2.5.0-shortNms/html/a02819_source.html

// --------------------------------------------------------------------------

//                   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

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//    may be used to endorse or promote products derived from this software

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// For a full list of authors, refer to the file AUTHORS.

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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

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// $Maintainer: Timo Sachsenberg $

// $Authors: Andreas Bertsch $

// --------------------------------------------------------------------------


#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_;


  };

}