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ElementDB Class Reference

Stores elements. More...

#include <OpenMS/CHEMISTRY/ElementDB.h>

Public Member Functions

Predicates
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...
 

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)
 
ElementDBoperator= (const ElementDB &db)
 
virtual ~ElementDB ()
 

Accessors

static const ElementDBgetInstance ()
 returns a pointer to the singleton instance of the element db More...
 
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 ElementgetElement (const String &name) const
 
const ElementgetElement (UInt atomic_number) const
 returns a pointer to the element of atomic number; if no element is found 0 is returned More...
 
ElementgetElement (const String &name)
 mutable access to the elements by name More...
 
ElementgetElement (UInt atomic_number)
 mutable access to the elements by atomic number More...
 

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 ( )
private
ElementDB ( const ElementDB db)
private
virtual ~ElementDB ( )
privatevirtual

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().

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

static const ElementDB* getInstance ( )
inlinestatic

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

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5