OpenMS
EnzymaticDigestionLogModel Class Reference

Class for the Log L model of enzymatic digestion of proteins. More...

#include <OpenMS/CHEMISTRY/EnzymaticDigestionLogModel.h>

Collaboration diagram for EnzymaticDigestionLogModel:
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Classes

struct  BindingSite_
 
struct  CleavageModel_
 

Public Member Functions

 EnzymaticDigestionLogModel ()
 Default constructor. More...
 
 EnzymaticDigestionLogModel (const EnzymaticDigestionLogModel &rhs)
 Copy constructor. More...
 
EnzymaticDigestionLogModeloperator= (const EnzymaticDigestionLogModel &rhs)
 Assignment operator. More...
 
String getEnzymeName () const
 Returns the enzyme for the digestion. More...
 
void setEnzyme (const String &name)
 Sets the enzyme for the digestion. More...
 
void digest (const AASequence &protein, std::vector< AASequence > &output) const
 Performs the enzymatic digestion of a protein. More...
 
Size peptideCount (const AASequence &protein)
 Returns the number of peptides a digestion of protein would yield under the current enzyme and missed cleavage settings. More...
 
double getLogThreshold () const
 Returns the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data) More...
 
void setLogThreshold (double threshold)
 

Protected Member Functions

void nextCleavageSite_ (const AASequence &sequence, AASequence::ConstIterator &p) const
 Moves the iterator p behind (i.e., C-term) the next cleavage site of the sequence. More...
 
bool isCleavageSite_ (const AASequence &sequence, const AASequence::ConstIterator &p) const
 Tests if position pointed to by p (N-term side) is a valid cleavage site. More...
 

Protected Attributes

const DigestionEnzymeenzyme_
 Used enzyme. More...
 
double log_model_threshold_
 Threshold to decide if position is cleaved or missed (only for the model) More...
 
std::map< BindingSite_, CleavageModel_model_data_
 Holds the cleavage model. More...
 

Detailed Description

Class for the Log L model of enzymatic digestion of proteins.

An alternative model for tryptic digestion. where the protein is cleaved only at positions where a cleavage model trained on real data, exceeds a certain threshold. The model is published in Siepen et al. (2007), "Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.", doi: 10.1021/pr060507u The model is only available for trypsin and ignores the missed cleavage setting. You should however use setLogThreshold() to adjust FP vs FN rates. A higher threshold increases the number of cleavages predicted.

Constructor & Destructor Documentation

◆ EnzymaticDigestionLogModel() [1/2]

Default constructor.

◆ EnzymaticDigestionLogModel() [2/2]

Copy constructor.

Member Function Documentation

◆ digest()

void digest ( const AASequence protein,
std::vector< AASequence > &  output 
) const

Performs the enzymatic digestion of a protein.

◆ getEnzymeName()

String getEnzymeName ( ) const

Returns the enzyme for the digestion.

◆ getLogThreshold()

double getLogThreshold ( ) const

Returns the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data)

◆ isCleavageSite_()

bool isCleavageSite_ ( const AASequence sequence,
const AASequence::ConstIterator p 
) const
protected

Tests if position pointed to by p (N-term side) is a valid cleavage site.

◆ nextCleavageSite_()

void nextCleavageSite_ ( const AASequence sequence,
AASequence::ConstIterator p 
) const
protected

Moves the iterator p behind (i.e., C-term) the next cleavage site of the sequence.

◆ operator=()

Assignment operator.

◆ peptideCount()

Size peptideCount ( const AASequence protein)

Returns the number of peptides a digestion of protein would yield under the current enzyme and missed cleavage settings.

◆ setEnzyme()

void setEnzyme ( const String name)

Sets the enzyme for the digestion.

◆ setLogThreshold()

void setLogThreshold ( double  threshold)

Sets the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data) Default is 0.25

Member Data Documentation

◆ enzyme_

const DigestionEnzyme* enzyme_
protected

Used enzyme.

◆ log_model_threshold_

double log_model_threshold_
protected

Threshold to decide if position is cleaved or missed (only for the model)

◆ model_data_

std::map<BindingSite_, CleavageModel_> model_data_
protected

Holds the cleavage model.