ElementDB.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch, Timo Sachsenberg, Chris Bielow, Jang Jang Jin$
// --------------------------------------------------------------------------
//
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
#include <OpenMS/CHEMISTRY/Element.h>
 
#include <map>
#include <string>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI ElementDB
  {
public:
    
    static const ElementDB* getInstance();
 
    const std::map<std::string, const Element *> & getNames() const;
 
    const std::map<std::string, const Element *> & getSymbols() const;
 
    const std::map<unsigned int, const Element *> & getAtomicNumbers() const;
 
    const Element * getElement(const std::string & name) const;
 
    const Element * getElement(unsigned int atomic_number) const;
 
 
    bool hasElement(const std::string& name) const;
 
    bool hasElement(unsigned int atomic_number) const;
 
protected:
 
    /*_ parses a Histogram given as a OpenMS String and return the distribution
 
            @throw throws exception ParseError
     */
    IsotopeDistribution parseIsotopeDistribution_(const std::map<unsigned int, double>& abundance, const std::map<unsigned int, double>& mass);
 
    /*_ calculates the average weight based on isotope abundance and mass
     */
    double calculateAvgWeight_(const std::map<unsigned int, double> & abundance, const std::map<unsigned int, double> & mass);
 
    /*_ calculates the mono weight based on the smallest isotope mass
     */
    double calculateMonoWeight_(const std::map<unsigned int, double> & Z_to_mass);
 
  // constructs element objects
    void storeElements_();
 
  // build element objects from given abundances, masses, name, symbol, and atomic number
    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);
 
  // add element objects to documentation maps
    void addElementToMaps_(const std::string& name, const std::string& symbol, const unsigned int an, const Element* e);
 
  // constructs isotope objects
    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);
 
    /*_ resets all containers
     */
    void clear_();
 
    std::map<std::string, const Element *> names_;
 
    std::map<std::string, const Element *> symbols_;
 
    std::map<unsigned int, const Element *> atomic_numbers_;
 
private:
    ElementDB();
    ~ElementDB();
    ElementDB(const ElementDB& db) = delete;
    ElementDB(const ElementDB&& db) = delete;
    ElementDB& operator=(const ElementDB& db) = delete;
 
  };
 
} // namespace OpenMS