Residue.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 2002-2020.
//
// 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: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
//
 
#pragma once
 
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
 
#include <iosfwd>
#include <set>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI Residue
  {
    friend class ResidueDB;
 
public:
 
 
    inline static const EmpiricalFormula& getInternalToFull()
    {
      static const EmpiricalFormula to_full = EmpiricalFormula("H2O");
      return to_full;
    }
 
    inline static const EmpiricalFormula& getInternalToNTerm()
    {
      static const EmpiricalFormula to_full = EmpiricalFormula("H");
      return to_full;
    }
 
    inline static const EmpiricalFormula& getInternalToCTerm()
    {
      static const EmpiricalFormula to_full = EmpiricalFormula("OH");
      return to_full;
    }
 
    inline static const EmpiricalFormula& getInternalToAIon()
    {
      // Mind the "-"
      static const EmpiricalFormula to_full =
        getInternalToNTerm() - EmpiricalFormula("CHO");
      return to_full;
    }
 
    inline static const EmpiricalFormula& getInternalToBIon()
    {
      // Mind the "-"
      static const EmpiricalFormula to_full =
        getInternalToNTerm() - EmpiricalFormula("H");
      return to_full;
    }
 
    inline static const EmpiricalFormula& getInternalToCIon()
    {
      static const EmpiricalFormula to_full =
        getInternalToNTerm() + EmpiricalFormula("NH2");
      return to_full;
    }
 
    inline static const EmpiricalFormula& getInternalToXIon()
    {
      // Mind the "-"
      static const EmpiricalFormula to_full =
        getInternalToCTerm() + EmpiricalFormula("CO") - EmpiricalFormula("H");
      return to_full;
    }
 
    inline static const EmpiricalFormula& getInternalToYIon()
    {
      static const EmpiricalFormula to_full =
        getInternalToCTerm() + EmpiricalFormula("H");
      return to_full;
    }
 
    inline static const EmpiricalFormula& getInternalToZIon()
    {
      // Mind the "-"
      static const EmpiricalFormula to_full =
        getInternalToCTerm() - EmpiricalFormula("NH2");
      return to_full;
    }
 
 
    enum ResidueType
    {
      Full = 0,       
      Internal,       
      NTerminal,      
      CTerminal,      
      AIon,           
      BIon,           
      CIon,           
      XIon,           
      YIon,           
      ZIon,           
      Precursor,      
      BIonMinusH20,   
      YIonMinusH20,   
      BIonMinusNH3,   
      YIonMinusNH3,   
      NonIdentified,  
      Unannotated,    
      SizeOfResidueType
    };
 
    static String getResidueTypeName(const ResidueType res_type);
 
 
 
    Residue();
 
    Residue(const Residue&) = default;
 
    Residue(Residue&&) = default;
 
    Residue(const String& name,
            const String& three_letter_code,
            const String& one_letter_code,
            const EmpiricalFormula& formula);
 
    virtual ~Residue();
 
 
    Residue& operator=(const Residue&) = default;
 
    Residue& operator=(Residue&&) & = default;
 
    void setName(const String& name);
 
    const String& getName() const;
 
    void setShortName(const String& short_name);
 
    const String& getShortName() const;
 
    void setSynonyms(const std::set<String>& synonyms);
 
    void addSynonym(const String& synonym);
 
    const std::set<String>& getSynonyms() const;
 
    void setThreeLetterCode(const String& three_letter_code);
 
    const String& getThreeLetterCode() const;
 
    void setOneLetterCode(const String& one_letter_code);
 
    const String& getOneLetterCode() const;
 
    void addLossFormula(const EmpiricalFormula&);
 
    void setLossFormulas(const std::vector<EmpiricalFormula>&);
 
    void addNTermLossFormula(const EmpiricalFormula&);
 
    void setNTermLossFormulas(const std::vector<EmpiricalFormula>&);
 
    const std::vector<EmpiricalFormula>& getLossFormulas() const;
 
    const std::vector<EmpiricalFormula>& getNTermLossFormulas() const;
 
    void setLossNames(const std::vector<String>& name);
 
    void setNTermLossNames(const std::vector<String>& name);
 
    void addLossName(const String& name);
 
    void addNTermLossName(const String& name);
 
    const std::vector<String>& getLossNames() const;
 
    const std::vector<String>& getNTermLossNames() const;
 
    void setFormula(const EmpiricalFormula& formula);
 
