Singleton that stores elements and isotopes. More...

#include <OpenMS/CHEMISTRY/ElementDB.h>

Collaboration diagram for ElementDB:

Predicates
std::unordered_map< std::string, const Element * >	names_

std::unordered_map< std::string, const Element * >	symbols_

std::unordered_map< unsigned int, const Element * >	atomic_numbers_

bool	hasElement (const std::string &name) const
	returns true if the db contains an element with the given name More...

bool	hasElement (unsigned int atomic_number) const
	returns true if the db contains an element with the given atomic_number More...

IsotopeDistribution	parseIsotopeDistribution_ (const std::map< unsigned int, double > &abundance, const std::map< unsigned int, double > &mass)

double	calculateAvgWeight_ (const std::map< unsigned int, double > &abundance, const std::map< unsigned int, double > &mass)

double	calculateMonoWeight_ (const std::map< unsigned int, double > &abundance, const std::map< unsigned int, double > &mass)

void	storeElements_ ()
	constructs element objects More...

void	buildElement_ (const std::string &name, const std::string &symbol, const unsigned int an, const std::map< unsigned int, double > &abundance, const std::map< unsigned int, double > &mass)
	build element objects from given abundances, masses, name, symbol, and atomic number More...

void	addElementToMaps_ (const std::string &name, const std::string &symbol, const unsigned int an, std::unique_ptr< const Element > e)
	add element objects to documentation maps More...

void	storeIsotopes_ (const std::string &name, const std::string &symbol, const unsigned int an, const std::map< unsigned int, double > &Z_to_mass, const IsotopeDistribution &isotopes)
	constructs isotope objects More...

void	clear_ ()

	ElementDB ()

	~ElementDB ()

	ElementDB (const ElementDB &db)=delete

	ElementDB (const ElementDB &&db)=delete

ElementDB &	operator= (const ElementDB &db)=delete

Accessors
static ElementDB *	getInstance ()

const std::unordered_map< std::string, const Element * > &	getNames () const
	returns a hashmap that contains names mapped to pointers to the elements More...

const std::unordered_map< std::string, const Element * > &	getSymbols () const
	returns a hashmap that contains symbols mapped to pointers to the elements More...

const std::unordered_map< unsigned int, const Element * > &	getAtomicNumbers () const
	returns a hashmap that contains atomic numbers mapped to pointers of the elements More...

const Element *	getElement (const std::string &name) const

const Element *	getElement (unsigned int atomic_number) const
	returns a pointer to the element of atomic number; if no element is found 0 is returned More...

void	addElement (const std::string &name, const std::string &symbol, const unsigned int an, const std::map< unsigned int, double > &abundance, const std::map< unsigned int, double > &mass, bool replace_existing)

Detailed Description

Singleton that stores elements and isotopes.

The elements weights (in the default file) are taken from "Isotopic Compositions of the Elements 1997", Pure Appl. Chem., 70(1), 217-235, 1998. (http://www.iupac.org/reports/1998/7001rosman/)

The isotope distributions (in the default file) are taken from "Atomic weights of the elements. Review 2000" (IUPAC Technical Report) Pure Appl. Chem., 2003, Vol. 75, No. 6, pp. 683-799 doi:10.1351/pac200375060683

Specific isotopes of elements can be accessed by writing the atomic number of the isotope in brackets followed by the element name, e.g. "(2)H" for deuterium.

Improvement:

include exact mass values for the isotopes (done) and update IsotopeDistribution (Andreas)

add exact isotope distribution based on exact isotope values (Andreas)

Constructor & Destructor Documentation

◆ ElementDB() [1/3]

ElementDB ( )

private

◆ ~ElementDB()

~ElementDB ( )

private

◆ ElementDB() [2/3]

ElementDB ( const ElementDB & db )

privatedelete

◆ ElementDB() [3/3]

ElementDB ( const ElementDB && db )

privatedelete

Member Function Documentation

◆ addElement()

void addElement	(	const std::string &	name,
		const std::string &	symbol,
		const unsigned int	an,
		const std::map< unsigned int, double > &	abundance,
		const std::map< unsigned int, double > &	mass,
		bool	replace_existing
	)

Adds or replaces a new element to the database

Adds a new element (or replaces an existing one if replace_existing is true).

Parameters

name	Common name of the element
symbol	Element symbol (one or two letter)
an	Atomic number (number of protons)
abundance	List of abundances for each isotope (e.g. {{12u, 0.9893}, {13u, 0.0107}} for Carbon)
mass	List of masses for each isotope (e.g. {{12u, 12.0}, {13u, 13.003355}} for Carbon)
replace_existing	If the element must be replaced (i.e. is not new), either allow that (=true), or throw an exception (=false).

