#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 Types inherited from BALL::Composite
typedef ForwardIterator < Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorIterator

typedef ConstForwardIterator < Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorConstIterator

typedef BidirectionalIterator < Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeIterator

typedef ConstBidirectionalIterator < Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeConstIterator

typedef std::reverse_iterator < ChildCompositeIterator >	ChildCompositeReverseIterator

typedef std::reverse_iterator < ChildCompositeConstIterator >	ChildCompositeConstReverseIterator

typedef BidirectionalIterator < Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeIterator

typedef ConstBidirectionalIterator < Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeConstIterator

typedef std::reverse_iterator < CompositeIterator >	CompositeReverseIterator

typedef std::reverse_iterator < CompositeConstIterator >	CompositeConstReverseIterator

enum	StampType { MODIFICATION = 1, SELECTION = 2, BOTH = 3 }

typedef UnaryPredicate< Composite >	KernelPredicateType

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

virtual void	persistentRead (PersistenceManager &pm)

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. More...

bool	applyInterBond (UnaryProcessor< Bond > &processor)
	Apply to all bonds connected to atoms outside this AtomContainer. More...

Public Member Functions inherited from BALL::Composite
template<typename T >
bool	applyLevel (ConstUnaryProcessor< T > &processor, long level) const

AncestorIterator	beginAncestor ()

AncestorIterator	endAncestor ()

AncestorConstIterator	beginAncestor () const

AncestorConstIterator	endAncestor () const

ChildCompositeIterator	beginChildComposite ()

ChildCompositeIterator	endChildComposite ()

ChildCompositeConstIterator	beginChildComposite () const

ChildCompositeConstIterator	endChildComposite () const

ChildCompositeReverseIterator	rbeginChildComposite ()

ChildCompositeReverseIterator	rendChildComposite ()

ChildCompositeConstReverseIterator	rbeginChildComposite () const

ChildCompositeConstReverseIterator	rendChildComposite () const

CompositeIterator	beginComposite ()

CompositeIterator	endComposite ()

CompositeConstIterator	beginComposite () const

CompositeConstIterator	endComposite () const

CompositeReverseIterator	rbeginComposite ()

CompositeReverseIterator	rendComposite ()

CompositeConstReverseIterator	rbeginComposite () const

CompositeConstReverseIterator	rendComposite () const

void	deleteChildrenList_ (std::list< Composite * > &composites)

template<typename T >
BALL_INLINE bool	apply (UnaryProcessor< T > &processor)

template<typename T >
BALL_INLINE bool	apply (ConstUnaryProcessor< T > &processor) const

template<typename T >
BALL_INLINE T *	getAncestor (const T &)

template<typename T >
BALL_INLINE const T *	getAncestor (const T &) const

template<typename T >
BALL_INLINE T *	getPrevious (const T &)

template<typename T >
BALL_INLINE const T *	getPrevious (const T &dummy) const

template<typename T >
BALL_INLINE T *	getNext (const T &)

template<typename T >
BALL_INLINE const T *	getNext (const T &dummy) const

template<typename T >
BALL_INLINE bool	hasAncestor (const T &dummy) const

	Composite ()

	Composite (const Composite &composite, bool deep=true)

virtual	~Composite ()

void	destroy (bool virtual_destroy)

void *	clone (Composite &root) const

bool	operator== (const Composite &composite) const

bool	operator!= (const Composite &composite) const

bool	isEmpty () const

bool	isRoot () const

bool	isRootOf (const Composite &composite) const

bool	isInterior () const

bool	hasChild () const

bool	isChildOf (const Composite &composite) const

bool	isFirstChild () const

bool	isFirstChildOf (const Composite &composite) const

bool	isLastChild () const

bool	isLastChildOf (const Composite &composite) const

bool	hasParent () const

bool	isParentOf (const Composite &composite) const

bool	hasSibling () const

bool	isSiblingOf (const Composite &composite) const

bool	hasPreviousSibling () const

bool	isPreviousSiblingOf (const Composite &composite) const

bool	hasNextSibling () const

bool	isNextSiblingOf (const Composite &composite) const

bool	isDescendantOf (const Composite &composite) const

template<typename T >
bool	hasAncestor (const T &dummy) const

bool	isAncestorOf (const Composite &composite) const

bool	isRelatedWith (const Composite &composite) const

bool	isHomomorph (const Composite &composite) const

bool	containsSelection () const

virtual bool	isAtom () const

virtual bool	isMolecule () const

virtual bool	isProtein () const

virtual bool	isFragment () const

virtual bool	isResidue () const

virtual bool	isChain () const

void	host (Visitor< Composite > &visitor)

