BALL::System Class Reference
[Molecular Datastructures]

#include <BALL/KERNEL/system.h>

Inheritance diagram for BALL::System:


Public Member Functions
bool	operator== (const System &system) const
bool	operator!= (const System &system) const
Constructors and Destructors
	System ()
	Default constructor.
	System (const System &system, bool deep=true)
	Copy constructor.
	System (const String &name)
	Detailled constructor.
virtual	~System ()
	Destructor.
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
Assignment
void	set (const System &system, bool deep=true)
System &	operator= (const System &system)
void	get (System &system, bool deep=true) const
Accessors
Molecule *	getMolecule (Position position)
const Molecule *	getMolecule (Position position) const
Protein *	getProtein (Position position)
const Protein *	getProtein (Position position) const
Size	countMolecules () const
Size	countFragments () const
Size	countAtoms () const
Size	countProteins () const
Size	countChains () const
Size	countSecondaryStructures () const
Size	countResidues () const
Size	countNucleicAcids () const
Size	countNucleotides () const
void	prepend (Molecule &molecule)
void	append (Molecule &molecule)
void	insert (Molecule &molecule)
void	insertBefore (Molecule &molecule, Composite &before)
void	insertAfter (Molecule &molecule, Composite &after)
bool	remove (Molecule &molecule)
void	spliceBefore (System &system)
void	spliceAfter (System &system)
void	splice (System &system)

Detailed Description

System class. This class is used to represent a system, i.e., a collection of molecules.

Constructor & Destructor Documentation

BALL::System::System ( )

Default constructor.

BALL::System::System	(	const System &	system,
		bool	deep = `true`
	)

Copy constructor.

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

Detailled constructor.

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

Destructor.

Member Function Documentation

void BALL::System::append ( Molecule & molecule )

Append a molecule after the last position.

Parameters:

molecule

the molecule to append

Size BALL::System::countAtoms ( ) const

Count the atoms in this system.

Returns:: Size the number of atoms

Reimplemented from BALL::AtomContainer.

Size BALL::System::countChains ( ) const

Count the chains in this system.

Returns:: Size the number of chains

Size BALL::System::countFragments ( ) const

Count the fragments in this system.

Returns:: Size the number of fragments

Size BALL::System::countMolecules ( ) const

Count the molecules in this system.

Returns:: Size the number of molecules

Size BALL::System::countNucleicAcids ( ) const

Count the nucleic acids in this system.

Returns:: Size the number of nucleic acids

Size BALL::System::countNucleotides ( ) const

Count the nucleotides in this system.

Returns:: Size the number of nucleotides

Size BALL::System::countProteins ( ) const

Count the proteins in this system.

Returns:: Size the number of proteins

Size BALL::System::countResidues ( ) const

Count the residues in this system.

Returns:: Size the number of residues

Size BALL::System::countSecondaryStructures ( ) const

Count the secondary structures in this system.

Returns:: Size the number of secondary structures

void BALL::System::get	(	System &	system,
		bool	deep = `true`
	)			const

Copying with cloning facility. The assignment is either deep or shallow (default).

Parameters:

System

the System to be assigned to

const Molecule* BALL::System::getMolecule ( Position position ) const

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

Note:: The current implementation of this function has linear complexity

Parameters:

position

the position of the child molecule

Returns:: Molecule* - constant pointer to the child Molecule at position

Molecule* BALL::System::getMolecule ( Position position )

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

Note:: The current implementation of this function has linear complexity

Parameters:

position

the position of the child molecule

Returns:: Molecule* - mutable pointer to the child Molecule at position

const Protein* BALL::System::getProtein ( Position position ) const

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

Note:: The current implementation of this function has linear complexity

Parameters:

position

the position of the child Protein

Returns:: Protien* - mutable pointer to the child Protein at position

Protein* BALL::System::getProtein ( Position position )

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

Note:: The current implementation of this function has linear complexity

Parameters:

position

the position of the child Protein

Returns:: Protien* - mutable pointer to the child Protein at position

void BALL::System::insert ( Molecule & molecule )

Insert a molecule after the last position.

Parameters:

molecule

the molecule to insert

void BALL::System::insertAfter	(	Molecule &	molecule,
		Composite &	after
	)

Insert a molecule after a given Composite object.

Parameters:

	molecule	the molecule to insert
	after	the Composite object to insert before

void BALL::System::insertBefore	(	Molecule &	molecule,
		Composite &	before
	)

Insert a molecule before a given Composite object.

Parameters:

	molecule	the molecule to insert
	before	the Composite object to insert before

bool BALL::System::operator!= ( const System & system ) const

Inequality operator

See also:: operator ==

System& BALL::System::operator= ( const System & system )

Assignment operator.

Parameters:

system

the System to be copied (cloned)

Returns:: System& - this instance

bool BALL::System::operator== ( const System & system ) const

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

See also:: Object::operator ==

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

Reads a System object from a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::AtomContainer.

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

Writes a System object to a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::AtomContainer.

void BALL::System::prepend ( Molecule & molecule )

Prepend a molecule at position 0.

Parameters:

molecule

the molecule to prepend

bool BALL::System::remove ( Molecule & molecule )

Remove a molecule.

Parameters:

molecule

the molecule to remove

void BALL::System::set	(	const System &	system,
		bool	deep = `true`
	)

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

Parameters:

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

void BALL::System::splice ( System & system )

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

void BALL::System::spliceAfter ( System & system )

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

Parameters:

system

the system to access

void BALL::System::spliceBefore ( System & system )

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

Parameters:

system

the system to access

BALL::System Class Reference [Molecular Datastructures]

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

BALL::System Class Reference
[Molecular Datastructures]