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>

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)

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...

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...

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

Protected Member Functions
void	initResidues_ ()
	initializes all residues by building 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...

Private Constructors
	ResidueDB ()
	default constructor More...

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

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

Protected Attributes
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_

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

Referenced by OpenMS::NuXLPresets::getPresets().

◆ getModifiedResidue() [1/3]

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.

◆ 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 Residue *	residue,
		const ResidueModification *	mod
	)

◆ 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

Referenced by OpenMS::NuXLPresets::getPresets().

◆ 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 String & name ) const

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

◆ hasResidue() [2/2]

bool hasResidue ( const Residue * residue ) const

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

◆ 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

Protected Attributes

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_