ElementDB Class Reference

Singleton that stores elements. More...

#include <OpenMS/CHEMISTRY/ElementDB.h>

Collaboration diagram for ElementDB:

Predicates
std::map< std::string, const Element * >	names_
std::map< std::string, const Element * >	symbols_
std::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 > &Z_to_mass)
void	storeElements_ ()
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)
void	addElementToMaps_ (const std::string &name, const std::string &symbol, const unsigned int an, const Element *e)
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)
void	clear_ ()
	ElementDB ()
	~ElementDB ()
	ElementDB (const ElementDB &db)=delete
	ElementDB (const ElementDB &&db)=delete
ElementDB &	operator= (const ElementDB &db)=delete

Accessors
static const ElementDB *	getInstance ()
const std::map< std::string, const Element * > &	getNames () const
	returns a hashmap that contains names mapped to pointers to the elements More...
const std::map< std::string, const Element * > &	getSymbols () const
	returns a hashmap that contains symbols mapped to pointers to the elements More...
const std::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...

Detailed Description

Singleton that stores elements.

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

addElementToMaps_()

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

protected

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

calculateAvgWeight_()

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

protected

calculateMonoWeight_()

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

protected

clear_()

void clear_ ( )

protected

getAtomicNumbers()

const std::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 const 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::map<std::string, const Element*>& getNames

(

)

const

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

getSymbols()

const std::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

storeElements_()

void storeElements_ ( )

protected

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

Member Data Documentation

atomic_numbers_

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

protected

names_

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

protected

symbols_

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

protected