BALL::AtomContainer Class Reference
[Molecular Datastructures]

#include <BALL/KERNEL/atomContainer.h>

Inheritance diagram for BALL::AtomContainer:

Public Types
Enums

enum	Property { NUMBER_OF_PROPERTIES = 0 }
	The number of predefined properties for AtomContainer. More...
Public Member Functions
Constructors and Destructors

	AtomContainer ()
	AtomContainer (const AtomContainer &atom_container, bool deep=true)
	AtomContainer (const String &name)
virtual	~AtomContainer ()
virtual void	clear ()
virtual void	destroy ()
Persistence

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

void	set (const AtomContainer &atom_container, bool deep=true)
AtomContainer &	operator= (const AtomContainer &atom_container)
void	get (AtomContainer &atom_container, bool deep=true) const
void	swap (AtomContainer &atom_container)
Predicates

bool	operator== (const AtomContainer &atom_container) const
bool	operator!= (const AtomContainer &atom_container) const
bool	isSubAtomContainerOf (const AtomContainer &atom_container) const
bool	isSuperAtomContainerOf (const AtomContainer &atom_container) const
Accessors

void	setName (const String &name)
const String &	getName () const
AtomContainer *	getSuperAtomContainer ()
const AtomContainer *	getSuperAtomContainer () const
AtomContainer *	getAtomContainer (Position position)
const AtomContainer *	getAtomContainer (Position position) const
Atom *	getAtom (Position position)
const Atom *	getAtom (Position position) const
Atom *	getAtom (const String &name)
const Atom *	getAtom (const String &name) const
Size	countAtomContainers () const
Size	countAtoms () const
Size	countBonds () const
Size	countInterBonds () const
Size	countIntraBonds () 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)
Size	removeHavingProperty (BALL::Property p)
Size	removeNotHavingProperty (BALL::Property p)
Size	removeHavingProperty (const string &name)
Size	removeNotHavingProperty (const string &name)
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)
Miscellaneous

void	destroyBonds ()


virtual bool	isValid () const
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
Internal Iteration

bool	applyIntraBond (UnaryProcessor< Bond > &processor)
	Apply to all bonds connecting two atoms inside this AtomContainer.
bool	applyInterBond (UnaryProcessor< Bond > &processor)
	Apply to all bonds connected to atoms outside this AtomContainer.
Private Attributes
String	name_

Detailed Description

Atom Container Base Class. The AtomContainer class is the base class of all kernel classes containing atoms.

Definition at line 32 of file atomContainer.h.

Member Enumeration Documentation

enum BALL::AtomContainer::Property

The number of predefined properties for AtomContainer.

Enumerator:

NUMBER_OF_PROPERTIES

Reimplemented in BALL::Chain, BALL::Fragment, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, and BALL::Residue.

Definition at line 45 of file atomContainer.h.

Constructor & Destructor Documentation

BALL::AtomContainer::AtomContainer ( )

Default constructor

BALL::AtomContainer::AtomContainer	(	const AtomContainer &	atom_container,
		bool	deep = `true`
	)

Copy constructor

Parameters:

	atom_container	the AtomContainer to construct from
	deep	a flag indicating cloning

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

Detailed Constructor

Parameters:

name

the name of the AtomContainer

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

Destructor

Member Function Documentation

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

Append an AtomContainer at the last position.

Parameters:

atom_container

the AtomContainer to prepend

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

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

Append an atom to the last position.

Parameters:

atom

the atom to append

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

bool BALL::AtomContainer::applyInterBond ( UnaryProcessor< Bond > & processor )

Apply to all bonds connected to atoms outside this AtomContainer.

bool BALL::AtomContainer::applyIntraBond ( UnaryProcessor< Bond > & processor )

Apply to all bonds connecting two atoms inside this AtomContainer.

virtual void BALL::AtomContainer::clear ( ) [virtual]

Clear the contents of this instance of AtomContainer. This methods clears the base fragment's name, destroys all its children (as in Composite::clear ), but does not remove it from its parent composite structures.

Reimplemented from BALL::Composite.

Reimplemented in BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, and BALL::SecondaryStructure.

Size BALL::AtomContainer::countAtomContainers ( ) const

Count the child AtomContainers.

Returns:: Size the number of AtomContainers

Reimplemented in BALL::Nucleotide, and BALL::Residue.

Size BALL::AtomContainer::countAtoms ( ) const

Count the child atoms.

Returns:: Size the number of atoms

Reimplemented in BALL::System.

Size BALL::AtomContainer::countBonds ( ) const

Count the child bonds.

Returns:: Size the number of bonds

Size BALL::AtomContainer::countInterBonds ( ) const

Count all bonds which connect atoms in this instance with atoms outside.

Returns:: Size the number of inter bonds

Size BALL::AtomContainer::countIntraBonds ( ) const

Count all bonds which connect 2 atoms in this instance.

Returns:: Size the number of intra bonds

virtual void BALL::AtomContainer::destroy ( ) [virtual]

Clear the contents of this instance of AtomContainer and removes it from parent composite structures. This methods clears the base fragment's name, destroys all its children (as in Composite::destroy ), and removes it from its parent composite structures.

Reimplemented from BALL::Composite.

Reimplemented in BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::destroyBonds ( )

Destroy all bonds in this instance.

virtual void BALL::AtomContainer::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::Composite.

Reimplemented in BALL::Chain, BALL::Fragment, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::get	(	AtomContainer &	atom_container,
		bool	deep = `true`
	)			const

Copy to another instance of AtomContainer. The assignment is either deep or shallow (default is deep).

Parameters:

atom_container

the AtomContainer to be assigned to

See also:: Composite::get

const Atom* BALL::AtomContainer::getAtom ( const String & name ) const

Get a pointer to a child atom with the name name . The pointer is 0 if this instance AtomContainer does not have an atom with this name.

