BALL::SecondaryStructure Class Reference
[Miscellaneous]

#include <BALL/KERNEL/secondaryStructure.h>

Inheritance diagram for BALL::SecondaryStructure:

Public Types
Enums

enum	Type { HELIX, COIL, STRAND, TURN, UNKNOWN, NUMBER_OF_TYPES }
Public Member Functions
Constructors and Destructors

	SecondaryStructure ()
	Default constructor.
	SecondaryStructure (const SecondaryStructure &secondary_structure, bool deep=true)
	Copy constructor.
	SecondaryStructure (const String &name)
virtual	~SecondaryStructure ()
	Destructor.
virtual void	clear ()
	Clear the contents of the secondary structure.
virtual void	destroy ()
	Clear the contents of the secondary structure and remove it from all composite structures.
Predicates

bool	operator== (const SecondaryStructure &secondary_structure) const
bool	operator!= (const SecondaryStructure &secondary_structure) const
Persistence

void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Write a SecondaryStructure object to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Read a SecondaryStructure object from a persistent stream.
Assignment

void	set (const SecondaryStructure &secondary_structure, bool deep=true)
SecondaryStructure &	operator= (const SecondaryStructure &secondary_structure)
void	get (SecondaryStructure &secondary_structure, bool deep=true) const
void	swap (SecondaryStructure &secondary_structure)
Accessors

Type	getType () const
	Return the type of secondary structure.
void	setType (Type type)
	Set the type of secondary structure.
Protein *	getProtein ()
const Protein *	getProtein () const
Chain *	getChain ()
const Chain *	getChain () const
Residue *	getResidue (Position position)
const Residue *	getResidue (Position position) const
Residue *	getNTerminal ()
const Residue *	getNTerminal () const
Residue *	getCTerminal ()
const Residue *	getCTerminal () const
PDBAtom *	getPDBAtom (Position position)
const PDBAtom *	getPDBAtom (Position position) const
Size	countResidues () const
Size	countPDBAtoms () const
void	prepend (Residue &residue)
void	append (Residue &residue)
void	insert (Residue &residue)
void	insertBefore (Residue &residue, Composite &before)
void	insertAfter (Residue &residue, Composite &after)
bool	remove (Residue &residue)
void	spliceBefore (SecondaryStructure &secondary_structure)
void	spliceAfter (SecondaryStructure &secondary_structure)
void	splice (SecondaryStructure &secondary_structure)
Debugging and Diagnostics

virtual bool	isValid () const
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
Protected Attributes
Type	type_
	The secondary structure type (helix, strand, coil, turn).
Private Member Functions
Fragment *	getFragment (Position position)
const Fragment *	getFragment (Position position) const
Atom *	getAtom (Position position)
const Atom *	getAtom (Position position) const
void	prepend (Atom &atom)
void	append (Atom &atom)
void	insert (Atom &atom)
void	insertBefore (Atom &atom, Composite &before)
void	insertAfter (Atom &atom, Composite &after)
bool	remove (Atom &atom)
void	prepend (AtomContainer &atom_container)
void	append (AtomContainer &atom_container)
void	insert (AtomContainer &atom_container)
void	insertBefore (AtomContainer &atom_container, Composite &before)
void	insertAfter (AtomContainer &atom_container, Composite &after)
void	spliceBefore (AtomContainer &atom_container)
void	spliceAfter (AtomContainer &atom_container)
void	splice (AtomContainer &atom_container)
bool	remove (AtomContainer &atom_container)

Detailed Description

Secondary structure class. This class is used to represent secondary structure elements of protein chains.

Definition at line 31 of file secondaryStructure.h.

Member Enumeration Documentation

enum BALL::SecondaryStructure::Type

Secondary structure type

Enumerator:

HELIX
COIL
STRAND
TURN
UNKNOWN
NUMBER_OF_TYPES

Definition at line 44 of file secondaryStructure.h.

Constructor & Destructor Documentation

BALL::SecondaryStructure::SecondaryStructure ( )

Default constructor.

BALL::SecondaryStructure::SecondaryStructure	(	const SecondaryStructure &	secondary_structure,
		bool	deep = `true`
	)

Copy constructor.

