EnzymaticDigestionLogModel Class Reference

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

#include <OpenMS/CHEMISTRY/EnzymaticDigestionLogModel.h>

Collaboration diagram for EnzymaticDigestionLogModel:

Classes
struct	BindingSite_
struct	CleavageModel_

Public Member Functions
	EnzymaticDigestionLogModel ()
	Default constructor. More...
	EnzymaticDigestionLogModel (const EnzymaticDigestionLogModel &rhs)
	Copy constructor. More...
EnzymaticDigestionLogModel &	operator= (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 DigestionEnzyme *	enzyme_
	Used enzyme. More...
double	log_model_threshold_
	Threshold to decide if position is cleaved or missed (only for the model) More...
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]

EnzymaticDigestionLogModel

(

)

Default constructor.

EnzymaticDigestionLogModel() [2/2]

EnzymaticDigestionLogModel

(

const EnzymaticDigestionLogModel &

rhs

)

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=()

EnzymaticDigestionLogModel& operator=

(

const EnzymaticDigestionLogModel &

rhs

)

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_

Map<BindingSite_, CleavageModel_> model_data_

protected

Holds the cleavage model.