ResidueDB Class Reference

residue data base which holds residues More...

#include <OpenMS/CHEMISTRY/ResidueDB.h>

Collaboration diagram for ResidueDB:

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...
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...

Protected Member Functions
Private Constructors
	ResidueDB ()
	default constructor More...
	ResidueDB (const ResidueDB &residue_db)
	copy constructor More...

Typedefs
typedef std::set< Residue * >::iterator	ResidueIterator
typedef std::set< const Residue * >::const_iterator	ResidueConstIterator
static ResidueDB *	getInstance ()
	this member function serves as a replacement of the constructor More...

Iterators
ResidueIterator	beginResidue ()
ResidueIterator	endResidue ()
ResidueConstIterator	beginResidue () const
ResidueConstIterator	endResidue () const
void	setResidues_ (const String &filename)
	sets the residues from given file More...

Assignment
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_
ResidueDB &	operator= (const ResidueDB &aa)
	assignment operator More...
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 and all lookup structures More...
void	clearResidueModifications_ ()
	clears the residue modifications and all lookup structures More...
void	buildResidueNames_ ()
	builds an index of residue names for fast access, synonyms are also considered More...
void	addResidue_ (Residue *residue)

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_ ( 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

clearResidueModifications_()

void clearResidueModifications_ ( )

protected

clears the residue modifications and all lookup structures

clearResidues_()

void clearResidues_ ( )

protected

clears the residues and all lookup structures

endResidue() [1/2]

ResidueIterator endResidue ( )

inline

endResidue() [2/2]

ResidueConstIterator endResidue ( ) const

inline

getInstance()

static ResidueDB* getInstance ( )

static

this member function serves as a replacement of the constructor

getModifiedResidue() [1/2]

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)

getModifiedResidue() [2/2]

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.

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)

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

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 )

protected

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