ModificationsDB Class Reference [Chemistry]

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

#include <OpenMS/CHEMISTRY/ModificationsDB.h>

List of all members.

Public Member Functions
Size	getNumberOfModifications () const
	returns the number of modifications read from the unimod.xml file
const ResidueModification &	getModification (Size index) const
	returns the modification with the given index
void	searchTerminalModifications (std::set< const ResidueModification * > &mods, const String &name, ResidueModification::Term_Specificity term_spec) const
	returns all modifications which have the given name as synonym
void	searchModifications (std::set< const ResidueModification * > &mods, const String &orgin, const String &mod_name, ResidueModification::Term_Specificity term_spec) const
	returns all modification which have the given name as synonym and the given origin
void	searchModifications (std::set< const ResidueModification * > &mods, const String &mod_name, ResidueModification::Term_Specificity term_spec) const
	returns all modification which have the given name as synonym
const ResidueModification &	getTerminalModification (const String &name, ResidueModification::Term_Specificity term_spec) const
	returns the modifications of the given name
const ResidueModification &	getModification (const String &residue_name, const String &mod_name, ResidueModification::Term_Specificity term_spec) const
	returns the modification with the given name and given residue
const ResidueModification &	getModification (const String &modification) const
Size	findModificationIndex (const String &mod_name) const
	returns the index of the modification in the mods_ vector; a unique name must be given
void	getTerminalModificationsByDiffMonoMass (std::vector< String > &mods, DoubleReal mass, DoubleReal error, ResidueModification::Term_Specificity term_spec)
	query the modifications DB to get the terminal modifications with mass
void	getModificationsByDiffMonoMass (std::vector< String > &mods, DoubleReal mass, DoubleReal error=0.0)
	query the modifications DB to get the modifications with mass, without any specific origin
void	getModificationsByDiffMonoMass (std::vector< String > &mods, const String &residue, DoubleReal mass, DoubleReal error=0.0)
	query the modifications DB to get modifications with the given mass at the given residue
void	readFromOBOFile (const String &filename)
	adds modifications from a given file in OBO format
void	readFromUnimodXMLFile (const String &filename)
	adds modifications from a given file in Unimod XML format
void	getAllSearchModifications (std::vector< String > &modifications)
	get all modifications that can be used for identification searches
Static Public Member Functions
static ModificationsDB *	getInstance ()
Protected Attributes
std::vector < ResidueModification * >	mods_
	stores the modifications
Map< String, std::set< const ResidueModification * > >	modification_names_
	stores the mappings of (unique) names to the modifications
Private Member Functions
Constructors and Destructors
	ModificationsDB ()
	default constructor
	ModificationsDB (const ModificationsDB &residue_db)
	copy constructor
virtual	~ModificationsDB ()
	destructor
Assignment
ModificationsDB &	operator= (const ModificationsDB &aa)
	assignment operator

---

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 there 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.

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Constructor & Destructor Documentation

ModificationsDB

(

)

[private]

default constructor

ModificationsDB

(

const ModificationsDB &

residue_db

)

[private]

copy constructor

virtual ~ModificationsDB

(

)

[private, virtual]

destructor

---

Member Function Documentation

Size findModificationIndex

(

const String &

mod_name

)

const

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

void getAllSearchModifications

(

std::vector< String > &

modifications

)

get all modifications that can be used for identification searches

static ModificationsDB* getInstance

(

)

[inline, static]

const ResidueModification& getModification

(

const String &

modification

)

const

const ResidueModification& getModification	(	const String &	residue_name,
		const String &	mod_name,
		ResidueModification::Term_Specificity	term_spec
	)			const

returns the modification with the given name and given residue

const ResidueModification& getModification

(

Size

index

)

const

returns the modification with the given index

void getModificationsByDiffMonoMass	(	std::vector< String > &	mods,
		const String &	residue,
		DoubleReal	mass,
		DoubleReal	error = 0.0
	)

query the modifications DB to get modifications with the given mass at the given residue

void getModificationsByDiffMonoMass	(	std::vector< String > &	mods,
		DoubleReal	mass,
		DoubleReal	error = 0.0
	)

query the modifications DB to get the modifications with mass, without any specific origin

Size getNumberOfModifications

(

)

const

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

const ResidueModification& getTerminalModification	(	const String &	name,
		ResidueModification::Term_Specificity	term_spec
	)			const

returns the modifications of the given name

This can either be the PSI-MOD identifier or every other unique identifier which can be found in the PSI-MOD definitions file.

To search for more than one modification searchModifications() can be used!

Exceptions:

ElementNotFound

is thrown if no or more than one element is found

void getTerminalModificationsByDiffMonoMass	(	std::vector< String > &	mods,
		DoubleReal	mass,
		DoubleReal	error,
		ResidueModification::Term_Specificity	term_spec
	)

query the modifications DB to get the terminal modifications with mass

ModificationsDB& operator=

(

const ModificationsDB &

aa

)

[private]

assignment operator

void readFromOBOFile

(

const String &

filename

)

adds modifications from a given file in OBO format

void readFromUnimodXMLFile

(

const String &

filename

)

adds modifications from a given file in Unimod XML format

void searchModifications	(	std::set< const ResidueModification * > &	mods,
		const String &	mod_name,
		ResidueModification::Term_Specificity	term_spec
	)			const

returns all modification which have the given name as synonym

void searchModifications	(	std::set< const ResidueModification * > &	mods,
		const String &	orgin,
		const String &	mod_name,
		ResidueModification::Term_Specificity	term_spec
	)			const

returns all modification which have the given name as synonym and the given origin

void searchTerminalModifications	(	std::set< const ResidueModification * > &	mods,
		const String &	name,
		ResidueModification::Term_Specificity	term_spec
	)			const

returns all modifications which have the given name as synonym

---

Member Data Documentation

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

stores the mappings of (unique) names to the modifications

std::vector<ResidueModification *> mods_ [protected]

stores the modifications