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

#include <OpenMS/CHEMISTRY/ProteaseDigestion.h>

Inheritance diagram for ProteaseDigestion:

Public Member Functions
void	setEnzyme (const String &name)
	Sets the enzyme for the digestion (by name) More...

Size	digest (const AASequence &protein, std::vector< AASequence > &output, Size min_length=1, Size max_length=0) 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...

bool	isValidProduct (const String &protein, int pep_pos, int pep_length, bool ignore_missed_cleavages=true, bool allow_nterm_protein_cleavage=false, bool allow_random_asp_pro_cleavage=false) const
	Variant of EnzymaticDigestion::isValidProduct() with support for n-term protein cleavage and random D\|P cleavage. More...

bool	isValidProduct (const AASequence &protein, int pep_pos, int pep_length, bool ignore_missed_cleavages=true, bool allow_nterm_protein_cleavage=false, bool allow_random_asp_pro_cleavage=false) const
	forwards to isValidProduct using protein.toUnmodifiedString() More...

void	setEnzyme (const DigestionEnzyme *enzyme)
	Sets the enzyme for the digestion. More...

Public Member Functions inherited from EnzymaticDigestion
	EnzymaticDigestion ()
	Default constructor. More...

virtual	~EnzymaticDigestion ()
	Destructor. 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 DigestionEnzyme *enzyme)
	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...

Size	digestUnmodified (const StringView &sequence, std::vector< StringView > &output, Size min_length=1, Size max_length=0) const
	Performs the enzymatic digestion of an unmodified sequence. More...

bool	isValidProduct (const String &sequence, int pos, int length, bool ignore_missed_cleavages=true) const
	Is the peptide fragment starting at position `pos` with length `length` within the sequence `sequence` generated by the current enzyme? More...

bool	filterByMissedCleavages (const String &sequence, std::function< bool(const Int)> filter) const
	Filter based on the number of missed cleavages. More...

Additional Inherited Members
Public Types inherited from EnzymaticDigestion
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...

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

Static Public Attributes inherited from EnzymaticDigestion
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 inherited from EnzymaticDigestion
bool	isValidProduct_ (const String &sequence, int pos, int length, bool ignore_missed_cleavages, bool allow_nterm_protein_cleavage, bool allow_random_asp_pro_cleavage) const
	supports functionality for ProteaseDigestion as well (which is deeply weaved into the function) To avoid code duplication, this is stored here and called by wrappers. Do not duplicate the code, just for the sake of semantics (unless we can come up with a clean separation) Note: the overhead of allow_nterm_protein_cleavage and allow_random_asp_pro_cleavage is marginal; the main runtime is spend during tokenize_() More...

std::vector< int >	tokenize_ (const String &sequence, int start=0, int end=-1) const
	Digests the sequence using the enzyme's regular expression. More...

Size	digestAfterTokenize_ (const std::vector< int > &fragment_positions, const StringView &sequence, std::vector< StringView > &output, Size min_length=0, Size max_length=-1) const
	Helper function for digestUnmodified() More...

Size	countMissedCleavages_ (const std::vector< int > &cleavage_positions, Size seq_start, Size seq_end) const
	Counts the number of missed cleavages in a sequence fragment. More...

Protected Attributes inherited from EnzymaticDigestion
Size	missed_cleavages_
	Number of missed cleavages. More...

const DigestionEnzyme *	enzyme_
	Used enzyme. More...

boost::regex	re_
	Regex for tokenizing (huge speedup by making this a member instead of stack object in tokenize_()) 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 allowed, 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 Function Documentation

◆ digest()

Size digest	(	const AASequence &	protein,
		std::vector< AASequence > &	output,
		Size	min_length = `1`,
		Size	max_length = `0`
	)		const

: Performs the enzymatic digestion of a protein.

Parameters

protein	Sequence to digest
output	Digestion products (peptides)
min_length	Minimal length of reported products
max_length	Maximal length of reported products (0 = no restriction)

Returns: Number of discarded digestion products (which are not matching length restrictions)

◆ isValidProduct() [1/2]

bool isValidProduct	(	const String &	protein,
		int	pep_pos,
		int	pep_length,
		bool	ignore_missed_cleavages = `true`,
		bool	allow_nterm_protein_cleavage = `false`,
		bool	allow_random_asp_pro_cleavage = `false`
	)		const

Variant of EnzymaticDigestion::isValidProduct() with support for n-term protein cleavage and random D|P cleavage.

Checks if peptide is a valid digestion product of the enzyme, taking into account specificity and the flags provided here.

Parameters

protein	Protein sequence
pep_pos	Starting index of potential peptide
pep_length	Length of potential peptide
ignore_missed_cleavages	Do not compare MC's of potential peptide to the maximum allowed MC's
allow_nterm_protein_cleavage	Regard peptide as n-terminal of protein if it starts only at pos=1 or 2 and protein starts with 'M'
allow_random_asp_pro_cleavage	Allow cleavage at D\|P sites to count as n/c-terminal.

Returns: True if peptide has correct n/c terminals (according to enzyme, specificity and above flags)

Referenced by PeptideIndexing::FoundProteinFunctor::addHit(), and IDFilter::DigestionFilter::operator()().

◆ isValidProduct() [2/2]

bool isValidProduct	(	const AASequence &	protein,
		int	pep_pos,
		int	pep_length,
		bool	ignore_missed_cleavages = `true`,
		bool	allow_nterm_protein_cleavage = `false`,
		bool	allow_random_asp_pro_cleavage = `false`
	)		const

forwards to isValidProduct using protein.toUnmodifiedString()

◆ 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() [1/2]

void setEnzyme

Sets the enzyme for the digestion.

◆ setEnzyme() [2/2]

void setEnzyme ( const String & name )

Sets the enzyme for the digestion (by name)

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

Public Member Functions

Additional Inherited Members