Simulates/Predicts retention times for peptides or peptide separation. More...

#include <OpenMS/SIMULATION/RTSimulation.h>

Inheritance diagram for RTSimulation:

Public Member Functions
RTSimulation &	operator= (const RTSimulation &source)
	Assignment operator. More...

void	predictRT (SimTypes::FeatureMapSim &features)
	Predict retention times for given peptide features based for HPLC or CE. More...

void	predictContaminantsRT (SimTypes::FeatureMapSim &)
	Set retention times randomly for given contaminants. More...

bool	isRTColumnOn () const
	Returns true if a RT column was simulated. More...

void	wrapSVM (std::vector< AASequence > &peptide_sequences, std::vector< double > &predicted_retention_times)
	Wrapper for the SVM RT Prediction (HPLC) using AASequences. More...

SimTypes::SimCoordinateType	getGradientTime () const

void	createExperiment (SimTypes::MSSimExperiment &experiment)
	Size experiment and assign retention time grid. More...

Constructors and Destructors
	RTSimulation ()
	Default constructor. More...

	RTSimulation (SimTypes::MutableSimRandomNumberGeneratorPtr random_generator)
	Constructor taking a random generator. More...

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

	~RTSimulation () override
	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
void	updateMembers_ () override
	Synchronize members with param class. More...

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

Protected Attributes
SimTypes::MutableSimRandomNumberGeneratorPtr	rnd_gen_
	Random number generator. 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...

Private Member Functions
void	setDefaultParams_ ()
	Set default parameters. More...

void	noRTColumn_ (SimTypes::FeatureMapSim &)
	Simply set all retention times to -1. More...

void	smoothRTDistortion_ (SimTypes::MSSimExperiment &experiment)
	smoothes the simulated distortion for the elution profiles with a moving average filter of size 3 More...

void	calculateMT_ (SimTypes::FeatureMapSim &features, std::vector< double > &predicted_retention_times)

void	getChargeContribution_ (Map< String, double > &q_cterm, Map< String, double > &q_nterm, Map< String, double > &q_aa_basic, Map< String, double > &q_aa_acidic)

Private Attributes
OpenMS::String	rt_model_file_

SimTypes::SimCoordinateType	total_gradient_time_
	Total gradient time. More...

SimTypes::SimCoordinateType	gradient_min_
	gradient ranges More...

SimTypes::SimCoordinateType	gradient_max_
	Maximal observed gradient time. More...

SimTypes::SimCoordinateType	rt_sampling_rate_
	bin size in rt dimension More...

double	egh_tau_location_
	EGH tau value. More...

double	egh_tau_scale_
	EGH tau scale parameter of the lorentzian variation. More...

double	egh_variance_location_
	EGH sigma value. More...

double	egh_variance_scale_
	EGH sigma scale parameter of the lorentzian variation. More...

Detailed Description

Simulates/Predicts retention times for peptides or peptide separation.

The retention times for the different peptides are determined based on a SVM model or are all set to -1 in case of simulations without a HPLC column.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
rt_column	string	HPLC	none, HPLC, CE	Modelling of an RT or CE column
auto_scale	string	true	true, false	Scale predicted RT's/MT's to given 'total_gradient_time'? If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence.
total_gradient_time	float	2500	min: 1e-05	The duration [s] of the gradient.
sampling_rate	float	2	min: 0.01 max: 60	Time interval [s] between consecutive scans
scan_window:min	float	500	min: 0	Start of RT Scan Window [s]
scan_window:max	float	1500	min: 1	End of RT Scan Window [s]
variation:feature_stddev	int	3		Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)
variation:affine_offset	int	0		Global offset in retention time [s] from predicted model
variation:affine_scale	int	1		Global scaling in retention time from predicted model
column_condition:distortion	int	0	min: 0 max: 10	Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be >4.
profile_shape:width:value	float	9	min: 0	Width of the Exponential Gaussian Hybrid distribution shape of the elution profile. This does not correspond directly to the width in [s].
profile_shape:width:variance	float	1.6	min: 0	Random component of the width (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be >= 0).
profile_shape:skewness:value	float	0.1		Asymmetric component of the EGH. Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile.
profile_shape:skewness:variance	float	0.3	min: 0	Random component of skewness (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be > 0).
HPLC:model_file	string	examples/simulation/RTPredict.model		SVM model for retention time prediction
CE:pH	float	3	min: 0 max: 14	pH of buffer
CE:alpha	float	0.5	min: 0 max: 1	Exponent Alpha used to calculate mobility
CE:mu_eo	float	0	min: 0 max: 5	Electroosmotic flow
CE:lenght_d	float	70	min: 0 max: 1000	Length of capillary [cm] from injection site to MS
CE:length_total	float	75	min: 0 max: 1000	Total length of capillary [cm]
CE:voltage	float	1000	min: 0	Voltage applied to capillary

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ RTSimulation() [1/3]

RTSimulation ( )

Default constructor.

