parse_linear_code()` | Literature |
| **LINUCS** | `parse_linucs()` | Glycan structure software |
| **KCF** | `parse_kcf()` | KEGG GLYCAN |
| **GlycoWorkbench** | `parse_gwb()` | GlycoWorkbench and GWS files |
| **pGlyco** | `parse_pglyco_struc()` | pGlyco software results |
| **StrucGP** | `parse_strucgp_struc()` | StrucGP software results |

The package includes an automatic parser and 13 format-specific parsers. Each
parser accepts a character vector of structure strings and returns a
`glyrepr::glycan_structure` object.

## Part 1: Automatic parsing

When the input format is not known in advance, use `auto_parse()`. It detects
the format one element at a time, so a vector can contain mixed formats.

```{r}
x <- c(
  "Gal(b1-3)GalNAc(b1-",
  "(N(F)(N(H(H(N))(H(N(H))))))",
  "WURCS=2.0/3,3,2/[a2122h-1b_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3/a4-b1_b3-c1"
)
auto_parse(x)
```

## Part 2: IUPAC notation

### IUPAC-condensed

This format is widely used in scientific literature and databases like UniCarbKB.

For more detail about this notation, see the
[`glyrepr` IUPAC vignette](https://glycoverse.github.io/glyrepr/articles/iupac.html).

```{r}
# Single structure
iupac_condensed <- "Neu5Ac(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-4)Gal(b1-4)Glc(a1-"
parse_iupac_condensed(iupac_condensed)
```

```{r}
# Multiple structures at once
glycans <- c(
  "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-",  # N-glycan core
  "Gal(b1-3)GalNAc(b1-",                                  # O-glycan core 1
  "Neu5Ac(a2-3)Gal(b1-3)[GlcNAc(b1-6)]GalNAc(b1-"         # O-glycan core 2
)
parse_iupac_condensed(glycans)
```

### IUPAC-short

This compact format is popular in research papers because it saves space:

```{r}
# The same structures in short format
iupac_short <- c(
  "Mana3(Mana6)Manb4GlcNAcb4GlcNAcb-",
  "Galb3GalNAcb-", 
  "Neu5Aca3Galb3(GlcNAcb6)GalNAcb-"
)
parse_iupac_short(iupac_short)
```

The parser infers common linkage positions when they are omitted.

### IUPAC-extended

This verbose format includes full chemical names and stereochemistry:

```{r}
iupac_extended <- paste0(
  "alpha-D-Galp-(1->3)-",
  "beta-D-Galp-(1->"
)
parse_iupac_extended(iupac_extended)
```

### IUPAC-compact

IUPAC-compact notation places the linkage immediately after each residue and
uses parentheses for branches.

```{r}
iupac_compact <- "Mana1-3(Mana1-6)Manb1-4GlcNAcb"
parse_iupac_compact(iupac_compact)
```

### GlyCAM IUPAC

GlyCAM IUPAC strings include configuration and ring markers such as `DManp`
and use a terminal `-OH` marker for the reducing end. The parser normalizes
these strings before parsing them.

```{r}
glycam <- "DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-OH"
parse_glycam_iupac(glycam)
```

## Part 3: Database and exchange formats

### GlycoCT

GlycoCT uses separate `RES` and `LIN` sections. It is verbose, but records
residue and linkage information explicitly.

```{r}
glycoct <- paste0(
  "RES\n",
  "1b:b-dglc-HEX-1:5\n",
  "2b:b-dgal-HEX-1:5\n", 
  "3b:a-dgal-HEX-1:5\n",
  "LIN\n",
  "1:1o(4+1)2d\n",
  "2:2o(3+1)3d"
)
parse_glycoct(glycoct)
```

### WURCS

WURCS (Web3 Unique Representation of Carbohydrate Structures) is a compact
standardised exchange format used by resources such as GlyTouCan.

```{r}
wurcs <- paste0(
  "WURCS=2.0/3,3,2/",
  "[a2122h-1b_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/",
  "1-2-3/a4-b1_b3-c1"
)
parse_wurcs(wurcs)
```

### KCF

KCF represents a glycan as a graph with `NODE` and `EDGE` sections. It is used
by KEGG GLYCAN.

```{r}
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)
```

### Linear Code

Linear Code is a compact notation used in literature and glycan software:
```{r}
linear_code <- "Ma3(Ma6)Mb4GNb4GNb"
parse_linear_code(linear_code)
```

### LINUCS

LINUCS expresses each residue as a token followed by a braced child list. A
linkage such as `[(4+1)]` records the parent and child positions.

```{r}
linucs <- "[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}"
parse_linucs(linucs)
```

## Part 4: Software-specific formats

### GlycoWorkbench

GlycoWorkbench strings describe the structure from the reducing end and may
include mass options after `$`. Those options are ignored because they are
not part of the glycan graph.

```{r}
gwb <- paste0(
  "freeEnd--1b1D-GlcNAc,p(--6a1L-Fuc,p)",
  "--4b1D-Gal,p--3a2D-NeuAc,p$MONO,Und,0,0,freeEnd"
)
parse_gwb(gwb)
```

### pGlyco

If you work with glycoproteomics, you may encounter pGlyco's parenthetical
notation:

```{r}
pglyco <- "(N(F)(N(H(H(N))(H(N(H))))))"
parse_pglyco_struc(pglyco)
```

In this notation:

- N = HexNAc
- F = Fuc
- H = Hex (Man or Gal)

### StrucGP

StrucGP uses a letter-based encoding system:

```{r}
strucgp <- "A2B2C1D1E2F1fedD1E2edcbB5ba"
parse_strucgp_struc(strucgp)
```

## Handling parsing failures

By default, a malformed structure stops the call with an informative error.
When processing a larger collection, `on_failure = "na"` preserves the input
positions and returns `NA` for records that cannot be parsed.

```{r}
parse_iupac_compact(
  c(valid = "Galb1-3GalNAca", invalid = "not a glycan"),
  on_failure = "na"
)
```