System Class Reference
[Molecular Datastructures]

#include <system.h>

Inheritance diagram for System:


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

Append a molecule after the last position.

Parameters:

molecule the molecule to append

Size System::countAtoms ( ) const throw ()

Count the atoms in this system.

Returns:
Size the number of atoms

Reimplemented from AtomContainer.

Size System::countChains ( ) const throw ()

Count the chains in this system.

Returns:
Size the number of chains

Size System::countFragments ( ) const throw ()

Count the fragments in this system.

Returns:
Size the number of fragments

Size System::countMolecules ( ) const throw ()

Count the molecules in this system.

Returns:
Size the number of molecules

Size System::countNucleicAcids ( ) const throw ()

Count the nucleic acids in this system.

Returns:
Size the number of nucleic acids

Size System::countNucleotides ( ) const throw ()

Count the nucleotides in this system.

Returns:
Size the number of nucleotides

Size System::countProteins ( ) const throw ()

Count the proteins in this system.

Returns:
Size the number of proteins

Size System::countResidues ( ) const throw ()

Count the residues in this system.

Returns:
Size the number of residues

Size System::countSecondaryStructures ( ) const throw ()

Count the secondary structures in this system.

Returns:
Size the number of secondary structures

void System::get ( System & system,

bool deep = true

) const throw ()

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

System the System to be assigned to

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

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* System::getMolecule ( Position position ) throw ()

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 System::insert ( Molecule & molecule ) throw ()

Insert a molecule after the last position.

Parameters:

molecule the molecule to insert

void System::insertAfter ( Molecule & molecule,

Composite & after

) throw ()

Insert a molecule after a given Composite object.

Parameters:

molecule the molecule to insert

after the Composite object to insert before

void System::insertBefore ( Molecule & molecule,

Composite & before

) throw ()

Insert a molecule before a given Composite object.

Parameters:

molecule the molecule to insert

before the Composite object to insert before

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

Inequality operator.

See also:
operator ==

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

Assignment operator.

Parameters:

system the System to be copied (cloned)

Returns:
System& - this instance

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

Equality operator.
Two instance of System are equal if they have the same handle.
See also:
Object::operator ==

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

Reads a System object from a persistent stream.

Parameters:

pm the persistence manager

Reimplemented from AtomContainer.

void 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 AtomContainer.

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

Prepend a molecule at position 0.

Parameters:

molecule the molecule to prepend

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

Remove a molecule.

Parameters:

molecule the molecule to remove

void System::set ( const System & system,

bool deep = true

) throw ()

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 System::splice ( System & system ) throw ()

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

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

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 System::spliceBefore ( System & system ) throw ()

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

System Class Reference [Molecular Datastructures]

Public Member Functions

Detailed Description

Member Function Documentation

System Class Reference
[Molecular Datastructures]