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typedef std::map< IonType, double > | IntensityMap |
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Size | precursor_charge_ |
| charge of the precursors used for training More...
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SvmModelParameterSet | mp_ |
| set of model parameters read from model file More...
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std::map< IonType, bool > | hide_type_ |
| whether ion types are hidden or not More...
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static std::map< String, Size > | aa_to_index_ |
| map AA to integers More...
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static std::map< String, double > | hydrophobicity_ |
| hydrophobicity values for each AA More...
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static std::map< String, double > | helicity_ |
| helicity values for each AA More...
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static std::map< String, double > | basicity_ |
| basicity values for each AA More...
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static bool | initializedMaps_ |
| flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized More...
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| SvmTheoreticalSpectrumGenerator () |
| Default constructor. More...
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| SvmTheoreticalSpectrumGenerator (const SvmTheoreticalSpectrumGenerator &source) |
| Copy constructor. More...
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SvmTheoreticalSpectrumGenerator & | operator= (const SvmTheoreticalSpectrumGenerator &tsg) |
| Assignment operator. More...
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| ~SvmTheoreticalSpectrumGenerator () override |
| Destructor. More...
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void | simulate (PeakSpectrum &spectrum, const AASequence &peptide, boost::random::mt19937_64 &rng, Size precursor_charge) |
| Generate the MS/MS according to the given probabilistic model. More...
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void | load () |
| Load a trained Svm and Prob. models. More...
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const std::vector< IonType > & | getIonTypes () |
| return the set of ion types that are modeled by the loaded SVMs More...
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void | scaleSingleFeature_ (double &value, double feature_min, double feature_max, double lower=-1.0, double upper=1.0) |
| scale value to the interval [lower,max] given the maximal and minimal entries for a feature More...
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void | scaleDescriptorSet_ (DescriptorSet &desc, double lower, double upper) |
| scale value to the interval [lower,max] given the maximal and minimal entries for a feature More...
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Size | generateDescriptorSet_ (AASequence peptide, Size position, IonType type, Size precursor_charge, DescriptorSet &desc_set) |
| generate the descriptors for an input peptide and a given fragmentation position More...
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String | ResidueTypeToString_ (Residue::ResidueType type) |
| Returns the ResidueType (e.g. AIon, BIon) as string for peak annotation. More...
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void | updateMembers_ () override |
| This method is used to update extra member variables at the end of the setParameters() method. More...
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static void | initializeMaps_ () |
| initialized the maps More...
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Simulates MS2 spectra with support vector machines.
The models are generated with the SvmTheoreticalSpectrumGeneratorTrainer.
Two modes are supported:
- Only a prediction of abundant/missing is performed and for abundant peaks are generated with user defined intensity.
- The intensity is predicted using SVM-regression (only for the primary ion types b and y). For the secondary types a Bayesian model is used.
Currently, only a test model is shipped with OpenMS.
Please find trained models at: http://sourceforge.net/projects/open-ms/files/Supplementary/Simulation/.
Parameters of this class are:
Name | Type | Default | Restrictions | Description |
svm_mode |
int | 1 |
| whether to predict abundant/missing using SVC (0) or predict intensities using SVR (1) |
model_file_name |
string | examples/simulation/SvmMSim.model |
| Name of the probabilistic Model file |
add_isotopes |
string | false |
true, false | If set to 1 isotope peaks of the product ion peaks are added |
max_isotope |
int | 2 |
| Defines the maximal isotopic peak which is added, add_isotopes must be set to 1 |
add_metainfo |
string | false |
true, false | Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++ |
add_first_prefix_ion |
string | false |
true, false | If set to true e.g. b1 ions are added |
hide_y_ions |
string | false |
true, false | Add peaks of y-ions to the spectrum |
hide_y2_ions |
string | false |
true, false | Add peaks of y-ions to the spectrum |
hide_b_ions |
string | false |
true, false | Add peaks of b-ions to the spectrum |
hide_b2_ions |
string | false |
true, false | Add peaks of b-ions to the spectrum |
hide_a_ions |
string | false |
true, false | Add peaks of a-ions to the spectrum |
hide_c_ions |
string | false |
true, false | Add peaks of c-ions to the spectrum |
hide_x_ions |
string | false |
true, false | Add peaks of x-ions to the spectrum |
hide_z_ions |
string | false |
true, false | Add peaks of z-ions to the spectrum |
hide_losses |
string | false |
true, false | Adds common losses to those ion expect to have them, only water and ammonia loss is considered |
y_intensity |
float | 1.0 |
| Intensity of the y-ions |
b_intensity |
float | 1.0 |
| Intensity of the b-ions |
a_intensity |
float | 1.0 |
| Intensity of the a-ions |
c_intensity |
float | 1.0 |
| Intensity of the c-ions |
x_intensity |
float | 1.0 |
| Intensity of the x-ions |
z_intensity |
float | 1.0 |
| Intensity of the z-ions |
relative_loss_intensity |
float | 0.1 |
| Intensity of loss ions, in relation to the intact ion intensity |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.