BALL::Residue Class Reference
[Molecular Datastructures]

#include <residue.h>

Inheritance diagram for BALL::Residue:

[legend]


Public Types
Enums
enum	Property { PROPERTY__NON_STANDARD = Fragment::NUMBER_OF_PROPERTIES + 1, PROPERTY__AMINO_ACID, PROPERTY__WATER, PROPERTY__HAS_SSBOND, PROPERTY__C_TERMINAL, PROPERTY__N_TERMINAL, PROPERTY__CYCLIC, NUMBER_OF_PROPERTIES }
	The number of predefined properties for AtomContainer. More...
enum	FullNameType { NO_VARIANT_EXTENSIONS, ADD_VARIANT_EXTENSIONS, ADD_RESIDUE_ID, ADD_VARIANT_EXTENSIONS_AND_ID }
	Enum used to describe the kind of name constructed by getFullName . More...
Public Member Functions
bool	operator== (const Residue &residue) const
	Equality operator.
bool	operator!= (const Residue &residue) const
	Inequality operator.
Constructors and Destructors
	Residue ()
	Default constructor.
	Residue (const Residue &residue, bool deep=true)
	Copy constructor.
	Residue (const String &name, const String &id=BALL_RESIDUE_DEFAULT_ID, char insertion_code=BALL_RESIDUE_DEFAULT_INSERTION_CODE)
	Detailled constructor.
virtual	~Residue ()
	Destructor.
virtual void	clear ()
	Clears the contents of this instance.
virtual void	destroy ()
	Clears the contents of this instance and removes it from all composite structures.
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Writes a Residue object to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Reads a Residue object from a persistent stream.
Assignment
void	set (const Residue &residue, bool deep=true)
	Assignment with cloning facility.
Residue &	operator= (const Residue &residue)
	Assignment operator.
void	get (Residue &residue, bool deep=true) const
	Assign a Residue object from another instance.
void	swap (Residue &residue)
	Swap the contents of two Residue objects.
Accessors
String	getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const
	Return the fully qualified name.
bool	hasTorsionPhi () const
	Check whether the torsion angle phi is defined.
Angle	getTorsionPhi () const
	Calculate the torsion angle phi.
bool	hasTorsionPsi () const
	Check whether the torsion angle psi is defined.
Angle	getTorsionPsi () const
	Calculate the torsion angle psi.
Protein *	getProtein ()
	Get a pointer to the parent protein.
const Protein *	getProtein () const
	Get a constant pointer to the parent protein.
Chain *	getChain ()
	Get a pointer to the parent chain.
const Chain *	getChain () const
	Get a pointer to the parent chain.
SecondaryStructure *	getSecondaryStructure ()
	Get a pointer to the parent secondary structure.
const SecondaryStructure *	getSecondaryStructure () const
	Get a pointer to the parent secondary structure.
PDBAtom *	getPDBAtom (Position position)
	Get a pointer to a child PDBAtom at a given position.
const PDBAtom *	getPDBAtom (Position position) const
	Get a pointer to a child PDBAtom at a given position.
void	setID (const String &id)
	Set the ID.
const String &	getID () const
	Retrieve the ID.
void	setInsertionCode (char insertion_code)
	Set the insertion code.
char	getInsertionCode () const
	Get the insertion code.
Size	countPDBAtoms () const
	Count the child PDBAtoms.
void	prepend (PDBAtom &atom)
	Prepend a PDBAtom at position 0.
void	append (PDBAtom &atom)
	Append a PDBAtom at the last position.
void	insert (PDBAtom &atom)
	Insert a PDBAtom at the last position.
void	insertBefore (PDBAtom &atom, Composite &before)
	Insert a PDBAtom before a given Composite object.
void	insertAfter (PDBAtom &atom, Composite &after)
	Insert a PDBAtom after a given Composite object.
bool	remove (PDBAtom &atom)
	Remove a PDBAtom.
void	spliceBefore (Residue &residue)
	Cut all children of `residue` and prepend them before the children of this instance.
void	spliceAfter (Residue &residue)
	Cut all children of `residue` and append them after the children of this instance.
void	splice (Residue &residue)
	Move the children of `residue` into this instance.
Predicates
bool	isAminoAcid () const
	Test if this residue is an amino acid.
bool	isTerminal () const
	Test if this residue is terminal.
bool	isNTerminal () const
	Test if this residue is N-terminal.
bool	isCTerminal () const
	Test if this residue is C-terminal.
Debugging and Diagnostics
virtual bool	isValid () const
	Internal state and consistency self-validation.
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
	Internal state dump.

