EnzymaticDigestion Class Reference

Class for the enzymatic digestion of proteins. More...

#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>

Public Types
enum	Specificity { SPEC_FULL, SPEC_SEMI, SPEC_NONE, SIZE_OF_SPECIFICITY }
	when querying for valid digestion products, this determines if the specificity of the two peptide ends is considered important More...

Public Member Functions
	EnzymaticDigestion ()
	Default constructor. More...
	EnzymaticDigestion (const EnzymaticDigestion &rhs)
	Copy constructor. More...
EnzymaticDigestion &	operator= (const EnzymaticDigestion &rhs)
	Assignment operator. More...
Size	getMissedCleavages () const
	Returns the number of missed cleavages for the digestion. More...
void	setMissedCleavages (Size missed_cleavages)
	Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when log model is used. More...
String	getEnzymeName () const
	Returns the enzyme for the digestion. More...
void	setEnzyme (const String name)
	Sets the enzyme for the digestion. More...
Specificity	getSpecificity () const
	Returns the specificity for the digestion. More...
void	setSpecificity (Specificity spec)
	Sets the specificity for the digestion (default is SPEC_FULL). More...
void	digest (const AASequence &protein, std::vector< AASequence > &output) const
	Performs the enzymatic digestion of a protein. More...
void	digestUnmodifiedString (const StringView sequence, std::vector< StringView > &output, Size min_length=1, Size max_length=0) const
	Performs the enzymatic digestion of a unmodified protein String. By returning only references into the original string it is much faster. max_length restricts the maximum length of reported peptides (0 = no restriction) 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...
bool	isValidProduct (const AASequence &protein, Size pep_pos, Size pep_length, bool methionine_cleavage=false, bool ignore_missed_cleavages=true) const
	Returns true if peptide at position pep_pos with length pep_length within protein protein was generated by the current model. More...
bool	isValidProduct (const String &protein, Size pep_pos, Size pep_length, bool methionine_cleavage=false, bool ignore_missed_cleavages=true) const

Static Public Member Functions
static Specificity	getSpecificityByName (const String &name)

Static Public Attributes
static const std::string	NamesOfSpecificity [SIZE_OF_SPECIFICITY]
	Names of the Specificity. More...
static const std::string	UnspecificCleavage
	Name for unspecific cleavage. More...

Protected Member Functions
std::vector< Size >	tokenize_ (const String &protein) const
	Returns the naive cleavage site positions without specificity (including '0' as first position, but not size() as last) More...
Size	countMissedCleavages_ (const std::vector< Size > &cleavage_positions, Size pep_start, Size pep_end) const

Protected Attributes
Size	missed_cleavages_
	Number of missed cleavages. More...
Enzyme	enzyme_
	Used enzyme. More...
Specificity	specificity_
	specificity of enzyme More...

Detailed Description

Class for the enzymatic digestion of proteins.

Digestion can be performed using simple regular expressions, e.g. [KR] | [^P] for trypsin. Also missed cleavages can be modeled, i.e. adjacent peptides are not cleaved due to enzyme malfunction/access restrictions. If n missed cleavages are given, all possible resulting peptides (cleaved and uncleaved) with up to n missed cleavages are returned. Thus no random selection of just n specific missed cleavage sites is performed.

An alternative model is also available in EnzymaticDigestionLogModel.

Member Enumeration Documentation

Specificity

enum Specificity

when querying for valid digestion products, this determines if the specificity of the two peptide ends is considered important

Enumerator
SPEC_FULL
SPEC_SEMI
SPEC_NONE
SIZE_OF_SPECIFICITY

Constructor & Destructor Documentation

EnzymaticDigestion() [1/2]

EnzymaticDigestion

(

)

Default constructor.

EnzymaticDigestion() [2/2]

EnzymaticDigestion

(

const EnzymaticDigestion &

rhs

)

Copy constructor.

Member Function Documentation

countMissedCleavages_()

Size countMissedCleavages_ ( const std::vector< Size > &  cleavage_positions, Size  pep_start, Size  pep_end  ) const

inlineprotected

Parameters

cleavage_positions	Positons of cleavage in protein as obtained from tokenize_()
pep_start	Index into protein sequence
pep_end	Past-the-end index into protein sequence

Returns

number of missed cleavages of peptide

digest()

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

Performs the enzymatic digestion of a protein.

digestUnmodifiedString()

void digestUnmodifiedString	(	const StringView	sequence,
		std::vector< StringView > &	output,
		Size	min_length = 1,
		Size	max_length = 0
	)		const

Performs the enzymatic digestion of a unmodified protein String. By returning only references into the original string it is much faster. max_length restricts the maximum length of reported peptides (0 = no restriction)

Referenced by SimpleSearchEngine::main_(), and RNPxlSearch::main_().

getEnzymeName()

String getEnzymeName

(

)

const

Returns the enzyme for the digestion.

getMissedCleavages()

Size getMissedCleavages

(

)

const

Returns the number of missed cleavages for the digestion.

getSpecificity()

Specificity getSpecificity

(

)

const

Returns the specificity for the digestion.

getSpecificityByName()

static Specificity getSpecificityByName ( const String &  name )

static

convert spec string name to enum returns SIZE_OF_SPECIFICITY if name is not valid

isValidProduct() [1/2]

bool isValidProduct	(	const AASequence &	protein,
		Size	pep_pos,
		Size	pep_length,
		bool	methionine_cleavage = false,
		bool	ignore_missed_cleavages = true
	)		const

Returns true if peptide at position pep_pos with length pep_length within protein protein was generated by the current model.

Referenced by IDFilter::DigestionFilter::operator()().

isValidProduct() [2/2]

bool isValidProduct	(	const String &	protein,
		Size	pep_pos,
		Size	pep_length,
		bool	methionine_cleavage = false,
		bool	ignore_missed_cleavages = true
	)		const

Returns true if peptide at position pep_pos with length pep_length within protein protein was generated by the current model

Note

: the protein sequence must be unmodified (i.e. only amino acid characters, no modifications or masses in brackets)

operator=()

EnzymaticDigestion& operator=

(

const EnzymaticDigestion &

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.

Referenced by TOPPOpenPepXLLF::main_(), SimpleSearchEngine::main_(), TOPPOpenPepXL::main_(), and RNPxlSearch::main_().

setMissedCleavages()

void setMissedCleavages

(

Size

missed_cleavages

)

Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when log model is used.

Referenced by TOPPOpenPepXLLF::main_(), SimpleSearchEngine::main_(), TOPPOpenPepXL::main_(), and RNPxlSearch::main_().

setSpecificity()

void setSpecificity

(

Specificity

spec

)

Sets the specificity for the digestion (default is SPEC_FULL).

tokenize_()

std::vector<Size> tokenize_ ( const String &  protein ) const

protected

Returns the naive cleavage site positions without specificity (including '0' as first position, but not size() as last)

Member Data Documentation

enzyme_

Enzyme enzyme_

protected

Used enzyme.

missed_cleavages_

Size missed_cleavages_

protected

Number of missed cleavages.

NamesOfSpecificity

const std::string NamesOfSpecificity[SIZE_OF_SPECIFICITY]

static

Names of the Specificity.

specificity_

Specificity specificity_

protected

specificity of enzyme

UnspecificCleavage

const std::string UnspecificCleavage

static

Name for unspecific cleavage.