◆ RTSimulation() [2/3]

RTSimulation ( SimTypes::MutableSimRandomNumberGeneratorPtr random_generator )

explicit

Constructor taking a random generator.

◆ RTSimulation() [3/3]

RTSimulation ( const RTSimulation & source )

Copy constructor.

◆ ~RTSimulation()

~RTSimulation ( )

override

Destructor.

Member Function Documentation

◆ calculateMT_()

void calculateMT_	(	SimTypes::FeatureMapSim &	features,
		std::vector< double > &	predicted_retention_times
	)

private

Wrapper for the Migration time calculation (CE)

Parameters

features	will get modified with metavalue "RT_CE_width_factor", describing widening of MT shape.
predicted_retention_times	will contain afterwards the predicted retention times.

◆ createExperiment()

void createExperiment ( SimTypes::MSSimExperiment & experiment )

Size experiment and assign retention time grid.

◆ getChargeContribution_()

void getChargeContribution_	(	Map< String, double > &	q_cterm,
		Map< String, double > &	q_nterm,
		Map< String, double > &	q_aa_basic,
		Map< String, double > &	q_aa_acidic
	)

private

◆ getGradientTime()

SimTypes::SimCoordinateType getGradientTime ( ) const

◆ isRTColumnOn()

bool isRTColumnOn ( ) const

Returns true if a RT column was simulated.

◆ noRTColumn_()

void noRTColumn_ ( SimTypes::FeatureMapSim & )

private

Simply set all retention times to -1.

◆ operator=()

RTSimulation& operator= ( const RTSimulation & source )

Assignment operator.

◆ predictContaminantsRT()

void predictContaminantsRT ( SimTypes::FeatureMapSim & )

Set retention times randomly for given contaminants.

◆ predictRT()

void predictRT ( SimTypes::FeatureMapSim & features )

Predict retention times for given peptide features based for HPLC or CE.

Parameters

features Feature map for which the retention times will be predicted

◆ setDefaultParams_()

void setDefaultParams_ ( )

private

Set default parameters.

◆ smoothRTDistortion_()

void smoothRTDistortion_ ( SimTypes::MSSimExperiment & experiment )

private

smoothes the simulated distortion for the elution profiles with a moving average filter of size 3

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

◆ wrapSVM()

void wrapSVM	(	std::vector< AASequence > &	peptide_sequences,
		std::vector< double > &	predicted_retention_times
	)

Wrapper for the SVM RT Prediction (HPLC) using AASequences.

Member Data Documentation

◆ egh_tau_location_

double egh_tau_location_

private

EGH tau value.

◆ egh_tau_scale_

double egh_tau_scale_

private

EGH tau scale parameter of the lorentzian variation.

◆ egh_variance_location_

double egh_variance_location_

private

EGH sigma value.

◆ egh_variance_scale_

double egh_variance_scale_

private

EGH sigma scale parameter of the lorentzian variation.

◆ gradient_max_

SimTypes::SimCoordinateType gradient_max_

private

Maximal observed gradient time.

◆ gradient_min_

SimTypes::SimCoordinateType gradient_min_

private

gradient ranges

Minimal observed gradient time

◆ rnd_gen_

SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_

protected

Random number generator.

◆ rt_model_file_

OpenMS::String rt_model_file_

private

◆ rt_sampling_rate_

SimTypes::SimCoordinateType rt_sampling_rate_

private

bin size in rt dimension

◆ total_gradient_time_

SimTypes::SimCoordinateType total_gradient_time_

private

Total gradient time.

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RTSimulation() [1/3]

◆ RTSimulation() [2/3]

◆ RTSimulation() [3/3]

◆ ~RTSimulation()

Member Function Documentation

◆ calculateMT_()

◆ createExperiment()

◆ getChargeContribution_()

◆ getGradientTime()

◆ isRTColumnOn()

◆ noRTColumn_()

◆ operator=()

◆ predictContaminantsRT()

◆ predictRT()

◆ setDefaultParams_()

◆ smoothRTDistortion_()

◆ updateMembers_()

◆ wrapSVM()

Member Data Documentation

◆ egh_tau_location_

◆ egh_tau_scale_

◆ egh_variance_location_

◆ egh_variance_scale_

◆ gradient_max_

◆ gradient_min_

◆ rnd_gen_

◆ rt_model_file_

◆ rt_sampling_rate_

◆ total_gradient_time_