DigestSimulation Class Reference

Simulates protein digestion. More...

#include <OpenMS/SIMULATION/DigestSimulation.h>

Inheritance diagram for DigestSimulation:

Collaboration diagram for DigestSimulation:

Constructors and Destructors
	DigestSimulation ()
	Default constructor. More...
	DigestSimulation (const DigestSimulation &source)
	Copy constructor. More...
	~DigestSimulation () override
	Destructor. More...
DigestSimulation &	operator= (const DigestSimulation &source)
	Assignment operator. More...
void	digest (SimTypes::FeatureMapSim &feature_map)
	Digest a set of proteins into peptides. More...
void	setDefaultParams_ ()
	set defaults 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 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
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...
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 protein digestion.

Supports all enzymes supported by EnzymaticDigestion.h and additionally incorporates abundance values, which are distributed evenly among digestion products of each protein.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
enzyme	string	Trypsin	Trypsin, Asp-N/B, Asp-N_ambic, Chymotrypsin, Chymotrypsin/P, CNBr, Formic_acid, Lys-C, Lys-N, Lys-C/P, PepsinA, TrypChymo, V8-DE, Trypsin/P, V8-E, leukocyte elastase, proline endopeptidase, Alpha-lytic protease, glutamyl endopeptidase, 2-iodobenzoate, iodosobenzoate, staphylococcal protease/D, proline-endopeptidase/HKR, Glu-C+P, PepsinA + P, cyanogen-bromide, Arg-C/P, Asp-N, Clostripain/P, Arg-C, elastase-trypsin-chymotrypsin, no cleavage, unspecific cleavage	Enzyme to use for digestion (select 'no cleavage' to skip digestion)
model	string	naive	trained, naive	The cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u).
min_peptide_length	int	3	min: 1	Minimum peptide length after digestion (shorter ones will be discarded)
model_trained:threshold	float	0.5	min: -2.0 max: 4.0	Model threshold for calling a cleavage. Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage.
model_naive:missed_cleavages	int	1	min: 0	Maximum number of missed cleavages considered. All possible resulting peptides will be created.

Note:

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

Constructor & Destructor Documentation

DigestSimulation() [1/2]

DigestSimulation

(

)

Default constructor.

DigestSimulation() [2/2]

DigestSimulation

(

const DigestSimulation &

source

)

Copy constructor.

~DigestSimulation()

~DigestSimulation ( )

override

Destructor.

Member Function Documentation

digest()

void digest

(

SimTypes::FeatureMapSim &

feature_map

)

Digest a set of proteins into peptides.

Digest proteins to peptides, with protein abundance distributes equally among created sibling peptides (this also applies for peptides with missed cleavages). Should a peptide be non-unique the abundances of its instances from proteins are summed up.

Parameters

feature_map

Input FeatureMap containing the proteins that should be digested as ProteinIdentification

operator=()

DigestSimulation& operator=

(

const DigestSimulation &

source

)

Assignment operator.

setDefaultParams_()

void setDefaultParams_ ( )

private

set defaults