ElementDB.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch, Timo Sachsenberg, Chris Bielow, Jang Jang Jin$
// --------------------------------------------------------------------------
//
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
 
#include <map>
#include <memory>
#include <unordered_map>
#include <string>
 
namespace OpenMS
{
  class Element;
 
  class OPENMS_DLLAPI ElementDB
  {
public:
 
    static ElementDB* getInstance();
 
    const std::unordered_map<std::string, const Element*>& getNames() const;
 
    const std::unordered_map<std::string, const Element*>& getSymbols() const;
 
    const std::unordered_map<unsigned int, const Element*>& getAtomicNumbers() const;
 
    const Element* getElement(const std::string& name) const;
 
    const Element* getElement(unsigned int atomic_number) const;
 
    void addElement(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,
                    bool replace_existing);
 
    bool hasElement(const std::string& name) const;
 
    bool hasElement(unsigned int atomic_number) const;
 
protected:
 
    IsotopeDistribution parseIsotopeDistribution_(const std::map<unsigned int, double>& abundance, const std::map<unsigned int, double>& mass);
 
    double calculateAvgWeight_(const std::map<unsigned int, double>& abundance, const std::map<unsigned int, double>& mass);
 
    double calculateMonoWeight_(const std::map<unsigned int, double>& abundance, const std::map<unsigned int, double>& mass);
 
    void storeElements_();
 
    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);
 
    void addElementToMaps_(const std::string& name, const std::string& symbol, const unsigned int an, std::unique_ptr<const Element> e);
 
    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);
 
    void clear_();
 
    std::unordered_map<std::string, const Element*> names_;
 
    std::unordered_map<std::string, const Element*> symbols_;
 
    std::unordered_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