BALL::Residue Class Reference
[Molecular Datastructures]

#include <BALL/KERNEL/residue.h>

Inheritance diagram for BALL::Residue:

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 }
Public Member Functions
bool	operator== (const Residue &residue) const
bool	operator!= (const Residue &residue) const
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)
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
Assignment

void	set (const Residue &residue, bool deep=true)
Residue &	operator= (const Residue &residue)
void	get (Residue &residue, bool deep=true) const
void	swap (Residue &residue)
Accessors

String	getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const
bool	hasTorsionPhi () const
Angle	getTorsionPhi () const
bool	hasTorsionPsi () const
Angle	getTorsionPsi () const
Protein *	getProtein ()
const Protein *	getProtein () const
Chain *	getChain ()
const Chain *	getChain () const
SecondaryStructure *	getSecondaryStructure ()
const SecondaryStructure *	getSecondaryStructure () const
PDBAtom *	getPDBAtom (Position position)
const PDBAtom *	getPDBAtom (Position position) const
void	setID (const String &id)
const String &	getID () const
void	setInsertionCode (char insertion_code)
char	getInsertionCode () const
Size	countPDBAtoms () const
void	prepend (PDBAtom &atom)
void	append (PDBAtom &atom)
void	insert (PDBAtom &atom)
void	insertBefore (PDBAtom &atom, Composite &before)
void	insertAfter (PDBAtom &atom, Composite &after)
bool	remove (PDBAtom &atom)
void	spliceBefore (Residue &residue)
void	spliceAfter (Residue &residue)
void	splice (Residue &residue)
Predicates

bool	isAminoAcid () const
bool	isTerminal () const
bool	isNTerminal () const
bool	isCTerminal () const
Debugging and Diagnostics

virtual bool	isValid () const
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
Private Member Functions
AtomContainer *	getAtomContainer (Position position)
const AtomContainer *	getAtomContainer (Position position) const
Size	countAtomContainers () const
void	prepend (AtomContainer &atom_container)
void	append (AtomContainer &atom_container)
void	insert (AtomContainer &atom_container)
void	insertBefore (AtomContainer &atom_container, Composite &composite)
void	insertAfter (AtomContainer &atom_container, Composite &composite)
void	spliceBefore (AtomContainer &atom_container)
void	spliceAfter (AtomContainer &base_ragment)
void	splice (AtomContainer &AtomContainer)
bool	remove (AtomContainer &AtomContainer)
bool	isSuperAtomContainerOf (const AtomContainer &atom_container) const
Private Attributes
String	id_
char	insertion_code_

Detailed Description

Residue class. This class is used to represent residues in proteins.

Definition at line 38 of file residue.h.

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).
ADD_RESIDUE_ID
ADD_VARIANT_EXTENSIONS_AND_ID

Definition at line 78 of file residue.h.

enum BALL::Residue::Property

The number of predefined properties for AtomContainer.

Enumerator:

PROPERTY__NON_STANDARD
PROPERTY__AMINO_ACID
PROPERTY__WATER
PROPERTY__HAS_SSBOND
PROPERTY__C_TERMINAL
PROPERTY__N_TERMINAL
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.
NUMBER_OF_PROPERTIES

Reimplemented from BALL::Fragment.

Definition at line 50 of file residue.h.

Constructor & Destructor Documentation

BALL::Residue::Residue ( )

Default constructor.

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

Copy constructor.

BALL::Residue::Residue	(	const String &	name,
		const String &	id = `BALL_RESIDUE_DEFAULT_ID`,
		char	insertion_code = `BALL_RESIDUE_DEFAULT_INSERTION_CODE`
	)

Detailled constructor.

virtual BALL::Residue::~Residue ( ) [virtual]

Destructor.

Member Function Documentation

void BALL::Residue::append ( AtomContainer & atom_container ) [private]

Append an AtomContainer at the last position.

Parameters:

atom_container

the AtomContainer to prepend

Reimplemented from BALL::AtomContainer.

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

Append a PDBAtom at the last position.

