ProtonDistributionModel.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 2002-2023.
//
// 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/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_;
 
  };
}