Generates theoretical spectra for cross-linked peptides. More...

#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGeneratorXLMS.h>

Inheritance diagram for TheoreticalSpectrumGeneratorXLMS:

Public Member Functions
TheoreticalSpectrumGeneratorXLMS &	operator= (const TheoreticalSpectrumGeneratorXLMS &tsg)
	assignment operator More...

virtual void	getCommonIonSpectrum (PeakSpectrum &spectrum, AASequence peptide, Size link_pos, bool frag_alpha, int charge=1, Size link_pos_2=0) const
	Generates fragment ions not containing the cross-linker for one peptide. More...

virtual void	getXLinkIonSpectrum (PeakSpectrum &spectrum, AASequence peptide, Size link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, Size link_pos_2=0) const
	Generates fragment ions containing the cross-linker for one peptide. More...

void	updateMembers_ ()
	overwrite More...

Constructors and Destructors
	TheoreticalSpectrumGeneratorXLMS ()
	default constructor More...

	TheoreticalSpectrumGeneratorXLMS (const TheoreticalSpectrumGeneratorXLMS &source)
	copy constructor More...

virtual	~TheoreticalSpectrumGeneratorXLMS ()
	destructor 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...

Protected Member Functions
virtual void	addCommonPeaks_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, AASequence peptide, Size link_pos, bool frag_alpha, Residue::ResidueType res_type, int charge=1, Size link_pos_2=0) const
	Adds cross-link-less ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays. More...

virtual void	addXLinkIonPeaks_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, AASequence peptide, Size link_pos, double precursor_mass, bool frag_alpha, Residue::ResidueType res_type, int charge, Size link_pos_2=0) const
	Adds cross-linked ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays. More...

void	addPeak_ (PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double pos, double intensity, Residue::ResidueType res_type, Size ion_index, int charge, String ion_type) const
	Adds a single peak to a spectrum and its charge and ion name to the given DataArrays. More...

char	residueTypeToIonLetter_ (Residue::ResidueType res_type) const
	helper for mapping residue type to letter More...

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

Protected Attributes
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_

bool	add_precursor_peaks_

bool	add_abundant_immonium_ions_

bool	multiple_fragmentation_mode_

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	pre_int_

double	pre_int_H2O_

double	pre_int_NH3_

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 cross-linked peptides.

Constructor & Destructor Documentation

◆ TheoreticalSpectrumGeneratorXLMS() [1/2]

TheoreticalSpectrumGeneratorXLMS ( )

default constructor

◆ TheoreticalSpectrumGeneratorXLMS() [2/2]

TheoreticalSpectrumGeneratorXLMS ( const TheoreticalSpectrumGeneratorXLMS & source )

copy constructor

◆ ~TheoreticalSpectrumGeneratorXLMS()

virtual ~TheoreticalSpectrumGeneratorXLMS ( )

virtual

destructor

Member Function Documentation

◆ addCommonPeaks_()

virtual void addCommonPeaks_	(	PeakSpectrum &	spectrum,
		DataArrays::IntegerDataArray &	charges,
		DataArrays::StringDataArray &	ion_names,
		AASequence	peptide,
		Size	link_pos,
		bool	frag_alpha,
		Residue::ResidueType	res_type,
		int	charge = `1`,
		Size	link_pos_2 = `0`
	)		const

protectedvirtual

Adds cross-link-less ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
charges	A DataArray collecting the charges of the added peaks
ion_names	A DataArray collecting the ion names of the added peaks
peptide	The peptide to fragment
link_pos	The position of the cross-linker on the given peptide
frag_alpha	True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
res_type	The ion type of the added peaks
charge	The charge of the added peaks
link_pos_2	A second position for the linker, in case it is a loop link

◆ addPeak_()

void addPeak_	(	PeakSpectrum &	spectrum,
		DataArrays::IntegerDataArray &	charges,
		DataArrays::StringDataArray &	ion_names,
		double	pos,
		double	intensity,
		Residue::ResidueType	res_type,
		Size	ion_index,
		int	charge,
		String	ion_type
	)		const

protected

Adds a single peak to a spectrum and its charge and ion name to the given DataArrays.

The ion_type is a string in this form: "alpha|xi", the first word can be either "alpha" or "beta" and indicates the fragmented peptide, the two letters at the end are either "ci" or "xi" for common ion or cross-linked ion.

