MonosaccharideDB Class Reference

Singleton database of monosaccharides for glycan notation. More...

#include <OpenMS/CHEMISTRY/MonosaccharideDB.h>

Collaboration diagram for MonosaccharideDB:

Classes
struct	Monosaccharide
	Structure representing a monosaccharide. More...

Accessors
std::map< String, Monosaccharide >	monosaccharides_
	Map from primary symbol to monosaccharide data.
std::map< String, String >	synonym_to_symbol_
	Map from synonyms to primary symbol (for lookup)
static MonosaccharideDB *	getInstance ()
bool	hasSymbol (const String &symbol) const
	Check if a symbol (or synonym) is a known monosaccharide.
const Monosaccharide *	getMonosaccharide (const String &symbol) const
	Get monosaccharide by symbol.
const Monosaccharide &	getMonosaccharideOrThrow (const String &symbol) const
	Get monosaccharide by symbol (throws if not found)
std::vector< String >	getAllSymbols () const
	Get all known primary symbols.
Size	getNumberOfMonosaccharides () const
	Get the number of monosaccharides in the database.
	MonosaccharideDB ()
	Private constructor (singleton pattern)
	~MonosaccharideDB ()=default
	Destructor.
	MonosaccharideDB (const MonosaccharideDB &)=delete
	Deleted copy constructor.
	MonosaccharideDB (MonosaccharideDB &&)=delete
	Deleted move constructor.
MonosaccharideDB &	operator= (const MonosaccharideDB &)=delete
	Deleted copy assignment.
MonosaccharideDB &	operator= (MonosaccharideDB &&)=delete
	Deleted move assignment.
void	loadFromJSON_ ()
	Load monosaccharide data from JSON file.

Detailed Description

Singleton database of monosaccharides for glycan notation.

This class provides access to monosaccharide symbols used in ProForma glycan notation. The data is loaded from a JSON file (CHEMISTRY/monosaccharides.json) which contains monosaccharide symbols, their full names, monoisotopic masses, chemical formulas, and synonyms.

The monosaccharide data originates from the HUPO-PSI ProForma specification: https://github.com/HUPO-PSI/ProForma

Common monosaccharides include:

• Hex (Hexose, 162.0528 Da)
• HexNAc (N-Acetylhexosamine, 203.0794 Da)
• Fuc (Fucose, 146.0579 Da)
• NeuAc / Neu5Ac (N-Acetylneuraminic acid / Sialic Acid, 291.0954 Da)
• NeuGc / Neu5Gc (N-Glycolylneuraminic acid, 307.0903 Da)

See also

https://github.com/HUPO-PSI/ProForma for the ProForma specification

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Class Documentation

OpenMS::MonosaccharideDB::Monosaccharide

struct OpenMS::MonosaccharideDB::Monosaccharide

Structure representing a monosaccharide.

Collaboration diagram for MonosaccharideDB::Monosaccharide:

Class Members
String	formula	Chemical formula (e.g., "C6H10O5")
double	mass	Monoisotopic mass in Daltons.
String	name	Full name or description.
String	symbol	Primary symbol (e.g., "Hex", "HexNAc")
vector< String >	synonyms	Alternative symbols/names.

Constructor & Destructor Documentation

MonosaccharideDB() [1/3]

MonosaccharideDB ( )

private

Private constructor (singleton pattern)

~MonosaccharideDB()

~MonosaccharideDB ( )

privatedefault

Destructor.

MonosaccharideDB() [2/3]

MonosaccharideDB ( const MonosaccharideDB &  )

privatedelete

Deleted copy constructor.

MonosaccharideDB() [3/3]

MonosaccharideDB ( MonosaccharideDB &&  )

privatedelete

Deleted move constructor.

Member Function Documentation

getAllSymbols()

std::vector< String > getAllSymbols

(

)

const

Get all known primary symbols.

getInstance()

static MonosaccharideDB * getInstance ( )

static

Returns a pointer to the singleton instance of the monosaccharide database This is thread-safe upon first and subsequent calls (Meyers' singleton)

getMonosaccharide()

const Monosaccharide * getMonosaccharide

(

const String &

symbol

)

const

Get monosaccharide by symbol.

Parameters

symbol

The monosaccharide symbol (e.g., "Hex") or a known synonym

Returns

Pointer to the monosaccharide, or nullptr if not found

getMonosaccharideOrThrow()

const Monosaccharide & getMonosaccharideOrThrow

(

const String &

symbol

)

const

Get monosaccharide by symbol (throws if not found)

Parameters

symbol

The monosaccharide symbol or synonym

Returns

Reference to the monosaccharide

Exceptions

Exception::ElementNotFound

if symbol is not known

getNumberOfMonosaccharides()

Size getNumberOfMonosaccharides

(

)

const

Get the number of monosaccharides in the database.

hasSymbol()

bool hasSymbol

(

const String &

symbol

)

const

Check if a symbol (or synonym) is a known monosaccharide.

loadFromJSON_()

void loadFromJSON_ ( )

private

Load monosaccharide data from JSON file.

operator=() [1/2]

MonosaccharideDB & operator= ( const MonosaccharideDB &  )

privatedelete

Deleted copy assignment.

operator=() [2/2]

MonosaccharideDB & operator= ( MonosaccharideDB &&  )

privatedelete

Deleted move assignment.

Member Data Documentation

monosaccharides_

std::map<String, Monosaccharide> monosaccharides_

private

Map from primary symbol to monosaccharide data.

synonym_to_symbol_

std::map<String, String> synonym_to_symbol_

private

Map from synonyms to primary symbol (for lookup)