ResidueModification.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: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
//
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
 
#include <set>
 
namespace OpenMS
{
  // forward declaration
  class Residue;
 
  class OPENMS_DLLAPI ResidueModification
  {
public:
 
    enum TermSpecificity
    {
      ANYWHERE = 0,        
      C_TERM = 1,          
      N_TERM = 2,          
      PROTEIN_C_TERM = 3,  
      PROTEIN_N_TERM = 4,  
      NUMBER_OF_TERM_SPECIFICITY
    };
 
    enum SourceClassification
    {
      ARTIFACT = 0,           
      HYPOTHETICAL,           
      NATURAL,                
      POSTTRANSLATIONAL,      
      MULTIPLE,               
      CHEMICAL_DERIVATIVE,    
      ISOTOPIC_LABEL,         
      PRETRANSLATIONAL,       
      OTHER_GLYCOSYLATION,    
      NLINKED_GLYCOSYLATION,  
      AA_SUBSTITUTION,        
      OTHER,                  
      NONSTANDARD_RESIDUE,    
      COTRANSLATIONAL,        
      OLINKED_GLYCOSYLATION,  
      UNKNOWN,                
      NUMBER_OF_SOURCE_CLASSIFICATIONS
    };
 
 
    ResidueModification();
 
    ResidueModification(const ResidueModification&) = default;
 
    ResidueModification(ResidueModification&&) = default;
 
    virtual ~ResidueModification();
 
 
    ResidueModification& operator=(const ResidueModification&) = default;
 
    ResidueModification& operator=(ResidueModification&&) & = default;
 
    void setId(const String& id);
 
    const String& getId() const;
 
    void setFullId(const String& full_id = "");
 
 
    const String& getFullId() const;
 
    void setUniModRecordId(const Int& id);
 
    const Int& getUniModRecordId() const;
 
    const String getUniModAccession() const;
 
    void setPSIMODAccession(const String& id);
 
    const String& getPSIMODAccession() const;
 
    void setFullName(const String& full_name);
 
    const String& getFullName() const;
 
    void setName(const String& name);
 
    const String& getName() const;
 
    void setTermSpecificity(TermSpecificity term_spec);
 
    void setTermSpecificity(const String& name);
 
    TermSpecificity getTermSpecificity() const;
 
    String getTermSpecificityName(TermSpecificity term_spec = NUMBER_OF_TERM_SPECIFICITY) const;
 
    void setOrigin(char origin);
 
    char getOrigin() const;
 
    void setSourceClassification(const String& classification);
 
    void setSourceClassification(SourceClassification classification);
 
    SourceClassification getSourceClassification() const;
 
    String getSourceClassificationName(SourceClassification classification = NUMBER_OF_SOURCE_CLASSIFICATIONS) const;
 
    void setAverageMass(double mass);
 
    double getAverageMass() const;
 
    void setMonoMass(double mass);
 
    double getMonoMass() const;
 
    void setDiffAverageMass(double mass);
 
    double getDiffAverageMass() const;
 
    void setDiffMonoMass(double mass);
 
    double getDiffMonoMass() const;
 
    void setFormula(const String& composition);
 
    const String& getFormula() const;
 
    void setDiffFormula(const EmpiricalFormula& diff_formula);
 
    const EmpiricalFormula& getDiffFormula() const;
 
    void setSynonyms(const std::set<String>& synonyms);
 
    void addSynonym(const String& synonym);
 
    const std::set<String>& getSynonyms() const;
 
    void setNeutralLossDiffFormulas(const std::vector<EmpiricalFormula>& diff_formulas);
 
    const std::vector<EmpiricalFormula>& getNeutralLossDiffFormulas() const;
 
    void setNeutralLossMonoMasses(std::vector<double> mono_masses);
 
    std::vector<double> getNeutralLossMonoMasses() const;
 
    void setNeutralLossAverageMasses(std::vector<double> average_masses);
 
    std::vector<double> getNeutralLossAverageMasses() const;
 
    bool hasNeutralLoss() const;
 
    bool isUserDefined() const;
 
    bool operator==(const ResidueModification& modification) const;
 
    bool operator!=(const ResidueModification& modification) const;
 
    bool operator<(const ResidueModification& modification) const;
 
 
 
    static const ResidueModification* createUnknownFromMassString(const String& mod,
                                                                  const double mass,
                                                                  const bool delta_mass,
                                                                  const TermSpecificity specificity,
                                                                  const Residue* residue = nullptr);
 
    static const ResidueModification* combineMods(const ResidueModification* base,
                                                  const std::set<const ResidueModification*>& addons,
                                                  bool allow_unknown_masses = false,
                                                  const Residue* residue = nullptr);
 
    String toString() const;
 
    static String getDiffMonoMassString(const double diff_mono_mass);
 
    static String getDiffMonoMassWithBracket(const double diff_mono_mass);
 
    static String getMonoMassWithBracket(const double mono_mass);
 
protected:
    String id_;
 
    String full_id_;
 
    String psi_mod_accession_;
 
    // The UniMod record id (an integer)
    Int unimod_record_id_;
 
    String full_name_;
 
    String name_;
 
    TermSpecificity term_spec_;
 
    char origin_;
 
    SourceClassification classification_;
 
    double average_mass_;
 
    double mono_mass_;
 
    double diff_average_mass_;
 
    double diff_mono_mass_;
 
    String formula_;
 
    EmpiricalFormula diff_formula_;
 
    std::set<String> synonyms_;
 
    std::vector<EmpiricalFormula> neutral_loss_diff_formulas_;
 
    std::vector<double> neutral_loss_mono_masses_;
 
    std::vector<double> neutral_loss_average_masses_;
  };
}