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| bool | add_b_ions_ |
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| bool | add_y_ions_ |
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| bool | add_a_ions_ |
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| bool | add_c_ions_ |
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| bool | add_x_ions_ |
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| bool | add_z_ions_ |
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| bool | add_zp1_ions_ |
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| bool | add_zp2_ions_ |
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| bool | add_first_prefix_ion_ |
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| bool | add_losses_ |
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| bool | add_metainfo_ |
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| bool | add_isotopes_ |
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| int | isotope_model_ |
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| bool | add_precursor_peaks_ |
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| bool | add_all_precursor_charges_ |
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| bool | add_abundant_immonium_ions_ |
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| bool | sort_by_position_ |
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| double | a_intensity_ |
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| double | b_intensity_ |
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| double | c_intensity_ |
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| double | x_intensity_ |
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| double | y_intensity_ |
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| double | z_intensity_ |
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| Int | max_isotope_ |
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| double | rel_loss_intensity_ |
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| double | max_isotope_probability_ |
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| double | pre_int_ |
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| double | pre_int_H2O_ |
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| double | pre_int_NH3_ |
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| virtual void | getSpectrum (PeakSpectrum &spec, const AASequence &peptide, Int min_charge, Int max_charge, Int precursor_charge=0) const |
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| void | updateMembers_ () override |
| | overwrite More...
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| static MSSpectrum | generateSpectrum (const Precursor::ActivationMethod &fm, const AASequence &seq, int precursor_charge) |
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| virtual void | addPeaks_ (PeakSpectrum &spectrum, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, MSSpectrum::Chunks &chunks, const Residue::ResidueType res_type, Int charge=1) const |
| | adds peaks to a spectrum of the given ion-type, peptide, charge, and intensity, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true More...
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| virtual void | addPrecursorPeaks_ (PeakSpectrum &spec, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, Int charge=1) const |
| | adds the precursor peaks to the spectrum, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true More...
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| void | addAbundantImmoniumIons_ (PeakSpectrum &spec, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges) const |
| | Adds the common, most abundant immonium ions to the theoretical spectra if the residue is contained in the peptide sequence, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true. More...
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| void | addIsotopeCluster_ (PeakSpectrum &spectrum, const AASequence &ion, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, const Residue::ResidueType res_type, Int charge, double intensity) const |
| | helper to add an isotope cluster to a spectrum, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true More...
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| void | addLosses_ (PeakSpectrum &spectrum, const AASequence &ion, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, double intensity, const Residue::ResidueType res_type, int charge) const |
| | helper to add full neutral loss ladders (for isotope clusters), also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true More...
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| void | addLossesFaster_ (PeakSpectrum &spectrum, double mz, const std::set< EmpiricalFormula > &f_losses, int ion_ordinal, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, const std::map< EmpiricalFormula, String > &formula_str_cache, double intensity, const Residue::ResidueType res_type, bool add_metainfo, int charge) const |
| | helper to add full neutral loss ladders (for single peaks), also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true More...
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Generates theoretical spectra for peptides with various options.
If the tool parameter add_metainfo is set to true, ion names like y8+ or [M-H2O+2H]++ are written as strings in a StringDataArray with the name corresponding to the constant Constants::UserParam::IonNames and charges are written as integers in an IntegerDataArray with the name "Charges" in the returned PeakSpectrum.
The getSpectrum function can be called with the same PeakSpectrum multiple times to add additional peaks. If the PeakSpectrum already has DataArrays, then the first StringDataArray and the first IntegerDataArray are extended. Therefore it is not recommended to add to or change the PeakSpectrum or these DataArrays between calls of the getSpectrum function with the same PeakSpectrum.
- Note
- The generation of neutral loss peaks is very slow in this class. Something similar to the neutral loss precalculation used in TheoreticalSpectrumGeneratorXLMS should be implemented here as well.
Parameters of this class are:
| Name | Type | Default | Restrictions | Description |
|---|
| isotope_model |
string | none |
none, coarse, fine | Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks. Note that adding isotopic peaks is very slow. |
| max_isotope |
int | 2 |
| Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse' |
| max_isotope_probability |
float | 0.05 |
| Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine' |
| add_metainfo |
string | false |
true, false | Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++ |
| add_losses |
string | false |
true, false | Adds common losses to those ion expect to have them, only water and ammonia loss is considered |
| sort_by_position |
string | true |
true, false | Sort output by position |
| add_precursor_peaks |
string | false |
true, false | Adds peaks of the unfragmented precursor ion to the spectrum |
| add_all_precursor_charges |
string | false |
true, false | Adds precursor peaks with all charges in the given range |
| add_abundant_immonium_ions |
string | false |
true, false | Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan) |
| add_first_prefix_ion |
string | false |
true, false | If set to true e.g. b1 ions are added |
| add_y_ions |
string | true |
true, false | Add peaks of y-ions to the spectrum |
| add_b_ions |
string | true |
true, false | Add peaks of b-ions to the spectrum |
| add_a_ions |
string | false |
true, false | Add peaks of a-ions to the spectrum |
| add_c_ions |
string | false |
true, false | Add peaks of c-ions to the spectrum |
| add_x_ions |
string | false |
true, false | Add peaks of x-ions to the spectrum |
| add_z_ions |
string | false |
true, false | Add peaks of z-ions to the spectrum (sometimes observed in CID and for some AAs in ExD due to H abstraction) |
| add_zp1_ions |
string | false |
true, false | Add peaks of z+1-radical cations (also [z+H]*^{+} or simply z*) to the spectrum (often observed in ExD) |
| add_zp2_ions |
string | false |
true, false | Add peaks of z+2-radical cations (also [z+2H]*^{2+} or simply z') to the spectrum (often observed in ExD esp. with higher precursor charges >3 and smaller z-ions.) |
| y_intensity |
float | 1.0 |
min: 0.0 | Intensity of the y-ions |
| b_intensity |
float | 1.0 |
min: 0.0 | Intensity of the b-ions |
| a_intensity |
float | 1.0 |
min: 0.0 | Intensity of the a-ions |
| c_intensity |
float | 1.0 |
min: 0.0 | Intensity of the c-ions |
| x_intensity |
float | 1.0 |
min: 0.0 | Intensity of the x-ions |
| z_intensity |
float | 1.0 |
min: 0.0 | Intensity of the z-ions |
| relative_loss_intensity |
float | 0.1 |
min: 0.0 max: 1.0 | Intensity of loss ions, in relation to the intact ion intensity |
| precursor_intensity |
float | 1.0 |
min: 0.0 | Intensity of the precursor peak |
| precursor_H2O_intensity |
float | 1.0 |
min: 0.0 | Intensity of the H2O loss peak of the precursor |
| precursor_NH3_intensity |
float | 1.0 |
min: 0.0 | Intensity of the NH3 loss peak of the precursor |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Public Member Functions inherited from DefaultParamHandler
1.9.1 
