libopenms-dev 1.11.1-5 / usr / include / OpenMS / CHEMISTRY / 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 2002-2013.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch, Timo Sachsenberg $
// --------------------------------------------------------------------------
//

#ifndef OPENMS_CHEMISTRY_ELEMENTDB_H
#define OPENMS_CHEMISTRY_ELEMENTDB_H

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CHEMISTRY/IsotopeDistribution.h>

namespace OpenMS
{
  class Element;

  /** @ingroup Chemistry

          @brief 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)
*/

  class OPENMS_DLLAPI ElementDB
  {
public:

    /** @name Accessors
    */
    //@{
    /// returns a pointer to the singleton instance of the element db
    inline static const ElementDB * getInstance()
    {
      static ElementDB * db_ = 0;
      if (db_ == 0)
      {
        db_ = new ElementDB;
      }
      return db_;
    }

    /// returns a hashmap that contains names mapped to pointers to the elements
    const Map<String, const Element *> & getNames() const;

    /// returns a hashmap that contains symbols mapped to pointers to the elements
    const Map<String, const Element *> & getSymbols() const;

    /// returns a hashmap that contains atomic numbers mapped to pointers of the elements
    const Map<UInt, const Element *> & getAtomicNumbers() 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
        *	@param name: name or symbol of the element
    */
    const Element * getElement(const String & name) const;

    /// returns a pointer to the element of atomic number; if no element is found 0 is returned
    const Element * getElement(UInt atomic_number) const;

    /// mutable access to the elements by name
    Element * getElement(const String & name);

    /// mutable access to the elements by atomic number
    Element * getElement(UInt atomic_number);

    //@}

    /** @name Predicates
    */
    //@{
    /// returns true if the db contains an element with the given name
    bool hasElement(const String & name) const;

    /// returns true if the db contains an element with the given atomic_number
    bool hasElement(UInt atomic_number) const;
    //@}

protected:

    /*_ parses a Histogram given as a OpenMS String and return the distribution

            @throw throws exception ParseError
     */
    IsotopeDistribution parseIsotopeDistribution_(const Map<UInt, double> & distribution);

    /*_ calculates the average weight based on isotope abundance and mass
     */
    double calculateAvgWeight_(const Map<UInt, double> & Z_to_abundance, const Map<UInt, double> & Z_to_mass);

    /*_ calculates the mono weight based on the smallest isotope mass
     */
    double calculateMonoWeight_(const Map<UInt, double> & Z_to_mass);

    /*_ read elements from a XML file, formated as a Param file.

            @throw throws ParseError if the file cannot be parsed
            @throw throws FileNotFound if the file could not be found
     */
    void readFromFile_(const String & file_name);

    /*_ resets all containers
     */
    void clear_();

    Map<String, const Element *> names_;

    Map<String, const Element *> symbols_;

    Map<UInt, const Element *> atomic_numbers_;

private:

    ElementDB();

    ElementDB(const ElementDB & db);

    ElementDB & operator=(const ElementDB & db);

    virtual ~ElementDB();
  };

} // namespace OpenMS
#endif