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OpenMS
2.8.0
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Generates theoretical spectra for peptides with various options. More...
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
Public Member Functions | |
Constructors and Destructors | |
TheoreticalSpectrumGenerator () | |
default constructor More... | |
TheoreticalSpectrumGenerator (const TheoreticalSpectrumGenerator &source) | |
copy constructor More... | |
~TheoreticalSpectrumGenerator () override | |
destructor More... | |
TheoreticalSpectrumGenerator & | operator= (const TheoreticalSpectrumGenerator &tsg) |
assignment operator More... | |
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DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
Acessors | |
bool | add_b_ions_ |
bool | add_y_ions_ |
bool | add_a_ions_ |
bool | add_c_ions_ |
bool | add_x_ions_ |
bool | add_z_ions_ |
bool | add_first_prefix_ion_ |
bool | add_losses_ |
bool | add_metainfo_ |
bool | add_isotopes_ |
int | isotope_model_ |
bool | add_precursor_peaks_ |
bool | add_all_precursor_charges_ |
bool | add_abundant_immonium_ions_ |
bool | sort_by_position_ |
double | a_intensity_ |
double | b_intensity_ |
double | c_intensity_ |
double | x_intensity_ |
double | y_intensity_ |
double | z_intensity_ |
Int | max_isotope_ |
double | rel_loss_intensity_ |
double | max_isotope_probability_ |
double | pre_int_ |
double | pre_int_H2O_ |
double | pre_int_NH3_ |
virtual void | getSpectrum (PeakSpectrum &spec, const AASequence &peptide, Int min_charge, Int max_charge, Int precursor_charge=0) const |
void | updateMembers_ () override |
overwrite More... | |
static MSSpectrum | generateSpectrum (const Precursor::ActivationMethod &fm, const AASequence &seq, int precursor_charge) |
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... | |
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... | |
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... | |
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... | |
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... | |
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... | |
static char | residueTypeToIonLetter_ (const Residue::ResidueType res_type) |
helper for mapping residue type to letter More... | |
Additional Inherited Members | |
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static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") |
Writes all parameters to meta values. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
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Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
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 "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.
Name | Type | Default | Restrictions | Description |
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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 |
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 |
default constructor
TheoreticalSpectrumGenerator | ( | const TheoreticalSpectrumGenerator & | source | ) |
copy constructor
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override |
destructor
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protected |
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.
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protected |
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
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protected |
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
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protected |
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
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protectedvirtual |
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
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protectedvirtual |
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
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static |
Generates a spectrum for a peptide sequence based on activation method and precursor charge. Activation method 'CID' or 'HCID' will generate only b- and y-ions. Activation method 'ECD' or 'ETD' will generate only c- and z-ions. If precursor charge is greater than 2 ions with charge 1 & 2 will be generated, else only ions of charge 1 will appear in the spectrum.
Exception::InvalidParameter | If fragmentation method is anything else than 'CID', 'HCID', 'ECD' or 'ETD'. |
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Generates a spectrum for a peptide sequence, with the ion types that are set in the tool parameters If precursor_charge is set to 0 max_charge + 1 will be used.
Exception::InvalidParameter | if precursor_charge < max_charge |
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
TheoreticalSpectrumGenerator& operator= | ( | const TheoreticalSpectrumGenerator & | tsg | ) |
assignment operator
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staticprotected |
helper for mapping residue type to letter
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overridevirtual |
overwrite
Reimplemented from DefaultParamHandler.
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