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

#include <OpenMS/CHEMISTRY/RNaseDigestion.h>

Inheritance diagram for RNaseDigestion:

Collaboration diagram for RNaseDigestion:

Classes
struct	CleavageSensitiveModGroups
	Cleavage-sensitive modification groups split by cleavage direction. More...

struct	DigestionProduct
	Detailed digestion product including sequence and parent coordinates. More...

Public Types
using	ConstRibonucleotidePtr = const Ribonucleotide *

Public Types inherited from EnzymaticDigestion
enum	Specificity { SPEC_NONE = 0 , SPEC_SEMI = 1 , SPEC_FULL = 2 , SPEC_UNKNOWN = 3 , SPEC_NOCTERM = 8 , SPEC_NONTERM = 9 , SIZE_OF_SPECIFICITY = 10 }
	when querying for valid digestion products, this determines if the specificity of the two peptide ends is considered important More...

Public Member Functions
void	setEnzyme (const DigestionEnzyme *enzyme) override
	Sets the enzyme for the digestion.

void	setEnzyme (const String &name)
	Sets the enzyme for the digestion (by name)

void	digest (const NASequence &rna, std::vector< NASequence > &output, Size min_length=0, Size max_length=0) const
	Performs the enzymatic digestion of a (potentially modified) RNA.

void	digest (const NASequence &rna, std::vector< DigestionProduct > &output, Size min_length=0, Size max_length=0) const
	Performs the enzymatic digestion of a RNA and returns fragments with parent coordinates.

std::vector< std::pair< Size, Size > >	getFragmentPositions (const NASequence &rna, Size min_length=0, Size max_length=0) const
	Returns the positions of digestion products in the RNA as pairs: (start, length)

CleavageSensitiveModGroups	inferCleavageSensitiveMods (const std::set< ConstRibonucleotidePtr > &variable_modifications) const
	Infer which variable modifications can block cleavage for the configured enzyme.

void	digestWithCleavageSensitiveMods (const NASequence &rna, const CleavageSensitiveModGroups &cleavage_sensitive_mods, Size max_sensitive_mods_per_fragment, std::vector< DigestionProduct > &output, Size min_length=0, Size max_length=0) const
	Digest RNA while allowing cleavage-sensitive modifications to block adjacent cuts.

void	digest (IdentificationData &id_data, Size min_length=0, Size max_length=0) const
	Performs the enzymatic digestion of all RNA parent sequences in `IdentificationData`.

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

	EnzymaticDigestion (const EnzymaticDigestion &rhs)
	Copy constructor.

EnzymaticDigestion &	operator= (const EnzymaticDigestion &rhs)
	Assignment operator.

virtual	~EnzymaticDigestion ()
	Destructor.

Size	getMissedCleavages () const
	Returns the number of missed cleavages for the digestion.

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.

String	getEnzymeName () const
	Returns the enzyme for the digestion.

Specificity	getSpecificity () const
	Returns the specificity for the digestion.

void	setSpecificity (Specificity spec)
	Sets the specificity for the digestion (default is SPEC_FULL).

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.

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

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

Size	countInternalCleavageSites (const String &sequence) const
	Counts the number of internal cleavage sites (missed cleavages) in a protein sequence.

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

Protected Member Functions
std::vector< std::pair< Size, Size > >	getFragmentPositions_ (const NASequence &rna, Size min_length, Size max_length) const
	Returns the positions of digestion products in the RNA as pairs: (start, length)

void	applyTerminalGains_ (NASequence &fragment, const std::pair< Size, Size > &pos, Size parent_size) const
	Apply enzyme-specific 5'/3' terminal gains to a fragment based on its parent coordinates.

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_()

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

Size	semiSpecificDigestion_ (const std::vector< int > &cleavage_positions, std::vector< std::pair< Size, Size > > &output, Size min_length=0, Size max_length=-1) const
	Generates semi-specific digestion products.

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()

Size	digestAfterTokenize_ (const std::vector< int > &fragment_positions, const StringView &sequence, std::vector< std::pair< Size, Size > > &output, Size min_length=0, Size max_length=-1) const

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.

Protected Attributes
const Ribonucleotide *	five_prime_gain_
	5' mod added by the enzyme

const Ribonucleotide *	three_prime_gain_
	3' mod added by the enzyme

std::vector< boost::regex >	cuts_after_regexes_
	a vector of reg. exp. for enzyme cutting pattern, each regex represents a single nucleotide

std::vector< boost::regex >	cuts_before_regexes_
	a vector reg. exp. for enzyme cutting pattern

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

const DigestionEnzyme *	enzyme_
	Used enzyme.

std::unique_ptr< boost::regex >	re_
	Regex for tokenizing (huge speedup by making this a member instead of stack object in tokenize_())

Specificity	specificity_
	specificity of enzyme

Additional Inherited Members
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.

static const std::string	NoCleavage
	Name for no cleavage.

static const std::string	UnspecificCleavage
	Name for unspecific cleavage.

Detailed Description

Class for the enzymatic digestion of RNAs.

See also: DigestionEnzymeRNA

Class Documentation

◆ OpenMS::RNaseDigestion::DigestionProduct

struct OpenMS::RNaseDigestion::DigestionProduct

Detailed digestion product including sequence and parent coordinates.

