OpenMS
ProtonDistributionModel.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2023.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34 
35 
36 #pragma once
37 
38 #include <OpenMS/CONCEPT/Types.h>
41 #include <vector>
42 
43 namespace OpenMS
44 {
45  class AASequence;
46 
70  class OPENMS_DLLAPI ProtonDistributionModel :
71  public DefaultParamHandler
72  {
73 public:
74 
80 
83 
87 
90 
96  {
97  ChargeDirected = 0,
99  SideChain
100  };
102 
111  void getProtonDistribution(std::vector<double> & bb_charges, std::vector<double> & sc_charges, const AASequence & peptide, Int charge, Residue::ResidueType res_type = Residue::YIon);
112 
124  //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);
125 
126 
127  void getChargeStateIntensities(const AASequence & peptide, const AASequence & n_term_ion, const AASequence & c_term_ion, Int charge, Residue::ResidueType n_term_type,
128  std::vector<double> & n_term_intensities, std::vector<double> & c_term_intensities, FragmentationType type);
129 
131  void setPeptideProtonDistribution(const std::vector<double> & bb_charge, const std::vector<double> & sc_charge);
132 
133 protected:
134 
135  // calculates the proton distribution
136  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);
137 
139  void calculateProtonDistributionCharge2_(const AASequence & peptide, Residue::ResidueType res_type, bool fixed_proton, Size cleavage_site, bool use_most_basic_site);
141 
142  void calculateProtonDistributionIonPair_(const AASequence & peptide, Residue::ResidueType type, Size cleavage_site);
143 
144  // returns the proton affinity of the peptide with the given charge and ion type
145  //double getProtonAffinity_(const AASequence& ion, Int charge, Residue::ResidueType res_type);
146 
147  // returns the (relative) Intensities of the possible charge states of the ion from peptide
148  //std::vector<double> getChargeStateIntensities_(const AASequence& peptide, const AASequence& ion, Int charge, Residue::ResidueType res_type);
149 
150 
151  void calcChargeStateIntensities_(const AASequence & peptide, const AASequence & n_term_ion, const AASequence & c_term_ion, Int charge,
152  Residue::ResidueType n_term_type, std::vector<double> & n_term_intensities, std::vector<double> & c_term_intensities, FragmentationType type);
153 
154  // calculates the intensities of the different possible charge states
155  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);
156 
157  // returns the left and right GB values, NH2 and COOH if at terminus
158  void getLeftAndRightGBValues_(const AASequence & peptide, double & left_gb, double & right_gb, Size position);
159 
160  std::vector<double> sc_charge_;
161  std::vector<double> bb_charge_;
162  std::vector<double> sc_charge_full_;
163  std::vector<double> bb_charge_full_;
164  std::vector<double> sc_charge_ion_n_term_;
165  std::vector<double> bb_charge_ion_n_term_;
166  std::vector<double> sc_charge_ion_c_term_;
167  std::vector<double> bb_charge_ion_c_term_;
168  double E_;
169  double E_c_term_;
170  double E_n_term_;
171 
172  };
173 }
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
A proton distribution model to calculate the proton distribution over charged peptides.
Definition: ProtonDistributionModel.h:72
ProtonDistributionModel(const ProtonDistributionModel &model)
copy constructor
double E_n_term_
Definition: ProtonDistributionModel.h:170
std::vector< double > bb_charge_ion_n_term_
Definition: ProtonDistributionModel.h:165
void calculateProtonDistributionCharge1_(const AASequence &peptide, Residue::ResidueType res_type)
void getLeftAndRightGBValues_(const AASequence &peptide, double &left_gb, double &right_gb, Size position)
FragmentationType
the type of fragmentation
Definition: ProtonDistributionModel.h:96
@ ChargeRemote
Definition: ProtonDistributionModel.h:98
std::vector< double > bb_charge_ion_c_term_
Definition: ProtonDistributionModel.h:167
void getProtonDistribution(std::vector< double > &bb_charges, std::vector< double > &sc_charges, const AASequence &peptide, Int charge, Residue::ResidueType res_type=Residue::YIon)
calculates a proton distribution of the given charged peptide
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)
double E_
Definition: ProtonDistributionModel.h:168
void calculateProtonDistributionGreater2_(const AASequence &peptide, Int charge, Residue::ResidueType res_type)
ProtonDistributionModel & operator=(const ProtonDistributionModel &pdm)
assignment operator
std::vector< double > sc_charge_full_
Definition: ProtonDistributionModel.h:162
std::vector< double > sc_charge_ion_c_term_
Definition: ProtonDistributionModel.h:166
double E_c_term_
Definition: ProtonDistributionModel.h:169
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)
calculates the charge state intensities of different charge states of the same ion
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 calculateProtonDistributionCharge2_(const AASequence &peptide, Residue::ResidueType res_type, bool fixed_proton, Size cleavage_site, bool use_most_basic_site)
std::vector< double > bb_charge_full_
Definition: ProtonDistributionModel.h:163
ProtonDistributionModel()
default constructor
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)
void setPeptideProtonDistribution(const std::vector< double > &bb_charge, const std::vector< double > &sc_charge)
sets the proton distributions of the whole peptide, they are needed for the getChargeStateIntensities...
~ProtonDistributionModel() override
destructor
std::vector< double > bb_charge_
Definition: ProtonDistributionModel.h:161
void calculateProtonDistributionIonPair_(const AASequence &peptide, Residue::ResidueType type, Size cleavage_site)
std::vector< double > sc_charge_ion_n_term_
Definition: ProtonDistributionModel.h:164
std::vector< double > sc_charge_
Definition: ProtonDistributionModel.h:160
ResidueType
Definition: Residue.h:152
@ YIon
MS:1001220 peptide bond up to the C-terminus.
Definition: Residue.h:161
int Int
Signed integer type.
Definition: Types.h:102
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48