ResidueDB Class Reference

residue data base which holds residues More...

#include <OpenMS/CHEMISTRY/ResidueDB.h>

Public Types
Typedefs
typedef std::set< Residue * >::iterator	ResidueIterator
typedef std::set< const Residue * >::const_iterator	ResidueConstIterator

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 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...
void	setResidues (const String &filename)
	sets the residues from given file More...
void	addResidue (const Residue &residue)
	adds a residue, i.e. a unknown residue, where only the weight is known 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...
Iterators
ResidueIterator	beginResidue ()
ResidueIterator	endResidue ()
ResidueConstIterator	beginResidue () const
ResidueConstIterator	endResidue () const

Static Public Member Functions
static ResidueDB *	getInstance ()
	this member function serves as a replacement of the constructor More...

Protected Member Functions
void	readResiduesFromFile_ (const String &filename)
	reads residues from the given file More...
Residue *	parseResidue_ (Map< String, String > &values)
	parses a residue, given the key/value pairs from i.e. an XML file More...
void	clear_ ()
	deletes all sub-instances of the stored data like modifications and residues More...
void	clearResidues_ ()
	clears the residues More...
void	buildResidueNames_ ()
	builds an index of residue names for fast access, synonyms are also considered More...
void	addResidue_ (Residue *residue)
Private Constructors
	ResidueDB ()
	default constructor More...
	ResidueDB (const ResidueDB &residue_db)
	copy constructor More...
Assignment
ResidueDB &	operator= (const ResidueDB &aa)
	assignment operator More...

Protected Attributes
boost::unordered_map< String, Residue * >	residue_names_
Residue *	residue_by_one_letter_code_ [256]
Map< String, Map< String, Residue * > >	residue_mod_names_
std::set< Residue * >	residues_
std::set< const Residue * >	const_residues_
std::set< Residue * >	modified_residues_
std::set< const Residue * >	const_modified_residues_
Map< String, std::set< const Residue * > >	residues_by_set_
std::set< String >	residue_sets_

Detailed Description

residue data base which holds residues

The residues stored in this DB are defined in a XML file under data/CHEMISTRY/residues.xml

By default no modified residues are stored in an instance. However, if one queries the instance with getModifiedResidue, a new modified residue is added.

Member Typedef Documentation

ResidueConstIterator

typedef std::set<const Residue*>::const_iterator ResidueConstIterator

ResidueIterator

typedef std::set<Residue*>::iterator ResidueIterator

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

addResidue()

void addResidue

(

const Residue &

residue

)

adds a residue, i.e. a unknown residue, where only the weight is known

addResidue_()

void addResidue_ ( Residue *  residue )

protected

beginResidue() [1/2]

ResidueIterator beginResidue ( )

inline

beginResidue() [2/2]

ResidueConstIterator beginResidue ( ) const

inline

buildResidueNames_()

void buildResidueNames_ ( )

protected

builds an index of residue names for fast access, synonyms are also considered

clear_()

void clear_ ( )

protected

deletes all sub-instances of the stored data like modifications and residues

clearResidues_()

void clearResidues_ ( )

protected

clears the residues

endResidue() [1/2]

ResidueIterator endResidue ( )

inline

endResidue() [2/2]

ResidueConstIterator endResidue ( ) const

inline

getInstance()

static ResidueDB* getInstance ( )

inlinestatic

this member function serves as a replacement of the constructor

getModifiedResidue() [1/2]

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() [2/2]

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)

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

The possible residues are defined in share/OpenMS/CHEMISTRY/Residues.xml. At the moment the following sets are available: All - all residues stored in the file 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)

Exceptions

Exception::ElementNotFound

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

operator=()

ResidueDB& operator= ( const ResidueDB &  aa )

protected

assignment operator

parseResidue_()

Residue* parseResidue_ ( Map< String, String > &  values )

protected

parses a residue, given the key/value pairs from i.e. an XML file

readResiduesFromFile_()

void readResiduesFromFile_ ( const String &  filename )

protected

reads residues from the given file

Exceptions

Exception::ParseError

if the file cannot be parsed

setResidues()

void setResidues

(

const String &

filename

)

sets the residues from given file

Member Data Documentation

const_modified_residues_

std::set<const Residue*> const_modified_residues_

protected

const_residues_

std::set<const Residue*> const_residues_

protected

modified_residues_

std::set<Residue*> modified_residues_

protected

residue_by_one_letter_code_

Residue* residue_by_one_letter_code_[256]

protected

residue_mod_names_

Map<String, Map<String, Residue*> > residue_mod_names_

protected

residue_names_

boost::unordered_map<String, Residue*> residue_names_

protected

residue_sets_

std::set<String> residue_sets_

protected

residues_

std::set<Residue*> residues_

protected

residues_by_set_

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

protected