Generates theoretical spectra for peptides with various options. More...

#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>

Inheritance diagram for TheoreticalSpectrumGenerator:

Collaboration diagram for TheoreticalSpectrumGenerator:

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...

Public Member Functions inherited from DefaultParamHandler
	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 &param)
	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
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes inherited from DefaultParamHandler
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...

Detailed Description

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.

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
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.

Constructor & Destructor Documentation

◆ TheoreticalSpectrumGenerator() [1/2]

TheoreticalSpectrumGenerator ( )

default constructor

◆ TheoreticalSpectrumGenerator() [2/2]

TheoreticalSpectrumGenerator ( const TheoreticalSpectrumGenerator & source )

copy constructor

◆ ~TheoreticalSpectrumGenerator()

~TheoreticalSpectrumGenerator ( )

override

destructor

Member Function Documentation

◆ addAbundantImmoniumIons_()

void addAbundantImmoniumIons_	(	PeakSpectrum &	spec,
		const AASequence &	peptide,
		DataArrays::StringDataArray &	ion_names,
		DataArrays::IntegerDataArray &	charges
	)		const

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.

◆ addIsotopeCluster_()

void addIsotopeCluster_	(	PeakSpectrum &	spectrum,
		const AASequence &	ion,
		DataArrays::StringDataArray &	ion_names,
		DataArrays::IntegerDataArray &	charges,
		const Residue::ResidueType	res_type,
		Int	charge,
		double	intensity
	)		const

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

◆ addLosses_()

void addLosses_	(	PeakSpectrum &	spectrum,
		const AASequence &	ion,
		DataArrays::StringDataArray &	ion_names,
		DataArrays::IntegerDataArray &	charges,
		double	intensity,
		const Residue::ResidueType	res_type,
		int	charge
	)		const

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

◆ addLossesFaster_()

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

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

◆ addPeaks_()

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

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

◆ addPrecursorPeaks_()

virtual void addPrecursorPeaks_	(	PeakSpectrum &	spec,
		const AASequence &	peptide,
		DataArrays::StringDataArray &	ion_names,
		DataArrays::IntegerDataArray &	charges,
		Int	charge = `1`
	)		const

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

◆ generateSpectrum()

static MSSpectrum generateSpectrum	(	const Precursor::ActivationMethod &	fm,
		const AASequence &	seq,
		int	precursor_charge
	)

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.

Exceptions

Exception::InvalidParameter If fragmentation method is anything else than 'CID', 'HCID', 'ECD' or 'ETD'.

◆ getSpectrum()

virtual void getSpectrum	(	PeakSpectrum &	spec,
		const AASequence &	peptide,
		Int	min_charge,
		Int	max_charge,
		Int	precursor_charge = `0`
	)		const

virtual

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.

Exceptions

Exception::InvalidParameter if precursor_charge < max_charge

Referenced by TOPPViewBase::showSpectrumGenerationDialog().

◆ operator=()

TheoreticalSpectrumGenerator& operator= ( const TheoreticalSpectrumGenerator & tsg )

assignment operator

◆ residueTypeToIonLetter_()

static char residueTypeToIonLetter_ ( const Residue::ResidueType res_type )

staticprotected

helper for mapping residue type to letter

◆ updateMembers_()

void updateMembers_ ( )

overridevirtual

overwrite

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ a_intensity_

double a_intensity_

protected

◆ add_a_ions_

bool add_a_ions_

protected

◆ add_abundant_immonium_ions_

bool add_abundant_immonium_ions_

protected

◆ add_all_precursor_charges_

bool add_all_precursor_charges_

protected

◆ add_b_ions_

bool add_b_ions_

protected

◆ add_c_ions_

bool add_c_ions_

protected

◆ add_first_prefix_ion_

bool add_first_prefix_ion_

protected

◆ add_isotopes_

bool add_isotopes_

protected

◆ add_losses_

bool add_losses_

protected

◆ add_metainfo_

bool add_metainfo_

protected

◆ add_precursor_peaks_

bool add_precursor_peaks_

protected

◆ add_x_ions_

bool add_x_ions_

protected

◆ add_y_ions_

bool add_y_ions_

protected

◆ add_z_ions_

bool add_z_ions_

protected

◆ b_intensity_

double b_intensity_

protected

◆ c_intensity_

double c_intensity_

protected

◆ isotope_model_

int isotope_model_

protected

◆ max_isotope_

Int max_isotope_

protected

◆ max_isotope_probability_

double max_isotope_probability_

protected

◆ pre_int_

double pre_int_

protected

◆ pre_int_H2O_

double pre_int_H2O_

protected

◆ pre_int_NH3_

double pre_int_NH3_

protected

◆ rel_loss_intensity_

double rel_loss_intensity_

protected

◆ sort_by_position_

bool sort_by_position_

protected

◆ x_intensity_

double x_intensity_

protected

◆ y_intensity_

double y_intensity_

protected

◆ z_intensity_

double z_intensity_

protected

Public Member Functions

Acessors

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TheoreticalSpectrumGenerator() [1/2]

◆ TheoreticalSpectrumGenerator() [2/2]

◆ ~TheoreticalSpectrumGenerator()

Member Function Documentation

◆ addAbundantImmoniumIons_()

◆ addIsotopeCluster_()

◆ addLosses_()

◆ addLossesFaster_()

◆ addPeaks_()

◆ addPrecursorPeaks_()

◆ generateSpectrum()

◆ getSpectrum()

◆ operator=()

◆ residueTypeToIonLetter_()

◆ updateMembers_()

Member Data Documentation

◆ a_intensity_

◆ add_a_ions_

◆ add_abundant_immonium_ions_

◆ add_all_precursor_charges_

◆ add_b_ions_

◆ add_c_ions_

◆ add_first_prefix_ion_

◆ add_isotopes_

◆ add_losses_

◆ add_metainfo_

◆ add_precursor_peaks_

◆ add_x_ions_

◆ add_y_ions_

◆ add_z_ions_

◆ b_intensity_

◆ c_intensity_

◆ isotope_model_

◆ max_isotope_

◆ max_isotope_probability_

◆ pre_int_

◆ pre_int_H2O_

◆ pre_int_NH3_

◆ rel_loss_intensity_

◆ sort_by_position_

◆ x_intensity_

◆ y_intensity_

◆ z_intensity_