BALL::SecondaryStructure::SecondaryStructure ( const String & name )

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

Destructor.

Member Function Documentation

void BALL::SecondaryStructure::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::SecondaryStructure::append ( Atom & atom ) [private]

Append an atom to the last position.

Parameters:

atom

the atom to append

Reimplemented from BALL::AtomContainer.

void BALL::SecondaryStructure::append ( Residue & residue )

Append a Residue after the last position.

Parameters:

residue

the Residue to append

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

Clear the contents of the secondary structure.

Reimplemented from BALL::AtomContainer.

Size BALL::SecondaryStructure::countPDBAtoms ( ) const

Count the PDBAtoms.

Returns:: Size the number of PDBAtoms

Size BALL::SecondaryStructure::countResidues ( ) const

Count the Residues.

Returns:: Size the number of residues

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

Clear the contents of the secondary structure and remove it from all composite structures.

Reimplemented from BALL::AtomContainer.

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

Internal state dump. Dump the current internal state of this instance to the output ostream s with dumping depth depth .

Parameters:

	s	output stream where to output the internal state of this instance
	depth	the dumping depth

Reimplemented from BALL::AtomContainer.

void BALL::SecondaryStructure::get	(	SecondaryStructure &	secondary_structure,
		bool	deep = `true`
	)			const

Assignment. The assignment is either deep or shallow (default).

Parameters:

secondary_structure

the SecondaryStructure to be assigned to

See also:: secondary_structure::set

const Atom* BALL::SecondaryStructure::getAtom ( Position position ) const [private]

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

Parameters:

position

the position of the child atom

Returns:: Atom* - constant pointer to the child

Reimplemented from BALL::AtomContainer.

Atom* BALL::SecondaryStructure::getAtom ( Position position ) [private]

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

Parameters:

position

the position of the child atom

Returns:: Atom* - mutable pointer to the child

Reimplemented from BALL::AtomContainer.

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

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

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

Chain* BALL::SecondaryStructure::getChain ( )

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

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

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

Get a pointer to the C-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns:: Residue* - constant pointer to the C-terminal Residue

Residue* BALL::SecondaryStructure::getCTerminal ( )

Get a pointer to the C-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns:: Residue* - mutable pointer to the C-terminal Residue

const Fragment* BALL::SecondaryStructure::getFragment ( Position position ) const [private]

Fragment* BALL::SecondaryStructure::getFragment ( Position position ) [private]

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

Get a pointer to the N-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns:: Residue* - constant pointer to the N-terminal Residue

Residue* BALL::SecondaryStructure::getNTerminal ( )

Get a pointer to the N-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns:: Residue* - mutable pointer to the N-terminal Residue

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

Get a pointer to a child PDBAtom at a given position. The pointer is 0 if this instance residue does not have a PDBAtom at this position.

Parameters:

position

the position of the child PDBAtom

Returns:: PDBAtom* - mutable pointer to the child

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

Get a pointer to a child PDBAtom at a given position. The pointer is 0 if this instance residue does not have a PDBAtom at this position.

Parameters:

position

the position of the child PDBAtom

Returns:: PDBAtom* - constant pointer to the child

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

Get a 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::SecondaryStructure::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 Residue* BALL::SecondaryStructure::getResidue ( Position position ) const

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

Parameters:

position

the position of the child Residue

Returns:: Residue* - constant pointer to the child

Residue* BALL::SecondaryStructure::getResidue ( Position position )

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

Parameters:

position

the position of the child Residue

Returns:: Residue* - mutable pointer to the child

Type BALL::SecondaryStructure::getType ( ) const [inline]

Return the type of secondary structure.

Definition at line 150 of file secondaryStructure.h.

void BALL::SecondaryStructure::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::SecondaryStructure::insert ( Atom & atom ) [private]

Insert an atom to the last position.

Parameters:

atom

the atom to insert

Reimplemented from BALL::AtomContainer.

void BALL::SecondaryStructure::insert ( Residue & residue )

Insert a Residue after the last position.

Parameters:

residue

the Residue to insert

void BALL::SecondaryStructure::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::SecondaryStructure::insertAfter	(	Atom &	atom,
		Composite &	after
	)			`[private]`

Insert an atom after a given Composite object.

