OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called. More...

#include <OpenMS/CHEMISTRY/ResidueDB.h>

Collaboration diagram for ResidueDB:

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Public Member Functions
Constructors and Destructors
virtual	~ResidueDB ()
	destructor More...

Accessors
Size	getNumberOfResidues () const
	returns the number of residues stored More...

Size	getNumberOfModifiedResidues () const
	returns the number of modified residues stored More...

const Residue *	getResidue (const String &name) const
	returns a pointer to the residue with name, 3 letter code or 1 letter code name More...

const Residue *	getResidue (const unsigned char &one_letter_code) const
	returns a pointer to the residue with 1 letter code name More...

const Residue *	getModifiedResidue (const String &name)
	Returns a pointer to a modified residue given a modification name. More...

const Residue *	getModifiedResidue (const Residue *residue, const String &name)
	Returns a pointer to a modified residue given a residue and a modification name. More...

const Residue *	getModifiedResidue (const Residue residue, const ResidueModification mod)
	Returns a pointer to a modified residue given a residue and a pointer to a modification from the ModificationsDB. More...

const std::set< const Residue * >	getResidues (const String &residue_set="All") const
	returns a set of all residues stored in this residue db More...

const std::set< String >	getResidueSets () const
	returns all residue sets that are registered which this instance More...

Static Public Member Functions
static ResidueDB *	getInstance ()
	singleton More...

Protected Member Functions
Private Constructors
	ResidueDB ()
	default constructor More...

	ResidueDB (const ResidueDB &residue_db)
	copy constructor More...

Assignment
std::map< String, std::map< String, const Residue * > >	residue_mod_names_

std::set< const Residue * >	const_residues_
	all (unmodified) residues More...

std::set< const Residue * >	const_modified_residues_
	all modified residues More...

std::set< String >	residue_sets_

std::unordered_map< String, const Residue * >	residue_names_
	lookup from name to residue More...

std::array< const Residue *, 256 >	residue_by_one_letter_code_ = {{nullptr}}
	fast lookup table for residues More...

std::map< String, std::set< const Residue * > >	residues_by_set_

ResidueDB &	operator= (const ResidueDB &aa)=delete
	assignment operator More...

void	buildResidues_ ()

void	insertResidueAndAssociateWithResidueSet_ (Residue *residue, const std::vector< String > &residue_sets)
	creates and adds residues to a lookup table including the residue set More...

void	addResidue_ (Residue *residue)
	add residue and add names to lookup More...

void	addResidueNames_ (const Residue *)
	adds names of single residue to the index More...

void	addModifiedResidueNames_ (const Residue *)
	adds names of single modified residue to the index More...

Predicates
bool	hasResidue (const String &name) const
	returns true if the db contains a residue with the given name More...

bool	hasResidue (const Residue *residue) const
	returns true if the db contains the residue of the given pointer More...

void	initResidues_ ()
	initializes all residues by building More...

Detailed Description

OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called.

Constructor & Destructor Documentation

◆ ~ResidueDB()

virtual ~ResidueDB ( )

virtual

destructor

◆ ResidueDB() [1/2]

ResidueDB ( )

protected

default constructor

◆ ResidueDB() [2/2]

ResidueDB ( const ResidueDB & residue_db )

protected

copy constructor

Member Function Documentation

◆ addModifiedResidueNames_()

void addModifiedResidueNames_ ( const Residue * )

protected

adds names of single modified residue to the index

◆ addResidue_()

void addResidue_ ( Residue * residue )

protected

add residue and add names to lookup

◆ addResidueNames_()

void addResidueNames_ ( const Residue * )

protected

adds names of single residue to the index

◆ buildResidues_()

void buildResidues_ ( )

protected

◆ getInstance()

static ResidueDB* getInstance ( )

static

singleton

◆ getModifiedResidue() [1/3]

const Residue* getModifiedResidue	(	const Residue *	residue,
		const ResidueModification *	mod
	)

Returns a pointer to a modified residue given a residue and a pointer to a modification from the ModificationsDB.

The modified residue is added to the database if it doesn't exist yet. The origin of the modification has to match the residue and the term has to be ResidueModification::Anywhere.

Exceptions

Exception::IllegalArgument if the residue was not found

◆ getModifiedResidue() [2/3]

const Residue* getModifiedResidue	(	const Residue *	residue,
		const String &	name
	)

Returns a pointer to a modified residue given a residue and a modification name.

The modified residue is added to the database if it doesn't exist yet.