    EmpiricalFormula getFormula(ResidueType res_type = Full) const;
 
    void setAverageWeight(double weight);
 
    double getAverageWeight(ResidueType res_type = Full) const;
 
    void setMonoWeight(double weight);
 
    double getMonoWeight(ResidueType res_type = Full) const;
 
    const ResidueModification* getModification() const;
 
    void setModification(const String& name);
 
    const String& getModificationName() const;
 
    void setLowMassIons(const std::vector<EmpiricalFormula>& low_mass_ions);
 
    const std::vector<EmpiricalFormula>& getLowMassIons() const;
 
    void setResidueSets(const std::set<String>& residues_sets);
 
    void addResidueSet(const String& residue_sets);
 
    const std::set<String>& getResidueSets() const;
 
    double getPka() const;
 
    double getPkb() const;
 
    double getPkc() const;
 
    double getPiValue() const;
 
    void setPka(double value);
 
    void setPkb(double value);
 
    void setPkc(double value);
 
    double getSideChainBasicity() const;
 
    void setSideChainBasicity(double gb_sc);
 
    double getBackboneBasicityLeft() const;
 
    void setBackboneBasicityLeft(double gb_bb_l);
 
    double getBackboneBasicityRight() const;
 
    void setBackboneBasicityRight(double gb_bb_r);
 
    bool hasNeutralLoss() const;
 
    bool hasNTermNeutralLosses() const;
 
    bool operator==(const Residue& residue) const;
 
    bool operator!=(const Residue& residue) const;
 
    bool operator==(char one_letter_code) const;
 
    bool operator!=(char one_letter_code) const;
 
    bool isModified() const;
 
    bool isInResidueSet(const String& residue_set);
 
    static char residueTypeToIonLetter(const ResidueType& res_type);
 
    friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Residue& residue);
 
protected:
 
    // basic
    String name_;
 
    String short_name_;
 
    std::set<String> synonyms_;
 
    String three_letter_code_;
 
    String one_letter_code_;
 
    EmpiricalFormula formula_;
 
    EmpiricalFormula internal_formula_;
 
    double average_weight_;
 
    double mono_weight_;
 
    // modification
    const ResidueModification* modification_;
 
    // loss
    std::vector<String> loss_names_;
 
    std::vector<EmpiricalFormula> loss_formulas_;
 
    std::vector<String> NTerm_loss_names_;
 
    std::vector<EmpiricalFormula> NTerm_loss_formulas_;
 
    double loss_average_weight_;
 
    double loss_mono_weight_;
 
    // low mass markers like immonium ions
    std::vector<EmpiricalFormula> low_mass_ions_;
 
    // pka values
    double pka_;
 
    // pkb values
    double pkb_;
 
    // pkc values
    double pkc_;
 
    double gb_sc_;
 
    double gb_bb_l_;
 
    double gb_bb_r_;
 
    // residue sets this amino acid is contained in
    std::set<String> residue_sets_;
 
    // precalculated residue type delta weights for more efficient weight calculation
    double internal_to_full_monoweight_ = getInternalToFull().getMonoWeight();
    double internal_to_nterm_monoweight_ = getInternalToNTerm().getMonoWeight();
    double internal_to_cterm_monoweight_ = getInternalToCTerm().getMonoWeight();
    double internal_to_a_monoweight_ = getInternalToAIon().getMonoWeight();
    double internal_to_b_monoweight_ = getInternalToBIon().getMonoWeight();
    double internal_to_c_monoweight_ = getInternalToCIon().getMonoWeight();
    double internal_to_x_monoweight_ = getInternalToXIon().getMonoWeight();
    double internal_to_y_monoweight_ = getInternalToYIon().getMonoWeight();
    double internal_to_z_monoweight_ = getInternalToZIon().getMonoWeight();
 
    void setModification_(const ResidueModification& mod);
 
  };
 
  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Residue& residue);
 
}