OpenMS  2.6.0
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RTSimulation Class Reference

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

#include <OpenMS/SIMULATION/RTSimulation.h>

Inheritance diagram for RTSimulation:
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Collaboration diagram for RTSimulation:
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Constructors and Destructors

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...
 
SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_
 Random number generator. More...
 
 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...
 
RTSimulationoperator= (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...
 
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)
 
void updateMembers_ () override
 Synchronize members with param class. 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...
 
virtual DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 &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< Stringsubsections_
 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/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:

NameTypeDefaultRestrictionsDescription
rt_column stringHPLC none, HPLC, CEModelling of an RT or CE column
auto_scale stringtrue true, falseScale 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 float2500.0 min: 1.0e-05The duration [s] of the gradient.
sampling_rate float2.0 min: 0.01 max: 60.0Time interval [s] between consecutive scans
scan_window:min float500.0 min: 0.0Start of RT Scan Window [s]
scan_window:max float1500.0 min: 1.0End of RT Scan Window [s]
variation:feature_stddev int3  Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)
variation:affine_offset int0  Global offset in retention time [s] from predicted model
variation:affine_scale int1  Global scaling in retention time from predicted model
column_condition:distortion int0 min: 0 max: 10Distortion 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 float9.0 min: 0.0Width 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 float1.6 min: 0.0Random 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 float0.1  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 float0.3 min: 0.0Random 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 stringexamples/simulation/RTPredict.model  SVM model for retention time prediction
CE:pH float3.0 min: 0.0 max: 14.0pH of buffer
CE:alpha float0.5 min: 0.0 max: 1.0Exponent Alpha used to calculate mobility
CE:mu_eo float0.0 min: 0.0 max: 5.0Electroosmotic flow
CE:lenght_d float70.0 min: 0.0 max: 1000.0Length of capillary [cm] from injection site to MS
CE:length_total float75.0 min: 0.0 max: 1000.0Total length of capillary [cm]
CE:voltage float1000.0 min: 0.0Voltage applied to capillary

Note:

Constructor & Destructor Documentation

◆ RTSimulation() [1/3]

Default constructor.

◆ RTSimulation() [2/3]

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
featureswill get modified with metavalue "RT_CE_width_factor", describing widening of MT shape.
predicted_retention_timeswill 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
featuresFeature 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_

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.