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

#include <OpenMS/CHEMISTRY/ModificationsDB.h>

Inheritance diagram for ModificationsDB:

Collaboration 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. note: out-of-bounds check is only performed in debug mode. 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 *	searchModification (const ResidueModification &mod_in) const
	Returns a pointer to an exact match of the given modification if present in the DB. More...

const ResidueModification *	searchModificationsFast (const String &mod_name, bool &multiple_matches, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Returns the modification which has the given name as synonym (fast version) 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 (const String &modification) const
	Returns true if the modification exists. More...

const ResidueModification *	addModification (std::unique_ptr< ResidueModification > new_mod)
	Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) it is not added. More...

const ResidueModification *	addModification (const ResidueModification &new_mod)
	Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) it is not added. A copy will be made on the heap and added to the ModificationsDB otherwise. 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 delta mass inside a tolerance window. More...

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

void	searchModificationsByDiffMonoMassSorted (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 delta mass inside a tolerance window and adds them sorted by mass difference. More...

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

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

void	writeTSV (const String &filename)
	Writes tab separated entries: FullId,FullName,Origin,AA,TerminusSpecificity,DiffMonoMass (including header) to TSV file. More...

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

static ModificationsDB *	initializeModificationsDB (OpenMS::String unimod_file="CHEMISTRY/unimod.xml", OpenMS::String custommod_file="CHEMISTRY/custom_mods.xml", OpenMS::String psimod_file="CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file="CHEMISTRY/XLMOD.obo")
	Initializes the modification DB with non-default modification files (can only be done once) More...

static bool	isInstantiated ()
	Check whether ModificationsDB was instantiated before. More...

Protected Member Functions
bool	residuesMatch_ (const char residue, const ResidueModification *curr_mod) 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...

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

Static Protected Attributes
static bool	is_instantiated_
	Stores whether ModificationsDB was instantiated before. More...

Private Member Functions

Constructors and Destructors

Parameters

unimod_file	Path to the Unimod XML file
psimod_file	Path to the PSI-MOD OBO file
xlmod_file	Path to the XLMOD OBO file

ModificationsDB (const OpenMS::String &unimod_file="CHEMISTRY/unimod.xml", const OpenMS::String &custommod_file="CHEMISTRY/custom_mods.xml", const OpenMS::String &psimod_file="CHEMISTRY/PSI-MOD.obo", const OpenMS::String &xlmod_file="CHEMISTRY/XLMOD.obo")

ModificationsDB (const ModificationsDB &residue_db)

Copy constructor. More...

virtual ~ModificationsDB ()

Destructor. More...

Assignment

ModificationsDB & operator= (const ModificationsDB &aa)

Assignment operator. More...

const ResidueModification * addNewModification_ (const ResidueModification &new_mod)

Add a new modification to ModificationsDB without checking if it was inside already. 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...

Friends
class	CrossLinksDB

class	Residue

class	AASequence

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.

In some scenarios, it might be useful to define different modification databases. This can be done by providing a path through initializeModificationsDB(), however it is important that this is done before* the first call to getInstance().

Constructor & Destructor Documentation

◆ ModificationsDB() [1/2]

ModificationsDB	(	const OpenMS::String &	unimod_file = `"CHEMISTRY/unimod.xml"`,
		const OpenMS::String &	custommod_file = `"CHEMISTRY/custom_mods.xml"`,
		const OpenMS::String &	psimod_file = `"CHEMISTRY/PSI-MOD.obo"`,
		const OpenMS::String &	xlmod_file = `"CHEMISTRY/XLMOD.obo"`
	)

explicitprivate

◆ ModificationsDB() [2/2]

ModificationsDB ( const ModificationsDB & residue_db )

private

Copy constructor.

◆ ~ModificationsDB()

virtual ~ModificationsDB ( )

privatevirtual

Destructor.

Member Function Documentation

◆ addModification() [1/2]

const ResidueModification* addModification ( const ResidueModification & new_mod )

Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) it is not added. A copy will be made on the heap and added to the ModificationsDB otherwise.

Returns: a pointer to the modification in the ModificationDB (which can differ from input if mod was already present).

Parameters

new_mod The new modification object. A copy will be made on the heap and added to the ModificationsDB if not already present.

◆ addModification() [2/2]

const ResidueModification* addModification ( std::unique_ptr< ResidueModification > new_mod )

Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) it is not added.

Returns: a pointer to the modification in the ModificationDB (which can differ from input if mod was already present).

Parameters

new_mod Owning pointer, which transfers ownership to ModificationsDB (mod might get deleted if already present!)

◆ addNewModification_()

const ResidueModification* addNewModification_ ( const ResidueModification & new_mod )

private

Add a new modification to ModificationsDB without checking if it was inside already.

Parameters

new_mod A copy will be made on the heap and added to the modification if not already present.

◆ findModificationIndex()

Size findModificationIndex ( const String & mod_name ) const

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

return numeric_limits<Size>::max() if not exactly one matching modification was found or no matching residue or modification were found

Exceptions

Exception::ElementNotFound if not exactly one matching modification was found.

◆ getAllSearchModifications()

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

Collects all modifications that can be used for identification searches.

◆ 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

mass	The monoisotopic mass of the residue including the mass of the modification
max_error	The maximal mass error in the modification search
residue	The residue at which the modifications occurs
term_spec	Only modifications with matching term specificity are considered.

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

◆ getInstance()

static ModificationsDB* getInstance ( )

static

Returns a pointer to the modifications DB (singleton)

◆ getModification() [1/2]

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.