Collaboration diagram for RNaseDigestion::DigestionProduct:

[legend]

Class Members
NASequence	fragment
pair< Size, Size >	position

Member Typedef Documentation

◆ ConstRibonucleotidePtr

using ConstRibonucleotidePtr = const Ribonucleotide*

Member Function Documentation

◆ applyTerminalGains_()

void applyTerminalGains_	(	NASequence &	fragment,
		const std::pair< Size, Size > &	pos,
		Size	parent_size
	)		const

protected

Apply enzyme-specific 5'/3' terminal gains to a fragment based on its parent coordinates.

◆ digest() [1/3]

void digest	(	const NASequence &	rna,
		std::vector< DigestionProduct > &	output,
		Size	min_length = `0`,
		Size	max_length = `0`
	)		const

Performs the enzymatic digestion of a RNA and returns fragments with parent coordinates.

Only fragments of appropriate length (between min_length and max_length) are returned. Enzyme-specific terminal gains are applied to the reported fragment sequences.

◆ digest() [2/3]

void digest	(	const NASequence &	rna,
		std::vector< NASequence > &	output,
		Size	min_length = `0`,
		Size	max_length = `0`
	)		const

Performs the enzymatic digestion of a (potentially modified) RNA.

Only fragments of appropriate length (between min_length and max_length) are returned.

Referenced by NucleicAcidSearchEngine::main_().

◆ digest() [3/3]

void digest	(	IdentificationData &	id_data,
		Size	min_length = `0`,
		Size	max_length = `0`
	)		const

Performs the enzymatic digestion of all RNA parent sequences in IdentificationData.

Digestion products are stored as IdentifiedOligos with corresponding ParentMatch annotations. Only fragments of appropriate length (between min_length and max_length) are included.

◆ digestWithCleavageSensitiveMods()

void digestWithCleavageSensitiveMods	(	const NASequence &	rna,
		const CleavageSensitiveModGroups &	cleavage_sensitive_mods,
		Size	max_sensitive_mods_per_fragment,
		std::vector< DigestionProduct > &	output,
		Size	min_length = `0`,
		Size	max_length = `0`
	)		const

Digest RNA while allowing cleavage-sensitive modifications to block adjacent cuts.

Starting from the regular digest fragments, additional fragments are generated recursively by applying cleavage-sensitive modifications at fragment boundaries. The number of such applied modifications is limited by max_sensitive_mods_per_fragment. Enzyme terminal gains are applied to all returned fragment sequences.

Referenced by NucleicAcidSearchEngine::main_().

◆ getFragmentPositions()

std::vector< std::pair< Size, Size > > getFragmentPositions	(	const NASequence &	rna,
		Size	min_length = `0`,
		Size	max_length = `0`
	)		const

Returns the positions of digestion products in the RNA as pairs: (start, length)

This is useful when callers need to associate digested fragments with parent coordinates.

◆ getFragmentPositions_()

std::vector< std::pair< Size, Size > > getFragmentPositions_	(	const NASequence &	rna,
		Size	min_length,
		Size	max_length
	)		const

protected

Returns the positions of digestion products in the RNA as pairs: (start, length)

◆ inferCleavageSensitiveMods()

CleavageSensitiveModGroups inferCleavageSensitiveMods ( const std::set< ConstRibonucleotidePtr > & variable_modifications ) const

Infer which variable modifications can block cleavage for the configured enzyme.

A modification is classified as cleavage-sensitive if its origin residue matches the enzyme cleavage regex at a boundary position, but the modified residue code no longer matches.

Referenced by NucleicAcidSearchEngine::main_().

◆ setEnzyme() [1/2]

void setEnzyme ( const DigestionEnzyme * enzyme )

overridevirtual

Sets the enzyme for the digestion.

Reimplemented from EnzymaticDigestion.

Referenced by NucleicAcidSearchEngine::main_().

◆ setEnzyme() [2/2]

void setEnzyme ( const String & name )

Sets the enzyme for the digestion (by name)

Member Data Documentation

◆ cuts_after_regexes_

std::vector<boost::regex> cuts_after_regexes_

protected

a vector of reg. exp. for enzyme cutting pattern, each regex represents a single nucleotide

◆ cuts_before_regexes_

std::vector<boost::regex> cuts_before_regexes_

protected

a vector reg. exp. for enzyme cutting pattern

◆ five_prime_gain_

const Ribonucleotide* five_prime_gain_

protected

5' mod added by the enzyme

◆ three_prime_gain_

const Ribonucleotide* three_prime_gain_

protected

3' mod added by the enzyme

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::RNaseDigestion::DigestionProduct

Member Typedef Documentation

◆ ConstRibonucleotidePtr

Member Function Documentation

◆ applyTerminalGains_()

◆ digest() [1/3]

◆ digest() [2/3]

◆ digest() [3/3]

◆ digestWithCleavageSensitiveMods()

◆ getFragmentPositions()

◆ getFragmentPositions_()

◆ inferCleavageSensitiveMods()

◆ setEnzyme() [1/2]

◆ setEnzyme() [2/2]

Member Data Documentation

◆ cuts_after_regexes_

◆ cuts_before_regexes_

◆ five_prime_gain_

◆ three_prime_gain_