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ProtonDistributionModel.h
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34 
35 
36 #ifndef OPENMS_ANALYSIS_ID_PROTONDISTRIBUTIONMODEL_H
37 #define OPENMS_ANALYSIS_ID_PROTONDISTRIBUTIONMODEL_H
38 
39 #include <OpenMS/CONCEPT/Types.h>
42 #include <vector>
43 
44 namespace OpenMS
45 {
46  class AASequence;
47 
71  class OPENMS_DLLAPI ProtonDistributionModel :
72  public DefaultParamHandler
73  {
74 public:
75 
81 
84 
86  virtual ~ProtonDistributionModel();
88 
90  ProtonDistributionModel & operator=(const ProtonDistributionModel & pdm);
91 
97  {
98  ChargeDirected = 0,
100  SideChain
101  };
103 
112  void getProtonDistribution(std::vector<double> & bb_charges, std::vector<double> & sc_charges, const AASequence & peptide, Int charge, Residue::ResidueType res_type = Residue::YIon);
113 
125  //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);
126 
127 
128  void getChargeStateIntensities(const AASequence & peptide, const AASequence & n_term_ion, const AASequence & c_term_ion, Int charge, Residue::ResidueType n_term_type,
129  std::vector<double> & n_term_intensities, std::vector<double> & c_term_intensities, FragmentationType type);
130 
132  void setPeptideProtonDistribution(const std::vector<double> & bb_charge, const std::vector<double> & sc_charge);
133 
134 protected:
135 
136  // calculates the proton distribution
137  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);
138 
139  void calculateProtonDistributionCharge1_(const AASequence & peptide, Residue::ResidueType res_type);
140  void calculateProtonDistributionCharge2_(const AASequence & peptide, Residue::ResidueType res_type, bool fixed_proton, Size cleavage_site, bool use_most_basic_site);
141  void calculateProtonDistributionGreater2_(const AASequence & peptide, Int charge, Residue::ResidueType res_type);
142 
143  void calculateProtonDistributionIonPair_(const AASequence & peptide, Residue::ResidueType type, Size cleavage_site);
144 
145  // returns the proton affinity of the peptide with the given charge and ion type
146  //double getProtonAffinity_(const AASequence& ion, Int charge, Residue::ResidueType res_type);
147 
148  // returns the (relative) Intensities of the possible charge states of the ion from peptide
149  //std::vector<double> getChargeStateIntensities_(const AASequence& peptide, const AASequence& ion, Int charge, Residue::ResidueType res_type);
150 
151 
152  void calcChargeStateIntensities_(const AASequence & peptide, const AASequence & n_term_ion, const AASequence & c_term_ion, Int charge,
153  Residue::ResidueType n_term_type, std::vector<double> & n_term_intensities, std::vector<double> & c_term_intensities, FragmentationType type);
154 
155  // calculates the intensities of the different possible charge states
156  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);
157 
158  // returns the left and right GB values, NH2 and COOH if at terminus
159  void getLeftAndRightGBValues_(const AASequence & peptide, double & left_gb, double & right_gb, Size position);
160 
161  std::vector<double> sc_charge_;
162  std::vector<double> bb_charge_;
163  std::vector<double> sc_charge_full_;
164  std::vector<double> bb_charge_full_;
165  std::vector<double> sc_charge_ion_n_term_;
166  std::vector<double> bb_charge_ion_n_term_;
167  std::vector<double> sc_charge_ion_c_term_;
168  std::vector<double> bb_charge_ion_c_term_;
169  double E_;
170  double E_c_term_;
171  double E_n_term_;
172 
173  };
174 }
175 #endif // OPENMS_ANALYSIS_ID_PROTONDISTRIBUTIONMODEL_H
Definition: Residue.h:154
std::vector< double > bb_charge_full_
Definition: ProtonDistributionModel.h:164
std::vector< double > sc_charge_
Definition: ProtonDistributionModel.h:161
std::vector< double > sc_charge_ion_n_term_
Definition: ProtonDistributionModel.h:165
A proton distribution model to calculate the proton distribution over charged peptides.
Definition: ProtonDistributionModel.h:71
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< double > sc_charge_full_
Definition: ProtonDistributionModel.h:163
std::vector< double > sc_charge_ion_c_term_
Definition: ProtonDistributionModel.h:167
std::vector< double > bb_charge_ion_n_term_
Definition: ProtonDistributionModel.h:166
Definition: ProtonDistributionModel.h:99
FragmentationType
the type of fragmentation
Definition: ProtonDistributionModel.h:96
double E_c_term_
Definition: ProtonDistributionModel.h:170
double E_n_term_
Definition: ProtonDistributionModel.h:171
ResidueType
Definition: Residue.h:144
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
std::vector< double > bb_charge_ion_c_term_
Definition: ProtonDistributionModel.h:168
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
int Int
Signed integer type.
Definition: Types.h:103
double E_
Definition: ProtonDistributionModel.h:169
std::vector< double > bb_charge_
Definition: ProtonDistributionModel.h:162

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13