Simulates MS2 spectra with support vector machines. More...

#include <OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGenerator.h>

Inheritance diagram for SvmTheoreticalSpectrumGenerator:

Collaboration diagram for SvmTheoreticalSpectrumGenerator:

Classes
struct	DescriptorSet
	A set of descriptors for a single training row. More...

struct	IonType
	nested class More...

struct	SvmModelParameterSet
	Simple container storing the model parameters required for simulation. More...

Friends
class	SvmTheoreticalSpectrumGeneratorTrainer

Constructors and Destructors
typedef std::map< IonType, double >	IntensityMap

Size	precursor_charge_
	charge of the precursors used for training More...

SvmModelParameterSet	mp_
	set of model parameters read from model file More...

std::map< IonType, bool >	hide_type_
	whether ion types are hidden or not More...

static std::map< String, Size >	aa_to_index_
	map AA to integers More...

static std::map< String, double >	hydrophobicity_
	hydrophobicity values for each AA More...

static std::map< String, double >	helicity_
	helicity values for each AA More...

static std::map< String, double >	basicity_
	basicity values for each AA More...

static bool	initializedMaps_
	flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized More...

	SvmTheoreticalSpectrumGenerator ()
	Default constructor. More...

	SvmTheoreticalSpectrumGenerator (const SvmTheoreticalSpectrumGenerator &source)
	Copy constructor. More...

SvmTheoreticalSpectrumGenerator &	operator= (const SvmTheoreticalSpectrumGenerator &tsg)
	Assignment operator. More...

	~SvmTheoreticalSpectrumGenerator () override
	Destructor. More...

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...

void	load ()
	Load a trained Svm and Prob. models. More...

const std::vector< IonType > &	getIonTypes () const
	return the set of ion types that are modeled by the loaded SVMs More...

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...

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...

Size	generateDescriptorSet_ (const AASequence &peptide, Size position, const IonType &type, Size precursor_charge, DescriptorSet &desc_set)
	generate the descriptors for an input peptide and a given fragmentation position More...

String	ResidueTypeToString_ (Residue::ResidueType type)
	Returns the ResidueType (e.g. AIon, BIon) as string for peak annotation. More...

void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

static void	initializeMaps_ ()
	initialized the maps More...

Additional Inherited Members
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...

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...

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

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	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.

Class Documentation

◆ OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet

struct OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet

A set of descriptors for a single training row.

Collaboration diagram for SvmTheoreticalSpectrumGenerator::DescriptorSet:

[legend]

Class Members
typedef vector< svm_node >	DescriptorSetType

Class Members
DescriptorSetType	descriptors

◆ OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet

struct OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet

Simple container storing the model parameters required for simulation.

Collaboration diagram for SvmTheoreticalSpectrumGenerator::SvmModelParameterSet:

[legend]

Class Members
vector< shared_ptr< SVMWrapper > >	class_models
map< pair< IonType, Size >, vector< vector< double > > >	conditional_prob
vector< double >	feature_max
vector< double >	feature_min
vector< double >	intensity_bin_boarders
vector< double >	intensity_bin_values
vector< IonType >	ion_types
Size	number_intensity_levels
Size	number_regions
vector< shared_ptr< SVMWrapper > >	reg_models
double	scaling_lower
double	scaling_upper
map< IonType, vector< IonType > >	secondary_types
map< ResidueType, double >	static_intensities

Member Typedef Documentation

◆ IntensityMap

typedef std::map<IonType, double> IntensityMap

protected

Constructor & Destructor Documentation

◆ SvmTheoreticalSpectrumGenerator() [1/2]

SvmTheoreticalSpectrumGenerator ( )

Default constructor.

◆ SvmTheoreticalSpectrumGenerator() [2/2]

SvmTheoreticalSpectrumGenerator ( const SvmTheoreticalSpectrumGenerator & source )

Copy constructor.

◆ ~SvmTheoreticalSpectrumGenerator()

~SvmTheoreticalSpectrumGenerator ( )

override

Destructor.

Member Function Documentation

◆ generateDescriptorSet_()

Size generateDescriptorSet_	(	const AASequence &	peptide,
		Size	position,
		const IonType &	type,
		Size	precursor_charge,
		DescriptorSet &	desc_set
	)

protected

generate the descriptors for an input peptide and a given fragmentation position

◆ getIonTypes()

const std::vector<IonType>& getIonTypes ( ) const

inline

return the set of ion types that are modeled by the loaded SVMs

◆ initializeMaps_()

static void initializeMaps_ ( )

staticprotected

initialized the maps

◆ load()

void load ( )

Load a trained Svm and Prob. models.

◆ operator=()

SvmTheoreticalSpectrumGenerator& operator= ( const SvmTheoreticalSpectrumGenerator & tsg )

Assignment operator.

◆ ResidueTypeToString_()

String ResidueTypeToString_ ( Residue::ResidueType type )

protected

Returns the ResidueType (e.g. AIon, BIon) as string for peak annotation.

◆ scaleDescriptorSet_()

void scaleDescriptorSet_	(	DescriptorSet &	desc,
		double	lower,
		double	upper
	)

protected

scale value to the interval [lower,max] given the maximal and minimal entries for a feature

◆ scaleSingleFeature_()

void scaleSingleFeature_	(	double &	value,
		double	feature_min,
		double	feature_max,
		double	lower = `-1.0`,
		double	upper = `1.0`
	)

inlineprotected

scale value to the interval [lower,max] given the maximal and minimal entries for a feature

◆ simulate()

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.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Friends And Related Function Documentation

◆ SvmTheoreticalSpectrumGeneratorTrainer

friend class SvmTheoreticalSpectrumGeneratorTrainer

friend

Member Data Documentation

◆ aa_to_index_

std::map<String, Size> aa_to_index_

staticprotected

map AA to integers

◆ basicity_

std::map<String, double> basicity_

staticprotected

basicity values for each AA

◆ helicity_

std::map<String, double> helicity_

staticprotected

helicity values for each AA

◆ hide_type_

std::map<IonType, bool> hide_type_

protected

whether ion types are hidden or not

◆ hydrophobicity_

std::map<String, double> hydrophobicity_

staticprotected

hydrophobicity values for each AA

◆ initializedMaps_

bool initializedMaps_

staticprotected

flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized

◆ mp_

SvmModelParameterSet mp_

protected

set of model parameters read from model file

◆ precursor_charge_

Size precursor_charge_

protected

charge of the precursors used for training

Classes

Friends

Constructors and Destructors

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet

◆ OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet

Member Typedef Documentation

◆ IntensityMap

Constructor & Destructor Documentation

◆ SvmTheoreticalSpectrumGenerator() [1/2]

◆ SvmTheoreticalSpectrumGenerator() [2/2]

◆ ~SvmTheoreticalSpectrumGenerator()

Member Function Documentation

◆ generateDescriptorSet_()

◆ getIonTypes()

◆ initializeMaps_()

◆ load()

◆ operator=()

◆ ResidueTypeToString_()

◆ scaleDescriptorSet_()

◆ scaleSingleFeature_()

◆ simulate()

◆ updateMembers_()

Friends And Related Function Documentation

◆ SvmTheoreticalSpectrumGeneratorTrainer

Member Data Documentation

◆ aa_to_index_

◆ basicity_

◆ helicity_

◆ hide_type_

◆ hydrophobicity_

◆ initializedMaps_

◆ mp_

◆ precursor_charge_