OpenMS
2.4.0
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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 > &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 | 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 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 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... | |
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.
include exact mass values for the isotopes (done) and update IsotopeDistribution (Andreas)
add exact isotope distribution based on exact isotope values (Andreas)
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returns a hashmap that contains atomic numbers mapped to pointers of the elements
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
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().
returns a pointer to the element of atomic number; if no element is found 0 is returned
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returns a pointer to the singleton instance of the element db
Referenced by MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide(), and MetaProSIPDecomposition::getNumberOfLabelingElements().
returns a hashmap that contains names mapped to pointers to the elements
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
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