BALL::SecondaryStructure Class Reference
[Miscellaneous]

Secondary structure class. More...

#include <secondaryStructure.h>

Inheritance diagram for BALL::SecondaryStructure:

[legend]


Public Types
Enums
enum	Type { HELIX, COIL, STRAND, TURN, UNKNOWN, NUMBER_OF_TYPES }
	Secondary structure type.
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
	Equality operator.
bool	operator!= (const SecondaryStructure &secondary_structure) const
	Inequality operator.
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)
	Assignment.
SecondaryStructure &	operator= (const SecondaryStructure &secondary_structure)
	Assignment operator.
void	get (SecondaryStructure &secondary_structure, bool deep=true) const
	Assignment.
void	swap (SecondaryStructure &secondary_structure)
	Swapping of two secondary structures.
Accessors
Type	getType () const
	Return the type of secondary structure.
void	setType (Type type)
	Set the type of secondary structure.
Protein *	getProtein ()
	Get a pointer to the parent protein.
const Protein *	getProtein () const
	Get a 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.
Residue *	getResidue (Position position)
	Get a pointer to a child Residue at a given position.
const Residue *	getResidue (Position position) const
	Get a pointer to a child Residue at a given position.
Residue *	getNTerminal ()
	Get a pointer to the N-terminal Residue.
const Residue *	getNTerminal () const
	Get a pointer to the N-terminal Residue.
Residue *	getCTerminal ()
	Get a pointer to the C-terminal Residue.
const Residue *	getCTerminal () const
	Get a pointer to the C-terminal Residue.
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.
Size	countResidues () const
	Count the Residues.
Size	countPDBAtoms () const
	Count the PDBAtoms.
void	prepend (Residue &residue)
	Prepend a Residue at position 0.
void	append (Residue &residue)
	Append a Residue after the last position.
void	insert (Residue &residue)
	Insert a Residue after the last position.
void	insertBefore (Residue &residue, Composite &before)
	Insert a Residue before a given Composite object.
void	insertAfter (Residue &residue, Composite &after)
	Insert a Residue after a given Composite object.
bool	remove (Residue &residue)
	Remove a Residue.
void	spliceBefore (SecondaryStructure &secondary_structure)
	Move the children of `secondary_structure` into this instance.
void	spliceAfter (SecondaryStructure &secondary_structure)
	Move the children of `secondary_structure` into this instance.
void	splice (SecondaryStructure &secondary_structure)
	Move the children of `secondary_structure` into this instance.
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.
Protected Attributes
Type	type_
	The secondary structure type (helix, strand, coil, turn).

Detailed Description

Secondary structure class.

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

Member Function Documentation

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

Append a Residue after the last position.

Parameters:

residue

the Residue to append

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::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 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 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

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

Insert a Residue after the last position.

Parameters:

residue

the Residue to insert

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	(	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::prepend ( Residue & residue )

Prepend a Residue at position 0.

Parameters:

residue

the Residue to prepend

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::splice ( SecondaryStructure & secondary_structure )

Move the children of secondary_structure into this instance.

The children are inserted using spliceBefore .

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 ( 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

BALL::SecondaryStructure Class Reference [Miscellaneous]

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

BALL::SecondaryStructure Class Reference
[Miscellaneous]