ProtonDistributionModel.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
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#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CHEMISTRY/Residue.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <vector>

namespace OpenMS
{
  class AASequence;

  class OPENMS_DLLAPI ProtonDistributionModel :
    public DefaultParamHandler
  {
public:

    ProtonDistributionModel();

    ProtonDistributionModel(const ProtonDistributionModel & model);

    ~ProtonDistributionModel() override;

    ProtonDistributionModel & operator=(const ProtonDistributionModel & pdm);

    enum FragmentationType
    {
      ChargeDirected = 0,
      ChargeRemote,
      SideChain
    };

    void getProtonDistribution(std::vector<double> & bb_charges, std::vector<double> & sc_charges, const AASequence & peptide, Int charge, Residue::ResidueType res_type = Residue::YIon);

    //void getChargeStateIntensities(const AASequence& peptide, const AASequence& n_term_ion, const AASequence& c_term_ion, Int charge, Residue::ResidueType n_term_type, double& n_term1,  double& c_term1, double& n_term2, double& c_term2, FragmentationType type);


    void getChargeStateIntensities(const AASequence & peptide, const AASequence & n_term_ion, const AASequence & c_term_ion, Int charge, Residue::ResidueType n_term_type,
                                   std::vector<double> & n_term_intensities, std::vector<double> & c_term_intensities, FragmentationType type);

    void setPeptideProtonDistribution(const std::vector<double> & bb_charge, const std::vector<double> & sc_charge);

protected:

    // calculates the proton distribution
    void calculateProtonDistribution_(const AASequence & peptide, Int charge, Residue::ResidueType res_type = Residue::YIon, bool fixed_proton = false, Size cleavage_site = 0, bool use_most_basic_site = false);

    void calculateProtonDistributionCharge1_(const AASequence & peptide, Residue::ResidueType res_type);
    void calculateProtonDistributionCharge2_(const AASequence & peptide, Residue::ResidueType res_type, bool fixed_proton, Size cleavage_site, bool use_most_basic_site);
    void calculateProtonDistributionGreater2_(const AASequence & peptide, Int charge, Residue::ResidueType res_type);

    void calculateProtonDistributionIonPair_(const AASequence & peptide, Residue::ResidueType type, Size cleavage_site);

    // returns the proton affinity of the peptide with the given charge and ion type
    //double getProtonAffinity_(const AASequence& ion, Int charge, Residue::ResidueType res_type);

    // returns the (relative) Intensities of the possible charge states of the ion from peptide
    //std::vector<double> getChargeStateIntensities_(const AASequence& peptide, const AASequence& ion, Int charge, Residue::ResidueType res_type);


    void calcChargeStateIntensities_(const AASequence & peptide, const AASequence & n_term_ion, const AASequence & c_term_ion, Int charge,
                                     Residue::ResidueType n_term_type, std::vector<double> & n_term_intensities, std::vector<double> & c_term_intensities, FragmentationType type);

    // calculates the intensities of the different possible charge states
    void calcChargeStateIntensities_(const AASequence & peptide, const AASequence & n_term_ion, const AASequence & c_term_ion, Int charge, Residue::ResidueType n_term_type, double & n_term1, double & c_term1, double & n_term2, double & c_term2, FragmentationType type);

    // returns the left and right GB values, NH2 and COOH if at terminus
    void getLeftAndRightGBValues_(const AASequence & peptide, double & left_gb, double & right_gb, Size position);

    std::vector<double> sc_charge_;
    std::vector<double> bb_charge_;
    std::vector<double> sc_charge_full_;
    std::vector<double> bb_charge_full_;
    std::vector<double> sc_charge_ion_n_term_;
    std::vector<double> bb_charge_ion_n_term_;
    std::vector<double> sc_charge_ion_c_term_;
    std::vector<double> bb_charge_ion_c_term_;
    double E_;
    double E_c_term_;
    double E_n_term_;

  };
}