Exceptions

Exception::IllegalArgument if element already exists in DB, but replace_existing is false

Note: Do not use this function inside parallel code as it modifies a singleton that is shared between threads.

◆ addElementToMaps_()

void addElementToMaps_	(	const std::string &	name,
		const std::string &	symbol,
		const unsigned int	an,
		std::unique_ptr< const Element >	e
	)

protected

add element objects to documentation maps

◆ buildElement_()

void buildElement_	(	const std::string &	name,
		const std::string &	symbol,
		const unsigned int	an,
		const std::map< unsigned int, double > &	abundance,
		const std::map< unsigned int, double > &	mass
	)

protected

build element objects from given abundances, masses, name, symbol, and atomic number

◆ calculateAvgWeight_()

double calculateAvgWeight_	(	const std::map< unsigned int, double > &	abundance,
		const std::map< unsigned int, double > &	mass
	)

protected

calculates the average weight based on isotope abundance and mass

◆ calculateMonoWeight_()

double calculateMonoWeight_	(	const std::map< unsigned int, double > &	abundance,
		const std::map< unsigned int, double > &	mass
	)

protected

_ calculates the mono weight based on the most abundant isotope

◆ clear_()

void clear_ ( )

protected

_ resets all containers

◆ getAtomicNumbers()

const std::unordered_map<unsigned int, const Element*>& getAtomicNumbers ( ) const

returns a hashmap that contains atomic numbers mapped to pointers of the elements

◆ getElement() [1/2]

const Element* getElement ( const std::string & name ) const

returns a pointer to the element with name or symbol given in parameter name; if no element exists with that name or symbol 0 is returned

Parameters

name	name or symbol of the element

◆ getElement() [2/2]

const Element* getElement ( unsigned int atomic_number ) const

returns a pointer to the element of atomic number; if no element is found 0 is returned

◆ getInstance()

static ElementDB* getInstance ( )

static

returns a pointer to the singleton instance of the element db This is thread safe upon first and subsequent calls.

◆ getNames()

const std::unordered_map<std::string, const Element*>& getNames ( ) const

returns a hashmap that contains names mapped to pointers to the elements

◆ getSymbols()

const std::unordered_map<std::string, const Element*>& getSymbols ( ) const

returns a hashmap that contains symbols mapped to pointers to the elements

◆ hasElement() [1/2]

bool hasElement ( const std::string & name ) const

returns true if the db contains an element with the given name

◆ hasElement() [2/2]

bool hasElement ( unsigned int atomic_number ) const

returns true if the db contains an element with the given atomic_number

◆ operator=()

ElementDB& operator= ( const ElementDB & db )

privatedelete

◆ parseIsotopeDistribution_()

IsotopeDistribution parseIsotopeDistribution_	(	const std::map< unsigned int, double > &	abundance,
		const std::map< unsigned int, double > &	mass
	)

protected

parses a isotope distribution of abundances and masses

◆ storeElements_()

void storeElements_ ( )

protected

constructs element objects

◆ storeIsotopes_()

void storeIsotopes_	(	const std::string &	name,
		const std::string &	symbol,
		const unsigned int	an,
		const std::map< unsigned int, double > &	Z_to_mass,
		const IsotopeDistribution &	isotopes
	)

protected

constructs isotope objects

Member Data Documentation

◆ atomic_numbers_

std::unordered_map<unsigned int, const Element*> atomic_numbers_

protected

◆ names_

std::unordered_map<std::string, const Element*> names_

protected

◆ symbols_

std::unordered_map<std::string, const Element*> symbols_

protected

Predicates

Accessors

Detailed Description

Constructor & Destructor Documentation

◆ ElementDB() [1/3]

◆ ~ElementDB()

◆ ElementDB() [2/3]

◆ ElementDB() [3/3]

Member Function Documentation

◆ addElement()

◆ addElementToMaps_()

◆ buildElement_()

◆ calculateAvgWeight_()

◆ calculateMonoWeight_()

◆ clear_()

◆ getAtomicNumbers()

◆ getElement() [1/2]

◆ getElement() [2/2]

◆ getInstance()

◆ getNames()

◆ getSymbols()

◆ hasElement() [1/2]

◆ hasElement() [2/2]

◆ operator=()

◆ parseIsotopeDistribution_()

◆ storeElements_()

◆ storeIsotopes_()

Member Data Documentation

◆ atomic_numbers_

◆ names_

◆ symbols_