BALL::Molecule Class Reference
[Molecular Datastructures]

#include <BALL/KERNEL/molecule.h>

Inheritance diagram for BALL::Molecule:

Public Types
Enums

enum	Property { IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES, NUMBER_OF_PROPERTIES }
Public Member Functions
bool	operator== (const Molecule &molecule) const
bool	operator!= (const Molecule &molecule) const
Constructors and Destructors

	Molecule ()
	Molecule (const Molecule &molecule, bool deep=true)
	Molecule (const String &name)
virtual	~Molecule ()
Persistence

void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
Assignment

void	set (const Molecule &molecule, bool deep=true)
Molecule &	operator= (const Molecule &molecule)
void	get (Molecule &molecule, bool deep=true) const
void	swap (Molecule &molecule)
Accessors

System *	getSystem ()
const System *	getSystem () 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)
Debugging and Diagnostics

virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
Protected Member Functions
Molecule *	getMolecule ()
const Molecule *	getMolecule () const
AtomContainer *	getSuperAtomContainer ()
const AtomContainer *	getSuperAtomContainer () const
void	prepend (Molecule &molecule)
void	append (Molecule &molecule)
void	insert (Molecule &molecule)
void	insertBefore (Molecule &molecule, Composite &composite)
void	insertAfter (Molecule &molecule, Composite &composite)
bool	remove (Molecule &molecule)
bool	isSubAtomContainerOf (const AtomContainer &atom_container) const

Detailed Description

Molecule class. Used to represent general molecules without specific properties.

Definition at line 31 of file molecule.h.

Member Enumeration Documentation

enum BALL::Molecule::Property

Properties

Enumerator:

IS_SOLVENT
NUMBER_OF_PROPERTIES

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::NucleicAcid, and BALL::Protein.

Definition at line 44 of file molecule.h.

Constructor & Destructor Documentation

BALL::Molecule::Molecule ( )

Default constructor.

BALL::Molecule::Molecule	(	const Molecule &	molecule,
		bool	deep = `true`
	)

Copy constructor.

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

Detailled constructor.

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

Destructor.

Member Function Documentation

void BALL::Molecule::append ( Molecule & molecule ) [protected]

void BALL::Molecule::append ( AtomContainer & atom_container )

Append an AtomContainer as the last child.

Parameters:

atom_container

the AtomContainer to add

Reimplemented from BALL::AtomContainer.

void BALL::Molecule::append ( Atom & atom )

Insert an atom as the last child.

Parameters:

atom

the atom to add

Reimplemented from BALL::AtomContainer.

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

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

Parameters:

	s	output stream where to output the internal state
	depth	the dumping depth

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::NucleicAcid, and BALL::Protein.

void BALL::Molecule::get	(	Molecule &	molecule,
		bool	deep = `true`
	)			const

Assign to another Molecule.

Parameters:

	molecule	the Molecule to be assigned to
	deep	make a deep (=`true`) or shallow (=`false`) copy

const Molecule* BALL::Molecule::getMolecule ( ) const [protected]

Molecule* BALL::Molecule::getMolecule ( ) [protected]

const AtomContainer* BALL::Molecule::getSuperAtomContainer ( ) const [protected]

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

Returns:: AtomContainer* - constant pointer to the parent AtomContainer

Reimplemented from BALL::AtomContainer.

AtomContainer* BALL::Molecule::getSuperAtomContainer ( ) [protected]

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

Returns:: AtomContainer* - mutable pointer to the parent AtomContainer

Reimplemented from BALL::AtomContainer.

const System* BALL::Molecule::getSystem ( ) const

Get a const pointer to the parent System.

Returns:: System* pointer to the parent System

System* BALL::Molecule::getSystem ( )

Access the parent System.

Returns:: System* pointer to the parent System

void BALL::Molecule::insert ( Molecule & molecule ) [protected]

void BALL::Molecule::insert ( AtomContainer & atom_container )

Insert an AtomContainer as the last child.

