| OpenMS 2.5.0

Public Member Functions | Private Member Functions | List of all members
DigestSimulation Class Reference
Simulation

Simulates protein digestion. More...

`#include <OpenMS/SIMULATION/DigestSimulation.h>`

Inheritance diagram for DigestSimulation:

## Public Member Functions

DigestSimulation & | operator= (const DigestSimulation &source)
| Assignment operator. More...
void | digest (SimTypes::FeatureMapSim &feature_map)
| Digest a set of proteins into peptides. More...
Constructors and Destructors
| DigestSimulation ()
| Default constructor. More...
| DigestSimulation (const DigestSimulation &source)
| Copy constructor. More...
| ~DigestSimulation () 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...

## Private Member Functions

void | setDefaultParams_ ()
| set defaults More...

## Additional Inherited Members

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 | PepsinA, Alpha-lytic protease, 2-iodobenzoate, Asp-N, Chymotrypsin, iodosobenzoate, Lys-C, staphylococcal protease/D, proline-endopeptidase/HKR, Lys-N, TrypChymo, Formic_acid, Trypsin/P, V8-DE, V8-E, Trypsin, CNBr, Lys-C/P, Asp-N_ambic, Asp-N/B, leukocyte elastase, Chymotrypsin/P, proline endopeptidase, Arg-C, Arg-C/P, glutamyl endopeptidase, PepsinA + P, Glu-C+P, Clostripain/P, cyanogen-bromide, 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