| OpenMS 2.5.0

ProtonDistributionModel.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/CHEMISTRY/Residue.h>
40 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.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
78 ProtonDistributionModel();
80
82 ProtonDistributionModel(const ProtonDistributionModel & model);
83
85 ~ProtonDistributionModel() override;
87
89 ProtonDistributionModel & operator=(const ProtonDistributionModel & pdm);
90
94 enum FragmentationType
96 {
97 ChargeDirected = 0,
98 ChargeRemote,
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
138 void calculateProtonDistributionCharge1_(const AASequence & peptide, Residue::ResidueType res_type);
139 void calculateProtonDistributionCharge2_(const AASequence & peptide, Residue::ResidueType res_type, bool fixed_proton, Size cleavage_site, bool use_most_basic_site);
140 void calculateProtonDistributionGreater2_(const AASequence & peptide, Int charge, Residue::ResidueType res_type);
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 }
OpenMS::ProtonDistributionModel::bb_charge_full_
std::vector< double > bb_charge_full_
Definition: ProtonDistributionModel.h:163
OpenMS::ProtonDistributionModel::E_
double E_
Definition: ProtonDistributionModel.h:168
OpenMS::ProtonDistributionModel::sc_charge_ion_n_term_
std::vector< double > sc_charge_ion_n_term_
Definition: ProtonDistributionModel.h:164
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::ProtonDistributionModel::bb_charge_ion_n_term_
std::vector< double > bb_charge_ion_n_term_
Definition: ProtonDistributionModel.h:165
seqan::position
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
OpenMS::ProtonDistributionModel::E_c_term_
double E_c_term_
Definition: ProtonDistributionModel.h:169
Residue.h
Types.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::ProtonDistributionModel::bb_charge_
std::vector< double > bb_charge_
Definition: ProtonDistributionModel.h:161
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProtonDistributionModel
A proton distribution model to calculate the proton distribution over charged peptides.
Definition: ProtonDistributionModel.h:70
OpenMS::ProtonDistributionModel::sc_charge_full_
std::vector< double > sc_charge_full_
Definition: ProtonDistributionModel.h:162
DefaultParamHandler.h
OpenMS::Residue::YIon
MS:1001220 peptide bond up to the C-terminus.
Definition: Residue.h:160
OpenMS::ProtonDistributionModel::FragmentationType
FragmentationType
the type of fragmentation
Definition: ProtonDistributionModel.h:95
int
OpenMS::ProtonDistributionModel::sc_charge_ion_c_term_
std::vector< double > sc_charge_ion_c_term_
Definition: ProtonDistributionModel.h:166
OpenMS::ProtonDistributionModel::bb_charge_ion_c_term_
std::vector< double > bb_charge_ion_c_term_
Definition: ProtonDistributionModel.h:167
OpenMS::ProtonDistributionModel::E_n_term_
double E_n_term_
Definition: ProtonDistributionModel.h:170
OpenMS::ProtonDistributionModel::ChargeRemote
Definition: ProtonDistributionModel.h:98
OpenMS::Residue::ResidueType
ResidueType
Definition: Residue.h:150
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ProtonDistributionModel::sc_charge_
std::vector< double > sc_charge_
Definition: ProtonDistributionModel.h:160