BALL::AtomContainer Class Reference

#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.
bool	applyInterBond (UnaryProcessor< Bond > &processor)
	Apply to all bonds connected to atoms outside this AtomContainer.
Public Member Functions inherited from BALL::Composite
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)
	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
void	host (Visitor< Composite > &visitor)
template<typename T >
bool	applyAncestor (UnaryProcessor< T > &processor)
template<typename T >
bool	applyChild (UnaryProcessor< T > &processor)
template<typename T >
bool	applyDescendantPreorder (UnaryProcessor< T > &processor)
template<typename T >
bool	applyDescendantPostorder (UnaryProcessor< T > &processor)
template<typename T >
bool	applyDescendant (UnaryProcessor< T > &processor)
template<typename T >
bool	applyPreorder (UnaryProcessor< T > &processor)
template<typename T >
bool	applyPostorder (UnaryProcessor< T > &processor)
template<typename T >
bool	apply (UnaryProcessor< T > &processor)
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.
	Object (const Object &object)
	Copy constructor.
virtual	~Object ()
	Destructor.
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.
BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor.
virtual	~PropertyManager ()
	Destructor.
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 string &name)
void	setProperty (const string &name, bool value)
void	setProperty (const string &name, int value)
void	setProperty (const string &name, unsigned int value)
void	setProperty (const string &name, float value)
void	setProperty (const string &name, double value)
void	setProperty (const string &name, const string &value)
void	setProperty (const string &name, const PersistentObject &value)
const NamedProperty &	getProperty (const string &name) const
NamedPropertyIterator	beginNamedProperty ()
NamedPropertyIterator	endNamedProperty ()
void	clearProperty (const string &name)
Size	countNamedProperties () const
bool	hasProperty (Property property) const
	Query for an unnamed property.
bool	hasProperty (const string &name) const
	Query for a named property.
bool	operator== (const PropertyManager &pm) const
bool	operator!= (const PropertyManager &pm) const
	Inequality operator.
void	write (PersistenceManager &pm) const
	Persistent stream writing.
bool	read (PersistenceManager &pm)
	Persistent stream reading.

Private Attributes
String	name_

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 30 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 43 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

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

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.

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

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::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

Reimplemented in BALL::Molecule.

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.

void BALL::AtomContainer::insert

(

Atom &

atom

)

Insert an atom to the last position.

Parameters

atom	the atom to insert

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

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::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::Nucleotide, and BALL::Molecule.

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.

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::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::Protein, BALL::Molecule, 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::Protein, BALL::Molecule, 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

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

void BALL::AtomContainer::prepend

(

AtomContainer &

atom_container

)

Prepend an AtomContainer at position 0.

Parameters

atom_container

the AtomContainer to prepend

Reimplemented in BALL::Molecule.

bool BALL::AtomContainer::remove

(

Atom &

atom

)

Remove an atom

Parameters

atom	the atom to remove

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

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.

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 .

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.

Member Data Documentation

String BALL::AtomContainer::name_

private

Definition at line 404 of file atomContainer.h.