database which holds all residue modifications from UniMod More...

#include <OpenMS/CHEMISTRY/ModificationsDB.h>

Inheritance diagram for ModificationsDB:

Public Member Functions
Size	getNumberOfModifications () const
	Returns the number of modifications read from the unimod.xml file. More...

const ResidueModification &	getModification (Size index) const
	Returns the modification with the given index. More...

void	searchModifications (std::set< const ResidueModification *> &mods, const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Collects all modifications which have the given name as synonym. More...

const ResidueModification &	getModification (const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Returns the modification with the given name. More...

bool	has (String modification) const
	Returns true if the modification exists. More...

void	addModification (ResidueModification *new_mod)
	Add a new modification to ModificationsDB. More...

Size	findModificationIndex (const String &mod_name) const
	Returns the index of the modification in the mods_ vector; a unique name must be given. More...

void	searchModificationsByDiffMonoMass (std::vector< String > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)
	Collects all modifications with matching delta mass. More...

const ResidueModification *	getBestModificationByMonoMass (double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)
	Returns the best matching modification for the given mass and residue. More...

const ResidueModification *	getBestModificationByDiffMonoMass (double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)
	Returns the best matching modification for the given delta mass and residue. More...

void	readFromOBOFile (const String &filename)
	Adds modifications from a given file in OBO format. More...

void	readFromUnimodXMLFile (const String &filename)
	Adds modifications from a given file in Unimod XML format. More...

void	getAllSearchModifications (std::vector< String > &modifications) const
	Collects all modifications that can be used for identification searches. More...

Static Public Member Functions
static ModificationsDB *	getInstance ()
	Returns a pointer to the modifications DB (singleton) More...

Protected Member Functions
bool	residuesMatch_ (const String &residue, char origin) const
	Helper function to check if a residue matches the origin for a modification. More...

Protected Attributes
std::vector< ResidueModification * >	mods_
	Stores the modifications. More...

Map< String, std::set< const ResidueModification * > >	modification_names_
	Stores the mappings of (unique) names to the modifications. More...

Private Member Functions
Constructors and Destructors
	ModificationsDB ()
	Default constructor. More...

	ModificationsDB (const ModificationsDB &residue_db)
	Copy constructor. More...

virtual	~ModificationsDB ()
	Destructor. More...

Assignment
ModificationsDB &	operator= (const ModificationsDB &aa)
	Assignment operator. More...

Friends
class	CrossLinksDB

Detailed Description

database which holds all residue modifications from UniMod

This singleton class serves as a storage of the available modifications represented by UniMod (www.unimod.org). The modifications are identified by their name and possibly other IDs from UniMod or the PSI-MOD ontology. Modifications can have different specificities, e.g. they can occur only at the termini, anywhere or only at specific amino acids.

The modifications are defined in share/OpenMS/CHEMISTRY/unimod.xml and in share/OpenMS/CHEMISTRY/PSI-MOD.obo. The unimod file can be directly downloaded from unimod.org and replaced if the modifications change.

To add a new modification, not contained in UniMod, one should follow the way described at the unimod.org website and download the file then from unimod.org. The same can be done to add support for the modifications to search engines, e.g. Mascot.

Constructor & Destructor Documentation

◆ ModificationsDB() [1/2]

ModificationsDB ( )

private

Default constructor.

◆ ModificationsDB() [2/2]

ModificationsDB ( const ModificationsDB & residue_db )

private

Copy constructor.

◆ ~ModificationsDB()

virtual ~ModificationsDB ( )

privatevirtual

Destructor.

Member Function Documentation

◆ addModification()

void addModification ( ResidueModification * new_mod )

Add a new modification to ModificationsDB.

Exceptions

Exception::InvalidValue if modification already exists (based on its fullID)

Referenced by RNPxlSearch::getPrecursorToFragmentAdducts_().

◆ findModificationIndex()

Size findModificationIndex ( const String & mod_name ) const

Returns the index of the modification in the mods_ vector; a unique name must be given.

Exceptions

Exception::ElementNotFound	if not exactly one matching modification was found
Exception::InvalidValue	if no matching residue or modification were found

◆ getAllSearchModifications()

void getAllSearchModifications ( std::vector< String > & modifications ) const

Collects all modifications that can be used for identification searches.

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

◆ getBestModificationByDiffMonoMass()

const ResidueModification* getBestModificationByDiffMonoMass	(	double	mass,
		double	max_error,
		const String &	residue = `""`,
		ResidueModification::TermSpecificity	term_spec = `ResidueModification::NUMBER_OF_TERM_SPECIFICITY`
	)

Returns the best matching modification for the given delta mass and residue.

Query the modifications DB to get the best matching modification with the given delta mass at the given residue (NULL pointer means no result, maybe the maximal error tolerance needs to be increased). Possible input for CAM modification would be a delta mass of 57 and a residue of "C".

Note: If there are multiple possible matches with equal masses, it will choose the _first_ match which defaults to the first matching UniMod entry.

Parameters

residue	The residue at which the modifications occurs
mass	The monoisotopic mass of the residue including the mass of the modification
max_error	The maximal mass error in the modification search

Returns: A pointer to the best matching modification (or NULL if none was found)

◆ getBestModificationByMonoMass()

const ResidueModification* getBestModificationByMonoMass	(	double	mass,
		double	max_error,
		const String &	residue = `""`,
		ResidueModification::TermSpecificity	term_spec = `ResidueModification::NUMBER_OF_TERM_SPECIFICITY`
	)

Returns the best matching modification for the given mass and residue.