Detailed Description

Residue class.

This class is used to represent residues in proteins.

Member Enumeration Documentation

enum BALL::Residue::FullNameType

Enum used to describe the kind of name constructed by getFullName .

Enumerator:

NO_VARIANT_EXTENSIONS	This returns the unmodified residue name only.
ADD_VARIANT_EXTENSIONS	Add the residue variant extensions (e.g. '-C' for C-terminal residues).

enum BALL::Residue::Property

The number of predefined properties for AtomContainer.

Enumerator:

PROPERTY__CYCLIC

Property for cyclic peptides.

This property is set by the build bonds processor, if an atom of the first and an atom of the last residue in a chain share a bond.

Reimplemented from BALL::Fragment.

Member Function Documentation

void BALL::Residue::append ( PDBAtom & atom )

Append a PDBAtom at the last position.

Parameters:

atom

the PDBAtom to append

Size BALL::Residue::countPDBAtoms ( ) const

Count the child PDBAtoms.

Returns:: Size the number of PDBAtoms

virtual void BALL::Residue::dump	(	std::ostream &	s = `std::cout`,
		Size	depth = `0`
	)			const `[virtual]`

Internal state dump.

Dump the current internal state to the output ostream s with dumping depth depth .

Parameters:

	s	output stream where to output the internal state
	depth	the dumping depth

Reimplemented from BALL::Fragment.

const Chain* BALL::Residue::getChain ( ) const

Get a pointer to the parent chain.

The pointer is 0 if this instance does not have a parent chain.

Returns:: Chain* - constant pointer to the parent chain

Chain* BALL::Residue::getChain ( )

Get a pointer to the parent chain.

The pointer is 0 if this instance does not have a parent chain.

Returns:: Chain* - mutable pointer to the parent chain

String BALL::Residue::getFullName ( FullNameType type = ADD_VARIANT_EXTENSIONS ) const

Return the fully qualified name.

Residue names are modified as follows:

-N is added for N terminal residues
-C is added for C terminal residue
[-]S is added for CYS involved in a disulphide bridge
-M is added for individual amino acids (C and N terminal)

Parameters:

type if type is set to NO_VARIANT_EXTENSIONS, the variant extension (-XX) is omitted.

Returns:: String the full fragment name

const String& BALL::Residue::getID ( ) const

Retrieve the ID.

Returns:: String the ID

char BALL::Residue::getInsertionCode ( ) const

Get the insertion code.

Returns:: char the insertion code

const PDBAtom* BALL::Residue::getPDBAtom ( Position position ) const

Get a pointer to a child PDBAtom at a given position.

The pointer is 0 if this instance does not have a PDBAtom at this position.

Parameters:

position

the position of the child PDBAtom

Returns:: PDBAtom* - constant pointer to the child

PDBAtom* BALL::Residue::getPDBAtom ( Position position )

Get a pointer to a child PDBAtom at a given position.

The pointer is 0 if this instance does not have a PDBAtom at this position.

Parameters:

position

the position of the child PDBAtom

Returns:: PDBAtom* - mutable pointer to the child

const Protein* BALL::Residue::getProtein ( ) const

Get a constant pointer to the parent protein.

The pointer is 0 if this instance does not have a parent protein.

Returns:: Protein* - constant pointer to the parent protein

Protein* BALL::Residue::getProtein ( )

Get a pointer to the parent protein.

The pointer is 0 if this instance does not have a parent protein.

Returns:: Protein* - mutable pointer to the parent protein

const SecondaryStructure* BALL::Residue::getSecondaryStructure ( ) const

Get a pointer to the parent secondary structure.

The pointer is 0 if this instance does not have a parent secondary structure.

Returns:: SecondaryStructure* - mutable pointer to the parent chain

SecondaryStructure* BALL::Residue::getSecondaryStructure ( )

Get a pointer to the parent secondary structure.

The pointer is 0 if this instance does not have a parent secondary structure.