template<typename T >
bool	applyAncestor (UnaryProcessor< T > &processor)

template<typename T >
bool	applyAncestor (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyChild (UnaryProcessor< T > &processor)

template<typename T >
bool	applyChild (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyDescendantPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPreorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyDescendantPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPostorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyDescendant (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendant (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPreorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPostorder (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	apply (UnaryProcessor< T > &processor)

template<typename T >
bool	apply (ConstUnaryProcessor< T > &processor) const

template<typename T >
bool	applyLevel (UnaryProcessor< T > &processor, long level)

void	set (const Composite &composite, bool deep=true)

Composite &	operator= (const Composite &composite)

void	get (Composite &composite, bool deep=true) const

Size	getDegree () const

Size	count (const KernelPredicateType &predicate) const

Size	countDescendants () const

Size	getPathLength (const Composite &composite) const

Size	getDepth () const

Size	getHeight () const

Composite &	getRoot ()

const Composite &	getRoot () const

Composite *	getLowestCommonAncestor (const Composite &composite)

const Composite *	getLowestCommonAncestor (const Composite &composite) const

template<typename T >
T *	getAncestor (const T &)

template<typename T >
const T *	getAncestor (const T &) const

template<typename T >
T *	getPrevious (const T &)

template<typename T >
const T *	getPrevious (const T &dummy) const

template<typename T >
T *	getNext (const T &)

template<typename T >
const T *	getNext (const T &dummy) const

Composite *	getParent ()

const Composite *	getParent () const

Composite *	getChild (Index index)

const Composite *	getChild (Index index) const

Composite *	getSibling (Index index)

const Composite *	getSibling (Index index) const

Composite *	getFirstChild ()

const Composite *	getFirstChild () const

Composite *	getLastChild ()

const Composite *	getLastChild () const

const PreciseTime &	getModificationTime () const

const PreciseTime &	getSelectionTime () const

void	stamp (StampType stamp=BOTH)

void	prependChild (Composite &composite)

void	appendChild (Composite &composite)

void	insertBefore (Composite &composite)

void	insertAfter (Composite &composite)

void	spliceBefore (Composite &composite)

void	spliceAfter (Composite &composite)

void	splice (Composite &composite)

bool	removeChild (Composite &child)

Size	removeSelected ()

Size	removeUnselected ()

void	replace (Composite &composite)

void	swap (Composite &composite)

virtual void	select ()

virtual void	deselect ()

Public Member Functions inherited from BALL::PersistentObject
	PersistentObject ()

virtual	~PersistentObject ()

PersistenceManager &	operator>> (PersistenceManager &pm) const

virtual void	finalize ()

Public Member Functions inherited from BALL::Object
	Object ()
	Default constructor. More...

	Object (const Object &object)
	Copy constructor. More...

virtual	~Object ()
	Destructor. More...

const Object &	operator= (const Object &)

bool	operator== (const Object &object) const

bool	operator!= (const Object &object) const

bool	operator< (const Object &object) const

bool	operator<= (const Object &object) const

bool	operator>= (const Object &object) const

bool	operator> (const Object &object) const

int	compare (const Object &object) const

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

Handle	getHandle () const

Public Member Functions inherited from BALL::AutoDeletable
virtual	~AutoDeletable ()

void *	operator new (size_t size)

void	operator delete (void *ptr)

void *	operator new (size_t size, void *ptr)

void	operator delete (void ptr, void )

bool	isAutoDeletable () const

void	setAutoDeletable (bool enable)

Public Member Functions inherited from BALL::Selectable
	Selectable ()

	Selectable (const Selectable &selectable, bool deep=true)

virtual	~Selectable ()

void	set (const Selectable &selectable, bool deep=true)

const Selectable &	operator= (const Selectable &selectable)

void	get (Selectable &selectable, bool deep=true) const

void	swap (Selectable &selectable)

virtual void	setSelected (bool selected)

bool	isSelected () const

bool	operator== (const Selectable &selectable) const

bool	operator!= (const Selectable &selectable) const

void	write (PersistenceManager &pm) const

bool	read (PersistenceManager &pm)

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

Public Member Functions inherited from BALL::PropertyManager
BALL_INLINE	PropertyManager ()
	Default constructor. More...

BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor. More...

virtual	~PropertyManager ()
	Destructor. More...

void	set (const PropertyManager &property_manager)

const PropertyManager &	operator= (const PropertyManager &property_manager)

void	get (PropertyManager &property_manager) const

void	swap (PropertyManager &property_manager)

BitVector &	getBitVector ()

const BitVector &	getBitVector () const

	operator BitVector & ()

void	setProperty (Property property)

void	clearProperty (Property property)

void	toggleProperty (Property property)

Size	countProperties () const

const NamedProperty &	getNamedProperty (Position index) const

NamedProperty &	getNamedProperty (Position index)

void	setProperty (const NamedProperty &property)

void	setProperty (const std::string &name)

void	setProperty (const std::string &name, bool value)

void	setProperty (const std::string &name, int value)

void	setProperty (const std::string &name, unsigned int value)

void	setProperty (const std::string &name, float value)

void	setProperty (const std::string &name, double value)

void	setProperty (const std::string &name, const std::string &value)

void	setProperty (const std::string &name, const PersistentObject &value)

const NamedProperty &	getProperty (const std::string &name) const

NamedPropertyIterator	beginNamedProperty ()

NamedPropertyIterator	endNamedProperty ()

void	clearProperty (const std::string &name)

Size	countNamedProperties () const

bool	hasProperty (Property property) const
	Query for an unnamed property. More...

bool	hasProperty (const std::string &name) const
	Query for a named property. More...

bool	operator== (const PropertyManager &pm) const

bool	operator!= (const PropertyManager &pm) const
	Inequality operator. More...

void	write (PersistenceManager &pm) const
	Persistent stream writing. More...

bool	read (PersistenceManager &pm)
	Persistent stream reading. More...

bool	isValid () const

void	dump (std::ostream &s=std::cout, Size depth=0) const

Additional Inherited Members
Static Public Member Functions inherited from BALL::Composite
static bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)

Static Public Member Functions inherited from BALL::Object
static Handle	getNextHandle ()

static Handle	getNewHandle ()

Static Public Member Functions inherited from BALL::AutoDeletable
static void	clearLastPtr ()

Static Public Attributes inherited from BALL::Composite
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR

static KernelPredicateType	DEFAULT_UNARY_PREDICATE

Protected Member Functions inherited from BALL::AutoDeletable
	AutoDeletable ()

	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)

Protected Attributes inherited from BALL::Selectable
bool	selected_

Detailed Description

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

Definition at line 29 of file atomContainer.h.

Member Enumeration Documentation

enum BALL::AtomContainer::Property

The number of predefined properties for AtomContainer.

Enumerator
NUMBER_OF_PROPERTIES

Definition at line 42 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 ( Atom & atom )

Append an atom to the last position.

Parameters

atom	the atom to append

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

Append an AtomContainer at the last position.

Parameters

atom_container the AtomContainer to prepend

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

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

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

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

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

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 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 ( 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 ( 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

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 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

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

Return the name.

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

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

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

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

Insert an atom to the last position.

Parameters

atom	the atom to insert

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

Insert an AtomContainer at the last position.

Parameters

atom_container the AtomContainer to insert

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

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

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

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

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

Test if an AtomContainer is a child.

Parameters

atom_container the AtomContainer to test

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

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 )

virtual

Read an AtomContainer object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Composite.

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

virtual void BALL::AtomContainer::persistentWrite	(	PersistenceManager &	pm,
		const char *	name = `0`
	)		const

virtual

Write an AtomContainer object to a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Composite.

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

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

Prepend an atom at position 0.

Parameters

atom	the atom to prepend

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

Prepend an AtomContainer at position 0.

Parameters

atom_container the AtomContainer to prepend

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

Remove an atom

Parameters

atom	the atom to remove

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

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

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

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

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

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 .

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

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

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

Swap the contents of two AtomContainers.

Parameters

atom_container the AtomContainer this instance is being swapped with.

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation