ResidueDB Class Reference [Chemistry]

residue data base which holds residues More...

#include <OpenMS/CHEMISTRY/ResidueDB.h>

List of all members.

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
Accessors
Size	getNumberOfResidues () const
	returns the number of residues stored
Size	getNumberOfModifiedResidues () const
const Residue *	getResidue (const String &name) const
	returns a pointer to the residue with name, 3 letter code or 1 letter code name
const Residue *	getModifiedResidue (const String &name)
const Residue *	getModifiedResidue (const Residue *residue, const String &name)
const std::set< const Residue * >	getResidues (const String &residue_set="All") const
	returns a set of all residues stored in this residue db
const std::set< String > &	getResidueSets () const
	returns all residue sets that are registered which this instance
void	setResidues (const String &filename)
	sets the residues from given file
void	addResidue (const Residue &residue)
	adds a residue, i.e. a unkown residue, where only the weight is known
Predicates
bool	hasResidue (const String &name) const
	returns true if the db contains a residue with the given name
bool	hasResidue (const Residue *residue) const
	returns true if the db contains the residue of the given pointer
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
Protected Member Functions
void	readResiduesFromFile_ (const String &filename)
	reads residues from the given file
Residue *	parseResidue_ (Map< String, String > &values)
	parses a residue, given the key/value pairs from i.e. an XML file
void	clear_ ()
	deletes all sub-instances of the stored data like modifications and residues
void	clearResidues_ ()
	clears the residues
void	buildResidueNames_ ()
	builds an index of residue names for fast access, synonyms are also considered
void	addResidue_ (Residue *residue)
Private Constructors
	ResidueDB ()
	default constructor
	ResidueDB (const ResidueDB &residue_db)
	copy constructor
Assignment
ResidueDB &	operator= (const ResidueDB &aa)
	assignment operator
Protected Attributes
Map< String, Residue * >	residue_names_
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

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

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

---

Constructor & Destructor Documentation

virtual ~ResidueDB

(

)

[virtual]

destructor

ResidueDB

(

)

[protected]

default constructor

ResidueDB

(

const ResidueDB &

residue_db

)

[protected]

copy constructor

---

Member Function Documentation

void addResidue

(

const Residue &

residue

)

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

void addResidue_

(

Residue *

residue

)

[protected]

ResidueIterator beginResidue

(

)

[inline]

ResidueConstIterator beginResidue

(

)

const [inline]

void buildResidueNames_

(

)

[protected]

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

void clear_

(

)

[protected]

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

void clearResidues_

(

)

[protected]

clears the residues

ResidueConstIterator endResidue

(

)

const [inline]

ResidueIterator endResidue

(

)

[inline]

static ResidueDB* getInstance

(

)

[inline, static]

this member function serves as a replacement of the constructor

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

const Residue* getModifiedResidue

(

const String &

name

)

Size getNumberOfModifiedResidues

(

)

const

Size getNumberOfResidues

(

)

const

returns the number of residues stored

const Residue* getResidue

(

const String &

name

)

const

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

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 occuring 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 occuring residues, including selenocysteine (U)

const std::set<String>& getResidueSets

(

)

const

returns all residue sets that are registered which this instance

bool hasResidue

(

const String &

name

)

const

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

bool hasResidue

(

const Residue *

residue

)

const

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

ResidueDB& operator=

(

const ResidueDB &

aa

)

[protected]

assignment operator

Residue* parseResidue_

(

Map< String, String > &

values

)

[protected]

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

void readResiduesFromFile_

(

const String &

filename

)

[protected]

reads residues from the given file

void setResidues

(

const String &

filename

)

sets the residues from given file

---

Member Data Documentation

std::set<const Residue *> const_modified_residues_ [protected]

std::set<const Residue *> const_residues_ [protected]

std::set<Residue *> modified_residues_ [protected]

Map<String, Map<String, Residue *> > residue_mod_names_ [protected]

Map<String, Residue *> residue_names_ [protected]

std::set<String> residue_sets_ [protected]

std::set<Residue *> residues_ [protected]

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