Residue.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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//

#ifndef OPENMS_CHEMISTRY_RESIDUE_H
#define OPENMS_CHEMISTRY_RESIDUE_H

#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>

#include <iostream>
#include <set>
#include <vector>

namespace OpenMS
{
  // forward declarations
  class ResidueModification;

  class OPENMS_DLLAPI Residue
  {
public:

    // Internal
    inline static const EmpiricalFormula & getInternalToFull()
    {
      static const EmpiricalFormula internal_to_full = EmpiricalFormula("H2O");
      return internal_to_full;
    }

    inline static DoubleReal getInternalToFullAverageWeight()
    {
      static const DoubleReal internal_to_full_average_weight = getInternalToFull().getAverageWeight();
      return internal_to_full_average_weight;
    }

    inline static DoubleReal getInternalToFullMonoWeight()
    {
      static const DoubleReal internal_to_full_mono_weight = getInternalToFull().getMonoWeight();
      return internal_to_full_mono_weight;
    }

    // N-terminal
    inline static const EmpiricalFormula & getNTerminalToFull()
    {
      static const EmpiricalFormula Nterminal_to_full = EmpiricalFormula("HO");
      return Nterminal_to_full;
    }

    inline static DoubleReal getNTerminalToFullAverageWeight()
    {
      static const DoubleReal Nterminal_to_full_average_weight = getNTerminalToFull().getAverageWeight();
      return Nterminal_to_full_average_weight;
    }

    inline static DoubleReal getNTerminalToFullMonoWeight()
    {
      static const DoubleReal Nterminal_to_full_mono_weight = getNTerminalToFull().getMonoWeight();
      return Nterminal_to_full_mono_weight;
    }

    // C-terminal
    inline static const EmpiricalFormula & getCTerminalToFull()
    {
      static const EmpiricalFormula Cterminal_to_full = EmpiricalFormula("H");
      return Cterminal_to_full;
    }

    inline static DoubleReal getCTerminalToFullAverageWeight()
    {
      static const DoubleReal Cterminal_to_full_average_weight = getCTerminalToFull().getAverageWeight();
      return Cterminal_to_full_average_weight;
    }

    inline static DoubleReal getCTerminalToFullMonoWeight()
    {
      static const DoubleReal Cterminal_to_full_mono_weight = getCTerminalToFull().getMonoWeight();
      return Cterminal_to_full_mono_weight;
    }

    // b ion
    inline static const EmpiricalFormula & getBIonToFull()
    {
      static const EmpiricalFormula b_ion_to_full = EmpiricalFormula("HO");
      return b_ion_to_full;
    }

    inline static DoubleReal getBIonToFullAverageWeight()
    {
      static const DoubleReal b_ion_to_full_average_weight = getBIonToFull().getAverageWeight();
      return b_ion_to_full_average_weight;
    }

    inline static DoubleReal getBIonToFullMonoWeight()
    {
      static const DoubleReal b_ion_to_full_mono_weight = getBIonToFull().getMonoWeight();
      return b_ion_to_full_mono_weight;
    }

    // a ion
    inline static const EmpiricalFormula & getAIonToFull()
    {
      static const EmpiricalFormula a_ion_to_full = EmpiricalFormula("HCO2");
      return a_ion_to_full;
    }

    inline static DoubleReal getAIonToFullAverageWeight()
    {
      static const DoubleReal a_ion_to_full_average_weight = getAIonToFull().getAverageWeight();
      return a_ion_to_full_average_weight;
    }

    inline static DoubleReal getAIonToFullMonoWeight()
    {
      static const DoubleReal a_ion_to_full_mono_weight = getAIonToFull().getMonoWeight();
      return a_ion_to_full_mono_weight;
    }

    // y ion
    inline static const EmpiricalFormula & getYIonToFull()
    {
      static const EmpiricalFormula y_ion_to_full = EmpiricalFormula("");
      return y_ion_to_full;
    }

    inline static DoubleReal getYIonToFullAverageWeight()
    {
      static const DoubleReal y_ion_to_full_average_weight = getYIonToFull().getAverageWeight();
      return y_ion_to_full_average_weight;
    }

    inline static DoubleReal getYIonToFullMonoWeight()
    {
      static const DoubleReal y_ion_to_full_mono_weight = getYIonToFull().getMonoWeight();
      return y_ion_to_full_mono_weight;
    }

