EmpiricalFormula.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow, Ahmed Khalil $
// $Authors: Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------
//
#pragma once

#include <iosfwd>
#include <map>
#include <set>
#include <string>

#include <OpenMS/CONCEPT/Types.h>

namespace OpenMS
{
  class String;
  class Element;
  class ElementDB;
  class IsotopeDistribution;
  class IsotopePatternGenerator;
  class CoarseIsotopePatternGenerator;

  class OPENMS_DLLAPI EmpiricalFormula
  {

protected:
    typedef std::map<const Element*, SignedSize> MapType_;

public:
    typedef MapType_::const_iterator ConstIterator;
    typedef MapType_::const_iterator const_iterator;
    typedef MapType_::iterator Iterator;
    typedef MapType_::iterator iterator;

    EmpiricalFormula();

    EmpiricalFormula(const EmpiricalFormula&) = default;

    EmpiricalFormula(EmpiricalFormula&&) = default;

    explicit EmpiricalFormula(const String& rhs);

    EmpiricalFormula(SignedSize number, const Element* element, SignedSize charge = 0);

    virtual ~EmpiricalFormula();

    static EmpiricalFormula fromString(const String& rhs)
    {
      EmpiricalFormula ef(rhs);
      return ef;
    }

    double getMonoWeight() const;

    double getAverageWeight() const;

    double calculateTheoreticalIsotopesNumber() const;

    bool estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P);

    bool estimateFromMonoWeightAndComp(double mono_weight, double C, double H, double N, double O, double S, double P);

    bool estimateFromWeightAndCompAndS(double average_weight, UInt S, double C, double H, double N, double O, double P);


    IsotopeDistribution getIsotopeDistribution(const IsotopePatternGenerator& method) const;

    IsotopeDistribution getConditionalFragmentIsotopeDist(const EmpiricalFormula& precursor,
                                                          const std::set<UInt>& precursor_isotopes,
                                                          const CoarseIsotopePatternGenerator& method) const;

    SignedSize getNumberOf(const Element* element) const;

    SignedSize getNumberOfAtoms() const;

    Int getCharge() const;

    void setCharge(Int charge);

    String toString() const;

    std::map<std::string, int> toMap() const;


    EmpiricalFormula& operator=(const EmpiricalFormula&) = default;

    EmpiricalFormula& operator=(EmpiricalFormula&&) & = default;

    EmpiricalFormula& operator+=(const EmpiricalFormula& rhs);

    EmpiricalFormula operator*(const SignedSize& times) const;

    EmpiricalFormula operator+(const EmpiricalFormula& rhs) const;

    EmpiricalFormula& operator-=(const EmpiricalFormula& rhs);

    EmpiricalFormula operator-(const EmpiricalFormula& rhs) const;


    bool isEmpty() const;

    bool isCharged() const;

    bool hasElement(const Element* element) const;

    bool contains(const EmpiricalFormula& ef) const;

    bool operator==(const EmpiricalFormula& rhs) const;

    bool operator!=(const EmpiricalFormula& rhs) const;

    bool operator<(const EmpiricalFormula& rhs) const;


    friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);

    inline ConstIterator begin() const { return formula_.begin(); }

    inline ConstIterator end() const { return formula_.end(); }

    inline Iterator begin() { return formula_.begin(); }

    inline Iterator end() { return formula_.end(); }

    // @TODO: make these static member variables instead?
    static EmpiricalFormula hydrogen(int n_atoms = 1);

    static EmpiricalFormula water(int n_molecules = 1);

protected:

    void removeZeroedElements_();

    MapType_ formula_;

    Int charge_;

    Int parseFormula_(std::map<const Element*, SignedSize>& ef, const String& formula) const;

  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);

} // namespace OpenMS