BALL::System Class Reference
[Molecular Datastructures]

#include <system.h>

Inheritance diagram for BALL::System:

[legend]


Public Member Functions
bool	operator== (const System &system) const
	Equality operator.
bool	operator!= (const System &system) const
	Inequality operator.
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)
	Writes a System object to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Reads a System object from a persistent stream.
Assignment
void	set (const System &system, bool deep=true)
	Assignment with cloning facility.
System &	operator= (const System &system)
	Assignment operator.
void	get (System &system, bool deep=true) const
	Copying with cloning facility.
Accessors
Molecule *	getMolecule (Position position)
	Get a pointer to a child Molecule at a given position.
const Molecule *	getMolecule (Position position) const
	Get a pointer to a child Molecule at a given position.
Size	countMolecules () const
	Count the molecules in this system.
Size	countFragments () const
	Count the fragments in this system.
Size	countAtoms () const
	Count the atoms in this system.
Size	countProteins () const
	Count the proteins in this system.
Size	countChains () const
	Count the chains in this system.
Size	countSecondaryStructures () const
	Count the secondary structures in this system.
Size	countResidues () const
	Count the residues in this system.
Size	countNucleicAcids () const
	Count the nucleic acids in this system.
Size	countNucleotides () const
	Count the nucleotides in this system.
void	prepend (Molecule &molecule)
	Prepend a molecule at position 0.
void	append (Molecule &molecule)
	Append a molecule after the last position.
void	insert (Molecule &molecule)
	Insert a molecule after the last position.
void	insertBefore (Molecule &molecule, Composite &before)
	Insert a molecule before a given Composite object.
void	insertAfter (Molecule &molecule, Composite &after)
	Insert a molecule after a given Composite object.
bool	remove (Molecule &molecule)
	Remove a molecule.
void	spliceBefore (System &system)
	Move the children of `system` into this instance.
void	spliceAfter (System &system)
	Move the children of `system` into this instance.
void	splice (System &system)
	Move the children of `system` into this instance.

Detailed Description

System class.

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

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.

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.

Parameters:

position

the position of the child molecule

Returns:: Molecule* - mutable pointer to the child molecule 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

Member Function Documentation

BALL::System Class Reference
[Molecular Datastructures]