    // c ion
    inline static const EmpiricalFormula & getCIonToFull()
    {
      static const EmpiricalFormula c_ion_to_full = EmpiricalFormula("H-1");
      return c_ion_to_full;
    }

    inline static DoubleReal getCIonToFullAverageWeight()
    {
      static const DoubleReal c_ion_to_full_average_weight = getCIonToFull().getAverageWeight();
      return c_ion_to_full_average_weight;
    }

    inline static DoubleReal getCIonToFullMonoWeight()
    {
      static const DoubleReal c_ion_to_full_mono_weight = getCIonToFull().getMonoWeight();
      return c_ion_to_full_mono_weight;
    }

    // c-1 ion
    inline static const EmpiricalFormula & getCIonMinusOneToFull()
    {
      static const EmpiricalFormula c_ion_to_full = EmpiricalFormula("H-2");
      return c_ion_to_full;
    }

    inline static DoubleReal getCIonMinusOneToFullAverageWeight()
    {
      static const DoubleReal c_ion_to_full_average_weight = getCIonMinusOneToFull().getAverageWeight();
      return c_ion_to_full_average_weight;
    }

    inline static DoubleReal getCIonMinusOneToFullMonoWeight()
    {
      static const DoubleReal c_ion_to_full_mono_weight = getCIonMinusOneToFull().getMonoWeight();
      return c_ion_to_full_mono_weight;
    }

    // c+1 ion
    inline static const EmpiricalFormula & getCIonPlusOneToFull()
    {
      static const EmpiricalFormula c_ion_to_full = EmpiricalFormula("");
      return c_ion_to_full;
    }

    inline static DoubleReal getCIonPlusOneToFullAverageWeight()
    {
      static const DoubleReal c_ion_to_full_average_weight = getCIonPlusOneToFull().getAverageWeight();
      return c_ion_to_full_average_weight;
    }

    inline static DoubleReal getCIonPlusOneToFullMonoWeight()
    {
      static const DoubleReal c_ion_to_full_mono_weight = getCIonPlusOneToFull().getMonoWeight();
      return c_ion_to_full_mono_weight;
    }

    // c+2 ion
    inline static const EmpiricalFormula & getCIonPlusTwoToFull()
    {
      static const EmpiricalFormula c_ion_to_full = EmpiricalFormula("H2");
      return c_ion_to_full;
    }

    inline static DoubleReal getCIonPlusTwoToFullAverageWeight()
    {
      static const DoubleReal c_ion_to_full_average_weight = getCIonPlusTwoToFull().getAverageWeight();
      return c_ion_to_full_average_weight;
    }

    inline static DoubleReal getCIonPlusTwoToFullMonoWeight()
    {
      static const DoubleReal c_ion_to_full_mono_weight = getCIonPlusTwoToFull().getMonoWeight();
      return c_ion_to_full_mono_weight;
    }

    // x ion
    inline static const EmpiricalFormula & getXIonToFull()
    {
      static const EmpiricalFormula x_ion_to_full = EmpiricalFormula("HCO");
      return x_ion_to_full;
    }

    inline static DoubleReal getXIonToFullAverageWeight()
    {
      static const DoubleReal x_ion_to_full_average_weight = getXIonToFull().getAverageWeight();
      return x_ion_to_full_average_weight;
    }

    inline static DoubleReal getXIonToFullMonoWeight()
    {
      static const DoubleReal x_ion_to_full_mono_weight = getXIonToFull().getMonoWeight();
      return x_ion_to_full_mono_weight;
    }

    // z ion
    inline static const EmpiricalFormula & getZIonToFull()
    {
      static const EmpiricalFormula z_ion_to_full = EmpiricalFormula("NH2");
      return z_ion_to_full;
    }

    inline static DoubleReal getZIonToFullAverageWeight()
    {
      static const DoubleReal z_ion_to_full_average_weight = getZIonToFull().getAverageWeight();
      return z_ion_to_full_average_weight;
    }

    inline static DoubleReal getZIonToFullMonoWeight()
    {
      static const DoubleReal z_ion_to_full_mono_weight = getZIonToFull().getMonoWeight();
      return z_ion_to_full_mono_weight;
    }

    // z-1 ion
    inline static const EmpiricalFormula & getZIonMinusOneToFull()
    {
      static const EmpiricalFormula z_ion_to_full = EmpiricalFormula("N2");
      return z_ion_to_full;
    }

    inline static DoubleReal getZIonMinusOneToFullAverageWeight()
    {
      static const DoubleReal z_ion_to_full_average_weight = getZIonMinusOneToFull().getAverageWeight();
      return z_ion_to_full_average_weight;
    }

    inline static DoubleReal getZIonMinusOneToFullMonoWeight()
    {
      static const DoubleReal z_ion_to_full_mono_weight = getZIonMinusOneToFull().getMonoWeight();
      return z_ion_to_full_mono_weight;
    }