Exceptions

Exception::IllegalArgument	if the residue was not found
Exception::InvalidValue	if no matching modification was found (via ModificationsDB::getModification)

◆ getModifiedResidue() [3/3]

const Residue* getModifiedResidue ( const String & name )

Returns a pointer to a modified residue given a modification name.

The "base" residue is looked up in ModificationsDB using the modification name. The modified residue is added to the database if it doesn't exist yet.

◆ getNumberOfModifiedResidues()

Size getNumberOfModifiedResidues ( ) const

returns the number of modified residues stored

◆ getNumberOfResidues()

Size getNumberOfResidues ( ) const

returns the number of residues stored

◆ getResidue() [1/2]

const Residue* getResidue ( const String & name ) const

returns a pointer to the residue with name, 3 letter code or 1 letter code name

◆ getResidue() [2/2]

const Residue* getResidue ( const unsigned char & one_letter_code ) const

returns a pointer to the residue with 1 letter code name

◆ getResidues()

const std::set<const Residue*> getResidues ( const String & residue_set = "All" ) const

returns a set of all residues stored in this residue db

Following sets are available: All - all residues Natural20 - default 20 naturally occurring residues Natural19WithoutI - default natural amino acids, excluding isoleucine (isobaric to leucine) Natural19WithoutL - default natural amino acids, excluding leucine (isobaric to isoleucine) Natural19J - default natural amino acids, (isobaric leucine/isoleucine are marked by 'J') AmbiguousWithoutX - all amino acids, including ambiguous ones: B (asparagine or aspartate), Z (glutamine or glutamate), J (isoleucine or leucine) Ambiguous - all amino acids including all ambiguous ones (X can be every other amino acid) AllNatural - naturally occurring residues, including selenocysteine (U)

returns an empty set if the specified residue set is not defined

◆ getResidueSets()

const std::set<String> getResidueSets ( ) const

returns all residue sets that are registered which this instance

◆ hasResidue() [1/2]

bool hasResidue ( const Residue * residue ) const

returns true if the db contains the residue of the given pointer

◆ hasResidue() [2/2]

bool hasResidue ( const String & name ) const

returns true if the db contains a residue with the given name

◆ initResidues_()

void initResidues_ ( )

protected

initializes all residues by building

◆ insertResidueAndAssociateWithResidueSet_()

void insertResidueAndAssociateWithResidueSet_	(	Residue *	residue,
		const std::vector< String > &	residue_sets
	)

protected

creates and adds residues to a lookup table including the residue set

◆ operator=()

ResidueDB& operator= ( const ResidueDB & aa )

protecteddelete

assignment operator

Member Data Documentation

◆ const_modified_residues_

std::set<const Residue*> const_modified_residues_

protected

all modified residues

◆ const_residues_

std::set<const Residue*> const_residues_

protected

all (unmodified) residues

◆ residue_by_one_letter_code_

std::array<const Residue*, 256> residue_by_one_letter_code_ = {{nullptr}}

protected

fast lookup table for residues

◆ residue_mod_names_

std::map<String, std::map<String, const Residue*> > residue_mod_names_

protected

◆ residue_names_

std::unordered_map<String, const Residue*> residue_names_

protected

lookup from name to residue

◆ residue_sets_

std::set<String> residue_sets_

protected

◆ residues_by_set_

std::map<String, std::set<const Residue*> > residues_by_set_

protected

Public Member Functions

Static Public Member Functions

Protected Member Functions

Assignment

Predicates

Detailed Description

Constructor & Destructor Documentation

◆ ~ResidueDB()

◆ ResidueDB() [1/2]

◆ ResidueDB() [2/2]

Member Function Documentation

◆ addModifiedResidueNames_()

◆ addResidue_()

◆ addResidueNames_()

◆ buildResidues_()

◆ getInstance()

◆ getModifiedResidue() [1/3]

◆ getModifiedResidue() [2/3]

◆ getModifiedResidue() [3/3]

◆ getNumberOfModifiedResidues()

◆ getNumberOfResidues()

◆ getResidue() [1/2]

◆ getResidue() [2/2]

◆ getResidues()

◆ getResidueSets()

◆ hasResidue() [1/2]

◆ hasResidue() [2/2]

◆ initResidues_()

◆ insertResidueAndAssociateWithResidueSet_()

◆ operator=()

Member Data Documentation

◆ const_modified_residues_

◆ const_residues_

◆ residue_by_one_letter_code_

◆ residue_mod_names_

◆ residue_names_

◆ residue_sets_

◆ residues_by_set_