Parameters

spectrum	The spectrum to which the new peak is added
charges	A DataArray collecting the charges of the added peaks
ion_names	A DataArray collecting the ion names of the added peaks
pos
intensity
res_type	The ion type of the added peak
ion_index	The index of the ion (fragmentation position)
charge	The charge of the ion
ion_type	Another cross-linking specific ion-type

◆ addXLinkIonPeaks_()

virtual void addXLinkIonPeaks_	(	PeakSpectrum &	spectrum,
		DataArrays::IntegerDataArray &	charges,
		DataArrays::StringDataArray &	ion_names,
		AASequence	peptide,
		Size	link_pos,
		double	precursor_mass,
		bool	frag_alpha,
		Residue::ResidueType	res_type,
		int	charge,
		Size	link_pos_2 = `0`
	)		const

protectedvirtual

Adds cross-linked ions of a specific ion type and charge to a spectrum and adds ion name and charge annotations to the DataArrays.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
charges	A DataArray collecting the charges of the added peaks
ion_names	A DataArray collecting the ion names of the added peaks
peptide	The peptide to fragment
link_pos	The position of the cross-linker on the given peptide
precursor_mass	The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
frag_alpha	True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
res_type	The ion type of the added peaks
charge	The charge of the added peaks
link_pos_2	A second position for the linker, in case it is a loop link

◆ getCommonIonSpectrum()

virtual void getCommonIonSpectrum	(	PeakSpectrum &	spectrum,
		AASequence	peptide,
		Size	link_pos,
		bool	frag_alpha,
		int	charge = `1`,
		Size	link_pos_2 = `0`
	)		const

virtual

Generates fragment ions not containing the cross-linker for one peptide.

B-ions are generated from the beginning of the peptide up to the first linked position, y-ions are generated from the second linked position up the end of the peptide. If link_pos_2 is 0, a mono-link or cross-link is assumed and the second position is the same as the first position. For a loop-link two different positions can be set and link_pos_2 must be larger than link_pos. The generated ion types and other additional settings are determined by the tool parameters.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
peptide	The peptide to fragment
link_pos	The position of the cross-linker on the given peptide
frag_alpha	True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
charge	The maximal charge of the ions
link_pos_2	A second position for the linker, in case it is a loop link

Referenced by TOPPOpenPepXLLF::main_(), and TOPPOpenPepXL::main_().

◆ getXLinkIonSpectrum()

virtual void getXLinkIonSpectrum	(	PeakSpectrum &	spectrum,
		AASequence	peptide,
		Size	link_pos,
		double	precursor_mass,
		bool	frag_alpha,
		int	mincharge,
		int	maxcharge,
		Size	link_pos_2 = `0`
	)		const

virtual

Generates fragment ions containing the cross-linker for one peptide.

B-ions are generated from the first linked position up to the end of the peptide, y-ions are generated from the beginning of the peptide up to the second linked position. If link_pos_2 is 0, a mono-link or cross-link is assumed and the second position is the same as the first position. For a loop-link two different positions can be set and link_pos_2 must be larger than link_pos. Since in the case of a cross-link a whole second peptide is attached to the other side of the cross-link, a precursor mass for the two peptides and the linker is needed. In the case of a loop link the precursor mass is the mass of the only peptide and the linker. The generated ion types and other additional settings are determined by the tool parameters.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
peptide	The peptide to fragment
link_pos	The position of the cross-linker on the given peptide
precursor_mass	The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
frag_alpha	True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
mincharge	The minimal charge of the ions
maxcharge	The maximal charge of the ions
link_pos_2	A second position for the linker, in case it is a loop link

Referenced by TOPPOpenPepXLLF::main_(), and TOPPOpenPepXL::main_().

◆ operator=()

TheoreticalSpectrumGeneratorXLMS& operator= ( const TheoreticalSpectrumGeneratorXLMS & tsg )

assignment operator

◆ residueTypeToIonLetter_()

char residueTypeToIonLetter_ ( Residue::ResidueType res_type ) const

protected

helper for mapping residue type to letter

◆ updateMembers_()

void updateMembers_ ( )

virtual

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_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

◆ max_isotope_

Int max_isotope_

protected

◆ multiple_fragmentation_mode_

bool multiple_fragmentation_mode_

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

◆ x_intensity_

double x_intensity_

protected

◆ y_intensity_

double y_intensity_

protected

◆ z_intensity_

double z_intensity_

protected

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TheoreticalSpectrumGeneratorXLMS() [1/2]

◆ TheoreticalSpectrumGeneratorXLMS() [2/2]

◆ ~TheoreticalSpectrumGeneratorXLMS()

Member Function Documentation

◆ addCommonPeaks_()

◆ addPeak_()

◆ addXLinkIonPeaks_()

◆ getCommonIonSpectrum()

◆ getXLinkIonSpectrum()

◆ operator=()

◆ residueTypeToIonLetter_()

◆ updateMembers_()

Member Data Documentation

◆ a_intensity_

◆ add_a_ions_

◆ add_abundant_immonium_ions_

◆ 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_

◆ max_isotope_

◆ multiple_fragmentation_mode_

◆ pre_int_

◆ pre_int_H2O_

◆ pre_int_NH3_

◆ rel_loss_intensity_

◆ x_intensity_

◆ y_intensity_

◆ z_intensity_