Parameters:

atom

the PDBAtom to append

virtual void BALL::Residue::clear ( ) [virtual]

Clears the contents of this instance.

Reimplemented from BALL::AtomContainer.

Size BALL::Residue::countAtomContainers ( ) const [private]

Count the child AtomContainers.

Returns:: Size the number of AtomContainers

Reimplemented from BALL::AtomContainer.

Size BALL::Residue::countPDBAtoms ( ) const

Count the child PDBAtoms.

Returns:: Size the number of PDBAtoms

virtual void BALL::Residue::destroy ( ) [virtual]

Clears the contents of this instance and removes it from all composite structures.

Reimplemented from BALL::AtomContainer.

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.

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

Assign a Residue object from another instance.

const AtomContainer* BALL::Residue::getAtomContainer ( Position position ) const [private]

Get a constant pointer to a child AtomContainer at a given position. The pointer is 0 if this instance does not have an AtomContainer at the given position.

Parameters:

position

of the child AtomContainer

Returns:: AtomContainer* - constant pointer to the child

Reimplemented from BALL::AtomContainer.

AtomContainer* BALL::Residue::getAtomContainer ( Position position ) [private]

Get a pointer to a child AtomContainer at a given position. The pointer is 0 if this instance does not have an AtomContainer at the given position.

Parameters:

position

of the child AtomContainer

Returns:: AtomContainer* - mutable pointer to the child

Reimplemented from BALL::AtomContainer.

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 ( AtomContainer & atom_container ) [private]

Insert an AtomContainer at the last position.

Parameters:

atom_container

the AtomContainer to insert

Reimplemented from BALL::AtomContainer.

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

Insert a PDBAtom at the last position.

Parameters:

atom

the PDBAtom to append

void BALL::Residue::insertAfter	(	AtomContainer &	atom_container,
		Composite &	after
	)			`[private]`

Insert an AtomContainer after a given Composite object.

Parameters:

	atom_container	the AtomContainer to insert
	after	the Composite object to insert after

Reimplemented from BALL::AtomContainer.

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	(	AtomContainer &	atom_container,
		Composite &	before
	)			`[private]`

Insert an AtomContainer before a given Composite object.

Parameters:

	atom_container	the AtomContainer to insert
	before	the Composite object to insert before

Reimplemented from BALL::AtomContainer.

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::isSuperAtomContainerOf ( const AtomContainer & atom_container ) const [private]

Test if an AtomContainer is the parent.

Parameters:

atom_container

the AtomContainer to test

Reimplemented from BALL::AtomContainer.

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 ==

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

Assignment 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 ( AtomContainer & atom_container ) [private]

Prepend an AtomContainer at position 0.

Parameters:

atom_container

the AtomContainer to prepend

Reimplemented from BALL::AtomContainer.

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

Prepend a PDBAtom at position 0.

Parameters:

atom

the PDBAtom to prepend

bool BALL::Residue::remove ( AtomContainer & atom_container ) [private]

Remove an AtomContainer

Parameters:

atom_container

the AtomContainer to remove

Returns:: false if {atom_container} could not be removed

Reimplemented from BALL::AtomContainer.

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 ( AtomContainer & atom_container ) [private]

Move the children of {atom_container} into this instance. The children of atom_container are inserted at its position if it is is a child of this. Otherwise the children are inserted using spliceBefore .

Reimplemented from BALL::AtomContainer.

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

Move the children of residue into this instance. The children are inserted using spliceBefore .

void BALL::Residue::spliceAfter ( AtomContainer & atom_container ) [private]

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

Parameters:

atom_container

the AtomContainer to access

Reimplemented from BALL::AtomContainer.

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 ( AtomContainer & atom_container ) [private]

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

Parameters:

atom_container

the AtomContainer to access

Reimplemented from BALL::AtomContainer.

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

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

Swap the contents of two Residue objects.

Member Data Documentation

String BALL::Residue::id_ [private]

Definition at line 423 of file residue.h.

char BALL::Residue::insertion_code_ [private]

Definition at line 425 of file residue.h.

BALL::Residue Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

BALL::Residue Class Reference
[Molecular Datastructures]