OpenMS  2.8.0
List of all members
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...
DigestSimulationoperator= (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 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 &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< 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 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:

enzyme stringTrypsin 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 cleavageEnzyme to use for digestion (select 'no cleavage' to skip digestion)
model stringnaive trained, naiveThe cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u).
min_peptide_length int3 min: 1Minimum peptide length after digestion (shorter ones will be discarded)
model_trained:threshold float0.5 min: -2.0 max: 4.0Model 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 int1 min: 0Maximum number of missed cleavages considered. All possible resulting peptides will be created.


Constructor & Destructor Documentation

◆ DigestSimulation() [1/2]

Default constructor.

◆ DigestSimulation() [2/2]

DigestSimulation ( const DigestSimulation source)

Copy constructor.

◆ ~DigestSimulation()

~DigestSimulation ( )


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.

feature_mapInput FeatureMap containing the proteins that should be digested as ProteinIdentification

◆ operator=()

DigestSimulation& operator= ( const DigestSimulation source)

Assignment operator.

◆ setDefaultParams_()

void setDefaultParams_ ( )

set defaults