ElementDB Class Reference [Chemistry]

Stores elements. More...

#include <OpenMS/CHEMISTRY/ElementDB.h>

List of all members.

Public Member Functions
Predicates
bool	hasElement (const String &name) const
	returns true if the db contains an element with the given name
bool	hasElement (UInt atomic_number) const
	returns true if the db contains an element with the given atomic_number
Protected Member Functions
IsotopeDistribution	parseIsotopeDistribution_ (const Map< UInt, double > &distribution)
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	clear_ ()
Protected Attributes
Map< String, const Element * >	names_
Map< String, const Element * >	symbols_
Map< UInt, const Element * >	atomic_numbers_
Private Member Functions
	ElementDB ()
	ElementDB (const ElementDB &db)
ElementDB &	operator= (const ElementDB &db)
virtual	~ElementDB ()
Accessors
static const ElementDB *	getInstance ()
	returns a pointer to the singleton instance of the element db
const Map< String, const Element * > &	getNames () const
	returns a hashmap that contains names mapped to pointers to the elements
const Map< String, const Element * > &	getSymbols () const
	returns a hashmap that contains symbols mapped to pointers to the elements
const Map< UInt, const Element * > &	getAtomicNumbers () const
	returns a hashmap that contains atomic numbers mapped to pointers of the elements
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
Element *	getElement (const String &name)
	mutable access to the elements by name
Element *	getElement (UInt atomic_number)
	mutable access to the elements by atomic number

---

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)

Improvement:

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

---

Constructor & Destructor Documentation

ElementDB

(

)

[private]

ElementDB

(

const ElementDB &

db

)

[private]

virtual ~ElementDB

(

)

[private, virtual]

---

Member Function Documentation

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

double calculateMonoWeight_

(

const Map< UInt, double > &

Z_to_mass

)

[protected]

void clear_

(

)

[protected]

const Map<UInt, const Element *>& getAtomicNumbers

(

)

const

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

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 FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

Element* getElement

(

UInt

atomic_number

)

mutable access to the elements by atomic number

const Element* getElement

(

UInt

atomic_number

)

const

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

Element* getElement

(

const String &

name

)

mutable access to the elements by name

static const ElementDB* getInstance

(

)

[inline, static]

returns a pointer to the singleton instance of the element db

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

const Map<String, const Element *>& getNames

(

)

const

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

const Map<String, const Element *>& getSymbols

(

)

const

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

bool hasElement

(

const String &

name

)

const

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

bool hasElement

(

UInt

atomic_number

)

const

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

ElementDB& operator=

(

const ElementDB &

db

)

[private]

IsotopeDistribution parseIsotopeDistribution_

(

const Map< UInt, double > &

distribution

)

[protected]

void readFromFile_

(

const String &

file_name

)

[protected]

---

Member Data Documentation

Map<UInt, const Element *> atomic_numbers_ [protected]

Map<String, const Element *> names_ [protected]

Map<String, const Element *> symbols_ [protected]