Note: Will never return a null pointer, instead will throw an exceptions.

Exceptions

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

◆ getModification() [2/2]

const ResidueModification* getModification ( Size index ) const

Returns the modification with the given index. note: out-of-bounds check is only performed in debug mode.

◆ getNumberOfModifications()

Size getNumberOfModifications ( ) const

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

◆ has()

bool has ( const String & modification ) const

Returns true if the modification exists.

◆ initializeModificationsDB()

static ModificationsDB* initializeModificationsDB	(	OpenMS::String	unimod_file = `"CHEMISTRY/unimod.xml"`,
		OpenMS::String	custommod_file = `"CHEMISTRY/custom_mods.xml"`,
		OpenMS::String	psimod_file = `"CHEMISTRY/PSI-MOD.obo"`,
		OpenMS::String	xlmod_file = `"CHEMISTRY/XLMOD.obo"`
	)

static

Initializes the modification DB with non-default modification files (can only be done once)

◆ isInstantiated()

static bool isInstantiated ( )

static

Check whether ModificationsDB was instantiated before.

◆ operator=()

ModificationsDB& operator= ( const ModificationsDB & aa )

private

Assignment operator.

◆ readFromOBOFile()

void readFromOBOFile ( const String & filename )

private

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 )

private

Adds modifications from a given file in Unimod XML format.

◆ residuesMatch_()

bool residuesMatch_	(	const char	residue,
		const ResidueModification *	curr_mod
	)		const

protected

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

Special cases are handled as follows:

if the origin of the modification is not "X" (everything), then the residue either needs to match the origin exactly or it must be one of "X", ".", or "?"
if the origin of the modification is "X" (can match any amino acid), then any residue should match – except if the modification is user-defined and maps to an unknown amino acid (indicated by "X")

Underlying logic to determine whether a given residue matches the modification: if the modification does not have origin of "X" (everything) then it is sufficient to check that the residue matches the origin

◆ searchModification()

const ResidueModification* searchModification ( const ResidueModification & mod_in ) const

Returns a pointer to an exact match of the given modification if present in the DB.

This should be used if e.g. only a stack copy of the modification is available but you need a pointer to the modification in the database.

Returns: The matching modification given the constraints. Returns nullptr if no modification exists that is an exact match accoring to the equals operator.

◆ 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.

Todo:: use set as return value. Would be more efficient in pyopenms

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 will be empty if no modification exists that fulfills the criteria.

◆ searchModificationsByDiffMonoMass() [1/2]

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

◆ searchModificationsByDiffMonoMass() [2/2]

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 delta mass inside a tolerance window.

Warning: This function adds the results in the order of appearance in the DB, not considering proximity in mass. Use searchModificationsByDiffMonoMassSorted for this.

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.

◆ searchModificationsByDiffMonoMassSorted() [1/2]

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

◆ searchModificationsByDiffMonoMassSorted() [2/2]

void searchModificationsByDiffMonoMassSorted	(	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 delta mass inside a tolerance window and adds them sorted by mass difference.

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.

◆ searchModificationsFast()

const ResidueModification* searchModificationsFast	(	const String &	mod_name,
		bool &	multiple_matches,
		const String &	residue = `""`,
		ResidueModification::TermSpecificity	term_spec = `ResidueModification::NUMBER_OF_TERM_SPECIFICITY`
	)		const

Returns the modification which has the given name as synonym (fast version)

Unlike searchModifications(), only returns the one occurrence of the modification (the last occurrence). It is therefore required to check multiple_matches to ensure that only a single modification was found.

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.

Returns: The matching modification given the constraints. Returns nullptr if no modification exists that fulfills the criteria. If multiple modifications are found, the multiple_matches flag will be set.

◆ writeTSV()

void writeTSV ( const String & filename )

Writes tab separated entries: FullId,FullName,Origin,AA,TerminusSpecificity,DiffMonoMass (including header) to TSV file.

Friends And Related Function Documentation

◆ AASequence

friend class AASequence

friend

◆ CrossLinksDB

friend class CrossLinksDB

friend

◆ Residue

friend class Residue

friend

Member Data Documentation

◆ is_instantiated_

bool is_instantiated_

staticprotected

Stores whether ModificationsDB was instantiated before.

◆ modification_names_

std::unordered_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

Static Protected Attributes

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ ModificationsDB() [1/2]

◆ ModificationsDB() [2/2]

◆ ~ModificationsDB()

Member Function Documentation

◆ addModification() [1/2]

◆ addModification() [2/2]

◆ addNewModification_()

◆ findModificationIndex()

◆ getAllSearchModifications()

◆ getBestModificationByDiffMonoMass()

◆ getInstance()

◆ getModification() [1/2]

◆ getModification() [2/2]

◆ getNumberOfModifications()

◆ has()

◆ initializeModificationsDB()

◆ isInstantiated()

◆ operator=()

◆ readFromOBOFile()

◆ readFromUnimodXMLFile()

◆ residuesMatch_()

◆ searchModification()

◆ searchModifications()

◆ searchModificationsByDiffMonoMass() [1/2]

◆ searchModificationsByDiffMonoMass() [2/2]

◆ searchModificationsByDiffMonoMassSorted() [1/2]

◆ searchModificationsByDiffMonoMassSorted() [2/2]

◆ searchModificationsFast()

◆ writeTSV()

Friends And Related Function Documentation

◆ AASequence

◆ CrossLinksDB

◆ Residue

Member Data Documentation

◆ is_instantiated_

◆ modification_names_

◆ mods_