    // z+1 ion
    inline static const EmpiricalFormula & getZIonPlusOneToFull()
    {
      static const EmpiricalFormula z_ion_to_full = EmpiricalFormula("NH3");
      return z_ion_to_full;
    }

    inline static DoubleReal getZIonPlusOneToFullAverageWeight()
    {
      static const DoubleReal z_ion_to_full_average_weight = getZIonPlusOneToFull().getAverageWeight();
      return z_ion_to_full_average_weight;
    }

    inline static DoubleReal getZIonPlusOneToFullMonoWeight()
    {
      static const DoubleReal z_ion_to_full_mono_weight = getZIonPlusOneToFull().getMonoWeight();
      return z_ion_to_full_mono_weight;
    }

    // z+2 ion
    inline static const EmpiricalFormula & getZIonPlusTwoToFull()
    {
      static const EmpiricalFormula z_ion_to_full = EmpiricalFormula("NH4");
      return z_ion_to_full;
    }

    inline static DoubleReal getZIonPlusTwoToFullAverageWeight()
    {
      static const DoubleReal z_ion_to_full_average_weight = getZIonPlusTwoToFull().getAverageWeight();
      return z_ion_to_full_average_weight;
    }

    inline static DoubleReal getZIonPlusTwoToFullMonoWeight()
    {
      static const DoubleReal z_ion_to_full_mono_weight = getZIonPlusTwoToFull().getMonoWeight();
      return z_ion_to_full_mono_weight;
    }


    enum ResidueType
    {
      Full = 0,           // with N-terminus and C-terminus
      Internal,           // internal, without any termini
      NTerminal,           // only N-terminus
      CTerminal,           // only C-terminus
      AIon,           // N-terminus up to the C-alpha/carbonyl carbon bond
      BIon,           // N-terminus up to the peptide bond
      CIonMinusOne,           // N-terminus up to the amide/C-alpha bond
      CIon,           // N-terminus up to the amide/C-alpha bond
      CIonPlusOne,           // N-terminus up to the amide/C-alpha bond
      CIonPlusTwo,           // N-terminus up to the amide/C-alpha bond
      XIon,           // amide/C-alpha bond up to the C-terminus
      YIon,           // peptide bond up to the C-terminus
      ZIonMinusOne,           // C-alpha/carbonyl carbon bond
      ZIon,            // C-alpha/carbonyl carbon bond
      ZIonPlusOne,            // C-alpha/carbonyl carbon bond
      ZIonPlusTwo,            // C-alpha/carbonyl carbon bond
      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(DoubleReal weight);

    DoubleReal getAverageWeight(ResidueType res_type = Full) const;

    void setMonoWeight(DoubleReal weight);

    DoubleReal getMonoWeight(ResidueType res_type = Full) const;

    void setModification(const String & name);

    const String & getModification() 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;

    DoubleReal getPka() const;

    DoubleReal getPkb() const;

    DoubleReal getPkc() const;

    DoubleReal getPiValue() const;

    void setPka(DoubleReal value);

    void setPkb(DoubleReal value);

    void setPkc(DoubleReal value);

    DoubleReal getSideChainBasicity() const;

    void setSideChainBasicity(DoubleReal gb_sc);

    DoubleReal getBackboneBasicityLeft() const;

    void setBackboneBasicityLeft(DoubleReal gb_bb_l);

    DoubleReal getBackboneBasicityRight() const;

    void setBackboneBasicityRight(DoubleReal 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_;

    DoubleReal average_weight_;

    DoubleReal mono_weight_;

    // modification
    bool is_modified_;

    String pre_mod_name_;

    String modification_;

    // loss
    std::vector<String> loss_names_;

    std::vector<EmpiricalFormula> loss_formulas_;

    std::vector<String> NTerm_loss_names_;

    std::vector<EmpiricalFormula> NTerm_loss_formulas_;

    DoubleReal loss_average_weight_;

    DoubleReal loss_mono_weight_;

    // low mass markers like immonium ions
    std::vector<EmpiricalFormula> low_mass_ions_;

    // pka values
    DoubleReal pka_;

    // pkb values
    DoubleReal pkb_;

    // pkc values
    DoubleReal pkc_;

    DoubleReal gb_sc_;

    DoubleReal gb_bb_l_;

    DoubleReal gb_bb_r_;

    // residue sets this amino acid is contained in
    std::set<String> residue_sets_;

  };

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

}

#endif