Parameters:

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

Reimplemented from BALL::AtomContainer.

void BALL::SecondaryStructure::insertAfter	(	Residue &	residue,
		Composite &	after
	)

Insert a Residue after a given Composite object.

Parameters:

	residue	the Residue to insert
	after	the Composite object to insert before

void BALL::SecondaryStructure::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::SecondaryStructure::insertBefore	(	Atom &	atom,
		Composite &	before
	)			`[private]`

Insert an atom before a given Composite object.

Parameters:

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

Reimplemented from BALL::AtomContainer.

void BALL::SecondaryStructure::insertBefore	(	Residue &	residue,
		Composite &	before
	)

Insert a Residue before a given Composite object.

Parameters:

	residue	the Residue to insert
	before	the Composite object to insert before

virtual bool BALL::SecondaryStructure::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::SecondaryStructure::operator!= ( const SecondaryStructure & secondary_structure ) const

Inequality operator

See also:: operator ==

SecondaryStructure& BALL::SecondaryStructure::operator= ( const SecondaryStructure & secondary_structure )

Assignment operator.

Parameters:

secondary_structure

the SecondaryStructure to be copied (cloned)

Returns:: Secondary_structure& - this instance

See also:: SecondaryStructure::set

bool BALL::SecondaryStructure::operator== ( const SecondaryStructure & secondary_structure ) const

Equality operator. Two instance of SecondaryStructure are equal if they have the same handle.

See also:: Object::operator ==

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

Read a SecondaryStructure object from a persistent stream.

Reimplemented from BALL::AtomContainer.

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

Write a SecondaryStructure object to a persistent stream.

Reimplemented from BALL::AtomContainer.

void BALL::SecondaryStructure::prepend ( AtomContainer & atom_container ) [private]

Prepend an AtomContainer at position 0.

Parameters:

atom_container

the AtomContainer to prepend

Reimplemented from BALL::AtomContainer.

void BALL::SecondaryStructure::prepend ( Atom & atom ) [private]

Prepend an atom at position 0.

Parameters:

atom

the atom to prepend

Reimplemented from BALL::AtomContainer.

void BALL::SecondaryStructure::prepend ( Residue & residue )

Prepend a Residue at position 0.

Parameters:

residue

the Residue to prepend

bool BALL::SecondaryStructure::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::SecondaryStructure::remove ( Atom & atom ) [private]

Remove an atom

Parameters:

atom

the atom to remove

Reimplemented from BALL::AtomContainer.

bool BALL::SecondaryStructure::remove ( Residue & residue )

Remove a Residue.

Parameters:

residue

the Residue to remove

void BALL::SecondaryStructure::set	(	const SecondaryStructure &	secondary_structure,
		bool	deep = `true`
	)

Assignment. The assignment is either deep or shallow (default).

Parameters:

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

void BALL::SecondaryStructure::setType ( Type type ) [inline]

Set the type of secondary structure.

Definition at line 153 of file secondaryStructure.h.

void BALL::SecondaryStructure::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::SecondaryStructure::splice ( SecondaryStructure & secondary_structure )

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

void BALL::SecondaryStructure::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::SecondaryStructure::spliceAfter ( SecondaryStructure & secondary_structure )

Move the children of secondary_structure into this instance. Cut all children of secondary_structure and append them after the children of this instance.

Parameters:

secondary_structure

the SecondaryStructure to access

void BALL::SecondaryStructure::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::SecondaryStructure::spliceBefore ( SecondaryStructure & secondary_structure )

Move the children of secondary_structure into this instance. Cut all children of secondary_structure and prepend them before the children of this instance.

Parameters:

secondary_structure

the SecondaryStructure to access

void BALL::SecondaryStructure::swap ( SecondaryStructure & secondary_structure )

Swapping of two secondary structures.

Parameters:

secondary_structure

to swap with this instance

Member Data Documentation

Type BALL::SecondaryStructure::type_ [protected]

The secondary structure type (helix, strand, coil, turn).

Definition at line 323 of file secondaryStructure.h.

BALL::SecondaryStructure Class Reference [Miscellaneous]

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

BALL::SecondaryStructure Class Reference
[Miscellaneous]