OpenMS  3.0.0
IonizationSimulation.h
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31 // $Maintainer: Chris Bielow$
32 // $Authors: Stephan Aiche, Chris Bielow$
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34 
35 #pragma once
36 
42 
43 // STL includes
44 #include <set>
45 
46 namespace OpenMS
47 {
48 
63  class OPENMS_DLLAPI IonizationSimulation :
64  public DefaultParamHandler,
65  public ProgressLogger
66  {
67 
68 public:
70  typedef enum
71  {
73  ESI
74  } IonizationType;
75 
78 
84 
87 
89  ~IonizationSimulation() override;
91 
93  IonizationSimulation& operator=(const IonizationSimulation& source);
94 
105  void ionize(SimTypes::FeatureMapSim& features, ConsensusMap& charge_consensus, SimTypes::MSSimExperiment& experiment);
106 
107 private:
108  class CompareCmpByEF_;
109 
111  void ionizeEsi_(SimTypes::FeatureMapSim&, ConsensusMap& charge_consensus);
112 
114  void ionizeMaldi_(SimTypes::FeatureMapSim&, ConsensusMap& charge_consensus);
115 
117  inline bool isFeatureValid_(const Feature& feature) const;
118 
120  void setFeatureProperties_(Feature& f,
121  const double& adduct_mass,
122  const String& adduct_formula,
123  const SimTypes::SimChargeType charge,
124  const SimTypes::SimIntensityType new_intensity,
125  const Size parent_index);
126 
128  void setDefaultParams_();
129 
131  void updateMembers_() override;
132 
138  UInt countIonizedResidues_(const AASequence&) const;
139 
140 
141  // Members //
142 
145 
146  /*
147  @brief List of residues that are counted as basic during execution of countBasicResidues_
148 */
149  std::set<String> basic_residues_;
150 
155 
159  std::vector<double> esi_impurity_probabilities_;
160 
161 
166 
171 
175  std::vector<double> maldi_probabilities_;
176 
181 
182 protected:
185  };
186 
187 }
188 
189 
DefaultParamHandler.h
SimTypes.h
OpenMS::IonizationSimulation::ionization_type_
IonizationType ionization_type_
ESI or MALDI ionization.
Definition: IonizationSimulation.h:144
OpenMS::Adduct::AdductsType
std::vector< Adduct > AdductsType
Definition: Adduct.h:48
double
OpenMS::IonizationSimulation::maldi_probabilities_
std::vector< double > maldi_probabilities_
Preprocessed table of discrete distribution (MALDI charges)
Definition: IonizationSimulation.h:175
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IonizationSimulation::max_adduct_charge_
Size max_adduct_charge_
Maximal charge that any impure adduct from parameter list has.
Definition: IonizationSimulation.h:170
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IonizationSimulation::maximal_mz_measurement_limit_
SimTypes::SimCoordinateType maximal_mz_measurement_limit_
Maximum m/z detected by mass analyser.
Definition: IonizationSimulation.h:178
OpenMS::SimTypes::MutableSimRandomNumberGeneratorPtr
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::IonizationSimulation::minimal_mz_measurement_limit_
SimTypes::SimCoordinateType minimal_mz_measurement_limit_
Minimum m/z detected by mass analyser.
Definition: IonizationSimulation.h:180
OpenMS::IonizationSimulation::esi_probability_
double esi_probability_
Probability for the binomial distribution of ESI charge states.
Definition: IonizationSimulation.h:154
OpenMS::IonizationSimulation::basic_residues_
std::set< String > basic_residues_
Definition: IonizationSimulation.h:149
OpenMS::IonizationSimulation
Simulates Protein ionization.
Definition: IonizationSimulation.h:63
OpenMS::IonizationSimulation::rnd_gen_
SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_
Random number generator.
Definition: IonizationSimulation.h:184
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::SimTypes::SimChargeType
Feature::ChargeType SimChargeType
Charge of a peptide.
Definition: SimTypes.h:65
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
float
OpenMS::IonizationSimulation::MALDI
Definition: IonizationSimulation.h:72
Adduct.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::IonizationSimulation::esi_impurity_probabilities_
std::vector< double > esi_impurity_probabilities_
Discrete distribution of impure charge adducts like Na+, K+, Ca++ etc besides the usual H+.
Definition: IonizationSimulation.h:159
OpenMS::IonizationSimulation::esi_adducts_
Adduct::AdductsType esi_adducts_
Corresponding table to esi_impurity_probabilities_ holding the actual element and its charge.
Definition: IonizationSimulation.h:165
OpenMS::IonizationSimulation::IonizationType
IonizationType
possible ionization methods
Definition: IonizationSimulation.h:70