Residue.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
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//

#ifndef OPENMS_CHEMISTRY_RESIDUE_H
#define OPENMS_CHEMISTRY_RESIDUE_H

#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:


    // Formulae that need to be added to the internal residues to get to fragment type
    // Formulae from http://www.matrixscience.com/help/fragmentation_help.html
    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,       // with N-terminus and C-terminus
      Internal,       // internal, without any termini
      NTerminal,      // only N-terminus
      CTerminal,      // only C-terminus
      AIon,           // MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond
      BIon,           // MS:1001224 N-terminus up to the peptide bond
      CIon,           // MS:1001231 N-terminus up to the amide/C-alpha bond
      XIon,           // MS:1001228 amide/C-alpha bond up to the C-terminus
      YIon,           // MS:1001220 peptide bond up to the C-terminus
      ZIon,           // MS:1001230 C-alpha/carbonyl carbon bond
      Precursor,      // MS:1001523 Precursor ion
      BIonMinusH20,   // MS:1001222 b ion without water
      YIonMinusH20,   // MS:1001223 y ion without water
      BIonMinusNH3,   // MS:1001232 b ion without ammonia
      YIonMinusNH3,   // MS:1001233 y ion without ammonia
      NonIdentified,  // MS:1001240 Non-identified ion
      Unannotated,    // no stored annotation
      SizeOfResidueType
    };

    static String getResidueTypeName(const ResidueType res_type);


    Residue();

    Residue(const Residue& residue);

    Residue(const String& name,
            const String& three_letter_code,
            const String& one_letter_code,
            const EmpiricalFormula& formula);

    virtual ~Residue();

    Residue& operator=(const Residue& residue);

    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;

    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;

    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 isModified() const;

    bool isInResidueSet(const String& residue_set);

    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_;

    void setModification_(const ResidueModification& mod);

  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Residue& residue);

}

#endif