ElementDB Class Reference

Stores elements. More...

#include <OpenMS/CHEMISTRY/ElementDB.h>

Accessors
static const ElementDB *	getInstance ()
const Map< String, const Element * > &	getNames () const
	returns a hashmap that contains names mapped to pointers to the elements More...
const Map< String, const Element * > &	getSymbols () const
	returns a hashmap that contains symbols mapped to pointers to the elements More...
const Map< UInt, const Element * > &	getAtomicNumbers () const
	returns a hashmap that contains atomic numbers mapped to pointers of the elements More...
const Element *	getElement (const String &name) const
const Element *	getElement (UInt atomic_number) const
	returns a pointer to the element of atomic number; if no element is found 0 is returned More...

Predicates
Map< String, const Element * >	names_
Map< String, const Element * >	symbols_
Map< UInt, const Element * >	atomic_numbers_
bool	hasElement (const String &name) const
	returns true if the db contains an element with the given name More...
bool	hasElement (UInt atomic_number) const
	returns true if the db contains an element with the given atomic_number More...
IsotopeDistribution	parseIsotopeDistribution_ (const Map< UInt, double > &Z_to_abundance, const Map< UInt, double > &Z_to_mass)
double	calculateAvgWeight_ (const Map< UInt, double > &Z_to_abundance, const Map< UInt, double > &Z_to_mass)
double	calculateMonoWeight_ (const Map< UInt, double > &Z_to_mass)
void	readFromFile_ (const String &file_name)
void	storeElement_ (const UInt an, const String &name, const String &symbol, const Map< UInt, double > &Z_to_abundancy, const Map< UInt, double > &Z_to_mass)
	store element after parsing it More...
void	clear_ ()
	ElementDB ()
	~ElementDB ()
	ElementDB (const ElementDB &db)=delete
	ElementDB (const ElementDB &&db)=delete
ElementDB &	operator= (const ElementDB &db)=delete

Detailed Description

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

This singleton stores all elements. The elements are taken from the publications given above and are stored in share/OpenMS/CHEMISTRY/Elements.xml.

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

calculateAvgWeight_()

double calculateAvgWeight_ ( const Map< UInt, double > &  Z_to_abundance, const Map< UInt, double > &  Z_to_mass  )

protected

calculateMonoWeight_()

double calculateMonoWeight_ ( const Map< UInt, double > &  Z_to_mass )

protected

clear_()

void clear_ ( )

protected

getAtomicNumbers()

const Map<UInt, const Element *>& getAtomicNumbers

(

)

const

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

getElement() [1/2]

const Element* getElement

(

const 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

Referenced by MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide(), and MetaProSIPDecomposition::getNumberOfLabelingElements().

getElement() [2/2]

const Element* getElement

(

UInt

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 Upon first call, the Elements.xml file is parsed This is thread safe upon first and subsequent calls.

Referenced by MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide(), and MetaProSIPDecomposition::getNumberOfLabelingElements().

getNames()

const Map<String, const Element *>& getNames

(

)

const

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

getSymbols()

const Map<String, const Element *>& getSymbols

(

)

const

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

hasElement() [1/2]

bool hasElement

(

const String &

name

)

const

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

hasElement() [2/2]

bool hasElement

(

UInt

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 Map< UInt, double > &  Z_to_abundance, const Map< UInt, double > &  Z_to_mass  )

protected

readFromFile_()

void readFromFile_ ( const String &  file_name )

protected

storeElement_()

void storeElement_ ( const UInt  an, const String &  name, const String &  symbol, const Map< UInt, double > &  Z_to_abundancy, const Map< UInt, double > &  Z_to_mass  )

protected

store element after parsing it

Member Data Documentation

atomic_numbers_

Map<UInt, const Element *> atomic_numbers_

protected

names_

Map<String, const Element *> names_

protected

symbols_

Map<String, const Element *> symbols_

protected