Parameters:

name

the name of the child atom

Returns:: Atom* - constant pointer to the child

Atom* BALL::AtomContainer::getAtom ( const String & name )

Get a pointer to a child atom with the name name . The pointer is 0 if this instance does not have an atom with this name.

Parameters:

name

the name of the child atom

Returns:: Atom* - mutable pointer to the child

const Atom* BALL::AtomContainer::getAtom ( Position position ) const

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

Parameters:

position

the position of the child atom

Returns:: Atom* - constant pointer to the child

Reimplemented in BALL::Chain, and BALL::SecondaryStructure.

Atom* BALL::AtomContainer::getAtom ( Position position )

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

Parameters:

position

the position of the child atom

Returns:: Atom* - mutable pointer to the child

Reimplemented in BALL::Chain, and BALL::SecondaryStructure.

const AtomContainer* BALL::AtomContainer::getAtomContainer ( Position position ) const

Get a constant pointer to a child AtomContainer at a given position. The pointer is 0 if this instance does not have an AtomContainer at the given position.

Parameters:

position

of the child AtomContainer

Returns:: AtomContainer* - constant pointer to the child

Reimplemented in BALL::Chain, BALL::Nucleotide, and BALL::Residue.

AtomContainer* BALL::AtomContainer::getAtomContainer ( Position position )

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

Parameters:

position

of the child AtomContainer

Returns:: AtomContainer* - mutable pointer to the child

Reimplemented in BALL::Chain, BALL::Nucleotide, and BALL::Residue.

const String& BALL::AtomContainer::getName ( ) const

Return the name.

Returns:: String& - constant reference to the name of this instance

const AtomContainer* BALL::AtomContainer::getSuperAtomContainer ( ) const

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 in BALL::Molecule.

AtomContainer* BALL::AtomContainer::getSuperAtomContainer ( )

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 in BALL::Molecule.

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

Insert an AtomContainer at the last position.

Parameters:

atom_container

the AtomContainer to insert

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

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

Insert an atom to the last position.

Parameters:

atom

the atom to insert

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

void BALL::AtomContainer::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 in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::insertAfter	(	Atom &	atom,
		Composite &	after
	)

Insert an atom after a given Composite object.

Parameters:

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

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

void BALL::AtomContainer::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 in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

void BALL::AtomContainer::insertBefore	(	Atom &	atom,
		Composite &	before
	)

Insert an atom before a given Composite object.

Parameters:

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

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

bool BALL::AtomContainer::isSubAtomContainerOf ( const AtomContainer & atom_container ) const

Test if an AtomContainer is a child.

Parameters:

atom_container

the AtomContainer to test

Reimplemented in BALL::Molecule.

bool BALL::AtomContainer::isSuperAtomContainerOf ( const AtomContainer & atom_container ) const

Test if an AtomContainer is the parent.

Parameters:

atom_container

the AtomContainer to test

Reimplemented in BALL::Nucleotide, and BALL::Residue.

virtual bool BALL::AtomContainer::isValid ( ) const [virtual]

Debugging and Diagnostics Internal state and consistency self-validation. If the internal state of this instance is correct (self-validated) and consistent true is returned, false otherwise.

Returns:: bool

Reimplemented from BALL::Composite.

Reimplemented in BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, and BALL::SecondaryStructure.

bool BALL::AtomContainer::operator!= ( const AtomContainer & atom_container ) const

Inequality operator.

See also:: operator ==

AtomContainer& BALL::AtomContainer::operator= ( const AtomContainer & atom_container )

Assignment operator. The assignment is deep.

Parameters:

atom_container

the AtomContainer to be copied (cloned)

Returns:: AtomContainer& - this instance AtomContainer

See also:: AtomContainer::set

bool BALL::AtomContainer::operator== ( const AtomContainer & atom_container ) const

Equality operator. Two instances of AtomContainer are equal if they have the same handle.

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

Read an AtomContainer object from a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Composite.

Reimplemented in BALL::Chain, BALL::Fragment, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, BALL::SecondaryStructure, and BALL::System.

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

Write an AtomContainer object to a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Composite.

Reimplemented in BALL::Chain, BALL::Fragment, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, BALL::SecondaryStructure, and BALL::System.

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

Prepend an AtomContainer at position 0.

Parameters:

atom_container

the AtomContainer to prepend

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

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

Prepend an atom at position 0.

Parameters:

atom

the atom to prepend

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

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

Remove an AtomContainer

Parameters:

atom_container

the AtomContainer to remove

Returns:: false if {atom_container} could not be removed

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

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

Remove an atom

Parameters:

atom

the atom to remove

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, and BALL::SecondaryStructure.

Size BALL::AtomContainer::removeHavingProperty ( const string & name )

Size BALL::AtomContainer::removeHavingProperty ( BALL::Property p )

Size BALL::AtomContainer::removeNotHavingProperty ( const string & name )

Size BALL::AtomContainer::removeNotHavingProperty ( BALL::Property p )

void BALL::AtomContainer::set	(	const AtomContainer &	atom_container,
		bool	deep = `true`
	)

Assign the contents of an AtomContainer The assignment is either deep or shallow (default is deep).

Parameters:

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

See also:: Composite::set

void BALL::AtomContainer::setName ( const String & name )

Set the name.

Parameters:

name

the new name

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

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

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

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

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

Parameters:

atom_container

the AtomContainer to access

Reimplemented in BALL::Chain, BALL::Molecule, BALL::Nucleotide, BALL::Residue, and BALL::SecondaryStructure.

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

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

Parameters:

atom_container

the AtomContainer to access