Returns:: SecondaryStructure* - mutable pointer to the parent chain

Angle BALL::Residue::getTorsionPhi ( ) const

Calculate the torsion angle phi.

Returns:: Angle - the torsion angle phi

Angle BALL::Residue::getTorsionPsi ( ) const

Calculate the torsion angle psi.

Returns:: Angle - the torsion angle phi

bool BALL::Residue::hasTorsionPhi ( ) const

Check whether the torsion angle phi is defined.

Returns:: bool

bool BALL::Residue::hasTorsionPsi ( ) const

Check whether the torsion angle psi is defined.

Returns:: bool

void BALL::Residue::insert ( PDBAtom & atom )

Insert a PDBAtom at the last position.

Parameters:

atom

the PDBAtom to append

void BALL::Residue::insertAfter	(	PDBAtom &	atom,
		Composite &	after
	)

Insert a PDBAtom after a given Composite object.

Parameters:

	atom	the PDBAtom to insert
	after	the Composite object to insert after

void BALL::Residue::insertBefore	(	PDBAtom &	atom,
		Composite &	before
	)

Insert a PDBAtom before a given Composite object.

Parameters:

	atom	the PDBAtom to insert
	before	the Composite object to insert before

bool BALL::Residue::isAminoAcid ( ) const

Test if this residue is an amino acid.

Returns true, if this instance has the property "PROPERTY__AMINO_ACID".

Returns:: bool

bool BALL::Residue::isCTerminal ( ) const

Test if this residue is C-terminal.

Returns true, if this instance has the property "PROPERTY__AMINO_ACID" and is the last amino acid residue in its parent chain.

Returns:: bool

bool BALL::Residue::isNTerminal ( ) const

Test if this residue is N-terminal.

Returns true, if this instance has the property "PROPERTY__AMINO_ACID" and is the first amino acid residue in its parent chain.

Returns:: bool

bool BALL::Residue::isTerminal ( ) const

Test if this residue is terminal.

Returns true, if this instance has the property "PROPERTY__AMINO_ACID" and is the first or last amino acid residue in its parent chain.

Returns:: bool

virtual bool BALL::Residue::isValid ( ) const [virtual]

Internal state and consistency self-validation.

Returns:: bool - true if the internal state is correct (self-validated) and consistent, false otherwise

Reimplemented from BALL::AtomContainer.

bool BALL::Residue::operator!= ( const Residue & residue ) const

Inequality operator.

See also:: operator ==

bool BALL::Residue::operator== ( const Residue & residue ) const

Equality operator.

Two residues are equal if they have the same handle.

See also:: Object::operator ==

void BALL::Residue::persistentRead ( PersistenceManager & pm ) throw (Exception::GeneralException) [virtual]

Reads a Residue object from a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Fragment.

void BALL::Residue::persistentWrite	(	PersistenceManager &	pm,
		const char *	name = `0`
	)			const throw (Exception::GeneralException) `[virtual]`

Writes a Residue object to a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Fragment.

void BALL::Residue::prepend ( PDBAtom & atom )

Prepend a PDBAtom at position 0.

Parameters:

atom

the PDBAtom to prepend

bool BALL::Residue::remove ( PDBAtom & atom )

Remove a PDBAtom.

Parameters:

atom

the PDBAtom to remove

void BALL::Residue::set	(	const Residue &	residue,
		bool	deep = `true`
	)

Assignment with cloning facility.

The assignment is either deep or shallow (default).

Parameters:

	residue	the Residue to be copied (cloned)
	deep	make a deep (=`true`) or shallow (=`false`) copy

void BALL::Residue::setID ( const String & id )

Set the ID.

Parameters:

id

the new ID

void BALL::Residue::setInsertionCode ( char insertion_code )

Set the insertion code.

Parameters:

insertion_code

the new insertion code

void BALL::Residue::splice ( Residue & residue )

Move the children of residue into this instance.

The children are inserted using spliceBefore .

void BALL::Residue::spliceAfter ( Residue & residue )

Cut all children of residue and append them after the children of this instance.

Parameters:

residue

the residue to access

void BALL::Residue::spliceBefore ( Residue & residue )

Cut all children of residue and prepend them before the children of this instance.

Parameters:

residue

the residue to access

BALL::Residue Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

Member Function Documentation

BALL::Residue Class Reference
[Molecular Datastructures]