BALL::AtomContainer Class Reference
[Molecular Datastructures]

Atom Container Base Class. More...

#include <atomContainer.h>

Inheritance diagram for BALL::AtomContainer:

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Public Types
Enums
enum	Property { NUMBER_OF_PROPERTIES = 0 }
	The number of predefined properties for AtomContainer.
Public Member Functions
Constructors and Destructors
	AtomContainer ()
	Default constructor.
	AtomContainer (const AtomContainer &atom_container, bool deep=true)
	Copy constructor.
	AtomContainer (const String &name)
	Detailed Constructor.
virtual	~AtomContainer ()
	Destructor.
virtual void	clear ()
	Clear the contents of this instance of AtomContainer.
virtual void	destroy ()
	Clear the contents of this instance of AtomContainer and removes it from parent composite structures.
Persistence
virtual void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Write an AtomContainer object to a persistent stream.
virtual void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Read an AtomContainer object from a persistent stream.
Assignment
void	set (const AtomContainer &atom_container, bool deep=true)
	Assign the contents of an AtomContainer The assignment is either deep or shallow (default is deep).
AtomContainer &	operator= (const AtomContainer &atom_container)
	Assignment operator.
void	get (AtomContainer &atom_container, bool deep=true) const
	Copy to another instance of AtomContainer.
void	swap (AtomContainer &atom_container)
	Swap the contents of two AtomContainers.
Predicates
bool	operator== (const AtomContainer &atom_container) const
	Equality operator.
bool	operator!= (const AtomContainer &atom_container) const
	Inequality operator.
Accessors
void	setName (const String &name)
	Set the name.
const String &	getName () const
	Return the name.
AtomContainer *	getSuperAtomContainer ()
	Get a mutable pointer to the parent AtomContainer.
const AtomContainer *	getSuperAtomContainer () const
	Get a constant pointer to the parent AtomContainer.
AtomContainer *	getAtomContainer (Position position)
	Get a pointer to a child AtomContainer at a given position.
const AtomContainer *	getAtomContainer (Position position) const
	Get a constant pointer to a child AtomContainer at a given position.
Atom *	getAtom (Position position)
	Get a pointer to a child atom at a given position.
const Atom *	getAtom (Position position) const
	Get a pointer to a child atom at a given position.
Atom *	getAtom (const String &name)
	Get a pointer to a child atom with the name name .
const Atom *	getAtom (const String &name) const
	Get a pointer to a child atom with the name name .
Size	countAtomContainers () const
	Count the child AtomContainers.
Size	countAtoms () const
	Count the child atoms.
Size	countBonds () const
	Count the child bonds.
Size	countInterBonds () const
	Count all bonds which connect atoms in this instance with atoms outside.
Size	countIntraBonds () const
	Count all bonds which connect 2 atoms in this instance.
void	prepend (Atom &atom)
	Prepend an atom at position 0.
void	append (Atom &atom)
	Append an atom to the last position.
void	insert (Atom &atom)
	Insert an atom to the last position.
void	insertBefore (Atom &atom, Composite &before)
	Insert an atom before a given Composite object.
void	insertAfter (Atom &atom, Composite &after)
	Insert an atom after a given Composite object.
bool	remove (Atom &atom)
	Remove an 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)
	Prepend an AtomContainer at position 0.
void	append (AtomContainer &atom_container)
	Append an AtomContainer at the last position.
void	insert (AtomContainer &atom_container)
	Insert an AtomContainer at the last position.
void	insertBefore (AtomContainer &atom_container, Composite &before)
	Insert an AtomContainer before a given Composite object.
void	insertAfter (AtomContainer &atom_container, Composite &after)
	Insert an AtomContainer after a given Composite object.
void	spliceBefore (AtomContainer &atom_container)
	Cut all children of `atom_container` and prepend them before the children of this instance.
void	spliceAfter (AtomContainer &atom_container)
	Cut all children of `atom_container` and append them after the children of this instance.
void	splice (AtomContainer &atom_container)
	Move the children of {atom_container} into this instance.
bool	remove (AtomContainer &atom_container)
	Remove an AtomContainer.
Miscellaneous
void	destroyBonds ()
	Destroy all bonds in this instance.
Predicates
bool	isSubAtomContainerOf (const AtomContainer &atom_container) const
	Test if an AtomContainer is a child.
bool	isSuperAtomContainerOf (const AtomContainer &atom_container) const
	Test if an AtomContainer is the parent.

virtual bool	isValid () const
	Debugging and Diagnostics.
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
	Internal state dump.
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.

Detailed Description

Atom Container Base Class.

The AtomContainer class is the base class of all kernel classes containing atoms.

Constructor & Destructor Documentation

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

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::Molecule.

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

Append an atom to the last position.

Parameters:

atom

the atom to append

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

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

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.

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

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

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

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

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::Molecule.

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

Insert an atom to the last position.

Parameters:

atom

the atom to insert

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

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::Molecule.

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::Molecule, and BALL::Nucleotide.

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::Molecule.

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::Molecule, and BALL::Nucleotide.

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

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::Molecule.

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

Prepend an atom at position 0.

Parameters:

atom

the atom to prepend

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

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::Molecule.

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

Remove an atom.

Parameters:

atom

the atom to remove

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

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::Molecule.

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::Molecule.

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

Reimplemented in BALL::Molecule.

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

Swap the contents of two AtomContainers.

Parameters:

atom_container

the AtomContainer this instance is being swapped with.

BALL::AtomContainer Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

BALL::AtomContainer Class Reference
[Molecular Datastructures]