Query the modifications DB to get the best matching modification with the given mass at the given residue (NULL pointer means no result, maybe the maximal error tolerance needs to be increased). Possible input for CAM modification would be a mass of 160 and a residue of "C".

Note: If there are multiple possible matches with equal masses, it will choose the _first_ match which defaults to the first matching UniMod entry.

Parameters

residue	The residue at which the modifications occurs
mass	The monoisotopic mass of the residue including the mass of the modification
max_error	The maximal mass error in the modification search

Returns: A pointer to the best matching modification (or NULL if none was found)

◆ getInstance()

static ModificationsDB* getInstance ( )

inlinestatic

Returns a pointer to the modifications DB (singleton)

Referenced by SimpleSearchEngine::getModifications_(), RNPxlSearch::getModifications_(), RNPxlSearch::getPrecursorToFragmentAdducts_(), RNPxlSearch::postScoreHits_(), SimpleSearchEngine::registerOptionsAndFlags_(), and RNPxlSearch::registerOptionsAndFlags_().

◆ getModification() [1/2]

const ResidueModification& getModification ( Size index ) const

Returns the modification with the given index.

Exceptions

Exception::IndexOverflow if the index is too large

Referenced by RNPxlSearch::getModifications_(), and RNPxlSearch::postScoreHits_().

◆ getModification() [2/2]

const ResidueModification& getModification	(	const String &	mod_name,
		const String &	residue = `""`,
		ResidueModification::TermSpecificity	term_spec = `ResidueModification::NUMBER_OF_TERM_SPECIFICITY`
	)		const

Returns the modification with the given name.

If residue is set, only modifications with matching residue of origin are considered. If term_spec is set, only modifications with matching term specificity are considered.

If more than one matching modification is found, the first one is returned with a warning.

Exceptions

Exception::ElementNotFound	if no modification named `mod_name` exists (via searchModifications())
Exception::InvalidValue	if no matching modification exists

◆ getNumberOfModifications()

Size getNumberOfModifications ( ) const

Returns the number of modifications read from the unimod.xml file.

◆ has()

bool has ( String modification ) const

Returns true if the modification exists.

◆ operator=()

ModificationsDB& operator= ( const ModificationsDB & aa )

private

Assignment operator.

◆ readFromOBOFile()

void readFromOBOFile ( const String & filename )

Adds modifications from a given file in OBO format.

Exceptions

Exception::ParseError if the file cannot be parsed correctly

◆ readFromUnimodXMLFile()

void readFromUnimodXMLFile ( const String & filename )

Adds modifications from a given file in Unimod XML format.

◆ residuesMatch_()

bool residuesMatch_	(	const String &	residue,
		char	origin
	)		const

protected

Helper function to check if a residue matches the origin for a modification.

◆ searchModifications()

void searchModifications	(	std::set< const ResidueModification *> &	mods,
		const String &	mod_name,
		const String &	residue = `""`,
		ResidueModification::TermSpecificity	term_spec = `ResidueModification::NUMBER_OF_TERM_SPECIFICITY`
	)		const

Collects all modifications which have the given name as synonym.

If residue is set, only modifications with matching residue of origin are considered. If term_spec is set, only modifications with matching term specificity are considered. The resulting set of modifications may be empty if no modification exists that fulfills the criteria.

Exceptions

Exception::ElementNotFound	if no modification named `mod_name` exists
Exception::InvalidValue	if no residue named `residue` exists

◆ searchModificationsByDiffMonoMass()

void searchModificationsByDiffMonoMass	(	std::vector< String > &	mods,
		double	mass,
		double	max_error,
		const String &	residue = `""`,
		ResidueModification::TermSpecificity	term_spec = `ResidueModification::NUMBER_OF_TERM_SPECIFICITY`
	)

Collects all modifications with matching delta mass.

If residue is set, only modifications with matching residue of origin are considered. If term_spec is set, only modifications with matching term specificity are considered.

Friends And Related Function Documentation

◆ CrossLinksDB

friend class CrossLinksDB

friend

Member Data Documentation

◆ modification_names_

Map<String, std::set<const ResidueModification*> > modification_names_

protected

Stores the mappings of (unique) names to the modifications.

◆ mods_

std::vector<ResidueModification*> mods_

protected

Stores the modifications.

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ ModificationsDB() [1/2]

◆ ModificationsDB() [2/2]

◆ ~ModificationsDB()

Member Function Documentation

◆ addModification()

◆ findModificationIndex()

◆ getAllSearchModifications()

◆ getBestModificationByDiffMonoMass()

◆ getBestModificationByMonoMass()

◆ getInstance()

◆ getModification() [1/2]

◆ getModification() [2/2]

◆ getNumberOfModifications()

◆ has()

◆ operator=()

◆ readFromOBOFile()

◆ readFromUnimodXMLFile()

◆ residuesMatch_()

◆ searchModifications()

◆ searchModificationsByDiffMonoMass()

Friends And Related Function Documentation

◆ CrossLinksDB

Member Data Documentation

◆ modification_names_

◆ mods_