Parameters:

atom_container

the AtomContainer to add

Reimplemented from BALL::AtomContainer.

void BALL::Molecule::insert ( Atom & atom )

Insert an atom as the last child.

Parameters:

atom

the atom to add

Reimplemented from BALL::AtomContainer.

void BALL::Molecule::insertAfter	(	Molecule &	molecule,
		Composite &	composite
	)			`[protected]`

void BALL::Molecule::insertAfter	(	AtomContainer &	atom_container,
		Composite &	after
	)

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::Molecule::insertAfter	(	Atom &	atom,
		Composite &	after
	)

Insert an atom after a Composite object.

Parameters:

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

Reimplemented from BALL::AtomContainer.

void BALL::Molecule::insertBefore	(	Molecule &	molecule,
		Composite &	composite
	)			`[protected]`

void BALL::Molecule::insertBefore	(	AtomContainer &	atom_container,
		Composite &	before
	)

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::Molecule::insertBefore	(	Atom &	atom,
		Composite &	before
	)

Insert an atom before a Composite object.

Parameters:

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

Reimplemented from BALL::AtomContainer.

bool BALL::Molecule::isSubAtomContainerOf ( const AtomContainer & atom_container ) const [protected]

Test if an AtomContainer is a child.

Parameters:

atom_container

the AtomContainer to test

Reimplemented from BALL::AtomContainer.

bool BALL::Molecule::operator!= ( const Molecule & molecule ) const

Inequality operator

See also:: operator ==

Molecule& BALL::Molecule::operator= ( const Molecule & molecule )

Assignment operator.

Parameters:

molecule

the Molecule to assign from

bool BALL::Molecule::operator== ( const Molecule & molecule ) const

Equality operator. Two molecules are equal if they have the same handle.

See also:: Object::operator ==.

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

Reads a Molecule object from a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::NucleicAcid, and BALL::Protein.

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

Writes a Molecule object to a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::NucleicAcid, and BALL::Protein.

void BALL::Molecule::prepend ( Molecule & molecule ) [protected]

void BALL::Molecule::prepend ( AtomContainer & atom_container )

Insert an AtomContainer as the first child.

Parameters:

atom_container

the AtomContainer to add

Reimplemented from BALL::AtomContainer.

void BALL::Molecule::prepend ( Atom & atom )

Insert an atom as the first child.

Parameters:

atom

the atom to add

Reimplemented from BALL::AtomContainer.

bool BALL::Molecule::remove ( Molecule & molecule ) [protected]

bool BALL::Molecule::remove ( AtomContainer & atom_container )

Remove an AtomContainer.

Parameters:

atom_container

the AtomContainer to remove

Reimplemented from BALL::AtomContainer.

bool BALL::Molecule::remove ( Atom & atom )

Remove an atom.

Parameters:

atom

the atom to remove

Reimplemented from BALL::AtomContainer.

void BALL::Molecule::set	(	const Molecule &	molecule,
		bool	deep = `true`
	)

Assign from another Molecule.

Parameters:

	molecule	the Molecule object to assign from
	deep	make a deep (=`true`) or shallow (=`false`) copy

void BALL::Molecule::splice ( AtomContainer & atom_container )

Move the children of atom_container into this molecule. The children of atom_container are inserted at the position of atom_container if it is a child of this. Otherwise the children are inserted using spliceBefore .

Reimplemented from BALL::AtomContainer.

void BALL::Molecule::spliceAfter ( AtomContainer & atom_container )

Cut all children of atom_container and append them after the children of this molecule.

Parameters:

atom_container

the AtomContainer to access

Reimplemented from BALL::AtomContainer.

void BALL::Molecule::spliceBefore ( AtomContainer & atom_container )

Cut all children of atom_container and prepend them before the children of this molecule.

Parameters:

atom_container

the AtomContainer to access

Reimplemented from BALL::AtomContainer.

void BALL::Molecule::swap ( Molecule & molecule )

Swap the contents of two molecules.

Parameters:

molecule

the Molecule to swap contents with

BALL::Molecule Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

BALL::Molecule Class Reference
[Molecular Datastructures]