#include <BALL/KERNEL/system.h>

Inheritance diagram for BALL::System:

Public Member Functions
bool	operator== (const System &system) const

bool	operator!= (const System &system) const

Constructors and Destructors
	System ()
	Default constructor. More...

	System (const System &system, bool deep=true)
	Copy constructor. More...

	System (const String &name)
	Detailled constructor. More...

virtual	~System ()
	Destructor. More...

Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const

void	persistentRead (PersistenceManager &pm)

Assignment
void	set (const System &system, bool deep=true)

System &	operator= (const System &system)

void	get (System &system, bool deep=true) const

Accessors
Molecule *	getMolecule (Position position)

const Molecule *	getMolecule (Position position) const

Protein *	getProtein (Position position)

const Protein *	getProtein (Position position) const

Size	countMolecules () const

Size	countFragments () const

Size	countAtoms () const

Size	countProteins () const

Size	countChains () const

Size	countSecondaryStructures () const

Size	countResidues () const

Size	countNucleicAcids () const

Size	countNucleotides () const

void	prepend (Molecule &molecule)

void	append (Molecule &molecule)

void	insert (Molecule &molecule)

void	insertBefore (Molecule &molecule, Composite &before)

void	insertAfter (Molecule &molecule, Composite &after)

bool	remove (Molecule &molecule)

void	spliceBefore (System &system)

void	spliceAfter (System &system)

void	splice (System &system)

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

	AtomContainer (const AtomContainer &atom_container, bool deep=true)

	AtomContainer (const String &name)

virtual	~AtomContainer ()

virtual void	clear ()

virtual void	destroy ()

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)

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

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)

void	destroyBonds ()

virtual bool	isValid () const

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

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
Public Types inherited from BALL::AtomContainer
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

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

System class. This class is used to represent a system, i.e., a collection of molecules.

Definition at line 38 of file KERNEL/system.h.

Constructor & Destructor Documentation

BALL::System::System ( )

Default constructor.

BALL::System::System	(	const System &	system,
		bool	deep = `true`
	)

Copy constructor.

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

Detailled constructor.

virtual BALL::System::~System ( )

virtual

Destructor.

Member Function Documentation

void BALL::System::append ( Molecule & molecule )

Append a molecule after the last position.

Parameters

molecule the molecule to append

Size BALL::System::countAtoms ( ) const

Count the atoms in this system.

Returns: Size the number of atoms

Size BALL::System::countChains ( ) const

Count the chains in this system.

Returns: Size the number of chains

Size BALL::System::countFragments ( ) const

Count the fragments in this system.

Returns: Size the number of fragments

Size BALL::System::countMolecules ( ) const

Count the molecules in this system.

Returns: Size the number of molecules

Size BALL::System::countNucleicAcids ( ) const

Count the nucleic acids in this system.

Returns: Size the number of nucleic acids

Size BALL::System::countNucleotides ( ) const

Count the nucleotides in this system.

Returns: Size the number of nucleotides

Size BALL::System::countProteins ( ) const

Count the proteins in this system.

Returns: Size the number of proteins

Size BALL::System::countResidues ( ) const

Count the residues in this system.

Returns: Size the number of residues

Size BALL::System::countSecondaryStructures ( ) const

Count the secondary structures in this system.

Returns: Size the number of secondary structures

void BALL::System::get	(	System &	system,
		bool	deep = `true`
	)		const

Copying with cloning facility. The assignment is either deep or shallow (default).

Parameters

System the System to be assigned to

Molecule* BALL::System::getMolecule ( Position position )

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

Note: The current implementation of this function has linear complexity

Parameters

position the position of the child molecule

Returns: Molecule* - mutable pointer to the child Molecule at position

const Molecule* BALL::System::getMolecule ( Position position ) const

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

Note: The current implementation of this function has linear complexity

Parameters

position the position of the child molecule

Returns: Molecule* - constant pointer to the child Molecule at position

Protein* BALL::System::getProtein ( Position position )

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

Note: The current implementation of this function has linear complexity

Parameters

position the position of the child Protein

Returns: Protien* - mutable pointer to the child Protein at position

const Protein* BALL::System::getProtein ( Position position ) const

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

Note: The current implementation of this function has linear complexity

Parameters

position the position of the child Protein

Returns: Protien* - mutable pointer to the child Protein at position

void BALL::System::insert ( Molecule & molecule )

Insert a molecule after the last position.

Parameters

molecule the molecule to insert

void BALL::System::insertAfter	(	Molecule &	molecule,
		Composite &	after
	)

Insert a molecule after a given Composite object.

Parameters

molecule	the molecule to insert
after	the Composite object to insert before

void BALL::System::insertBefore	(	Molecule &	molecule,
		Composite &	before
	)

Insert a molecule before a given Composite object.

Parameters

molecule	the molecule to insert
before	the Composite object to insert before

bool BALL::System::operator!= ( const System & system ) const

Inequality operator

See also: operator ==

System& BALL::System::operator= ( const System & system )

Assignment operator.

Parameters

system the System to be copied (cloned)

Returns: System& - this instance

bool BALL::System::operator== ( const System & system ) const

Equality operator. Two instance of System are equal if they have the same handle.

See also: Object::operator ==

void BALL::System::persistentRead ( PersistenceManager & pm )

virtual

Reads a System object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

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

virtual

Writes a System object to a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

void BALL::System::prepend ( Molecule & molecule )

Prepend a molecule at position 0.

Parameters

molecule the molecule to prepend

bool BALL::System::remove ( Molecule & molecule )

Remove a molecule.

Parameters

molecule the molecule to remove

void BALL::System::set	(	const System &	system,
		bool	deep = `true`
	)

Assignment with cloning facility. The assignment is either deep or shallow (default).

Parameters

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

void BALL::System::splice ( System & system )

Move the children of system into this instance. The children are inserted using spliceBefore .

void BALL::System::spliceAfter ( System & system )

Move the children of system into this instance. Cut all children of system and append them after the children of this instance.

Parameters

system the system to access

void BALL::System::spliceBefore ( System & system )

Move the children of system into this instance. Cut all children of system and prepend them before the children of this instance.

Parameters

system the system to access

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation