#include <BALL/KERNEL/nucleicAcid.h>

Inheritance diagram for BALL::NucleicAcid:

Public Types
Enums
enum	Property { NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES }

Public Types inherited from BALL::Molecule
enum	Property { IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES, NUMBER_OF_PROPERTIES }

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

Public Member Functions
bool	operator== (const NucleicAcid &nucleic_acid) const

bool	operator!= (const NucleicAcid &nucleic_acid) const

Constructors and Destructors
	NucleicAcid ()

	NucleicAcid (const NucleicAcid &nucleic_acid, bool deep=true)

	NucleicAcid (const String &name, const String &id=BALL_NUCLEICACID_DEFAULT_ID)

virtual	~NucleicAcid ()

virtual void	clear ()

virtual void	destroy ()

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

void	persistentRead (PersistenceManager &pm)

Assignment Methods
void	set (const NucleicAcid &nucleic_acid, bool deep=true)

NucleicAcid &	operator= (const NucleicAcid &nucleic_acid)

void	get (NucleicAcid &nucleic_acid, bool deep=true) const

void	swap (NucleicAcid &nucleic_acid)

Accessors
Nucleotide *	getNucleotide (Position position)

const Nucleotide *	getNucleotide (Position position) const

Nucleotide *	get3Prime ()

const Nucleotide *	get3Prime () const

Nucleotide *	get5Prime ()

const Nucleotide *	get5Prime () const

void	setID (const String &id)

const String &	getID () const

Size	countNucleotides () const

Debugging and Diagnostics
virtual bool	isValid () const

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

Public Member Functions inherited from BALL::Molecule
bool	operator== (const Molecule &molecule) const

bool	operator!= (const Molecule &molecule) const

	Molecule ()

	Molecule (const Molecule &molecule, bool deep=true)

	Molecule (const String &name)

virtual	~Molecule ()

void	set (const Molecule &molecule, bool deep=true)

Molecule &	operator= (const Molecule &molecule)

void	get (Molecule &molecule, bool deep=true) const

void	swap (Molecule &molecule)

System *	getSystem ()

const System *	getSystem () 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)

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)

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

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

	AtomContainer (const String &name)

virtual	~AtomContainer ()

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 ()

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
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 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

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. 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 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. More...

bool	hasProperty (const 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

Private Attributes
String	id_

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::Molecule
Molecule *	getMolecule ()

const Molecule *	getMolecule () const

AtomContainer *	getSuperAtomContainer ()

const AtomContainer *	getSuperAtomContainer () const

void	prepend (Molecule &molecule)

void	append (Molecule &molecule)

void	insert (Molecule &molecule)

void	insertBefore (Molecule &molecule, Composite &composite)

void	insertAfter (Molecule &molecule, Composite &composite)

bool	remove (Molecule &molecule)

bool	isSubAtomContainerOf (const AtomContainer &atom_container) const

Protected Attributes inherited from BALL::Selectable
bool	selected_

Detailed Description

Nucleic acid class.

Definition at line 27 of file nucleicAcid.h.

Member Enumeration Documentation

enum BALL::NucleicAcid::Property

Enumerator
NUMBER_OF_PROPERTIES

Definition at line 40 of file nucleicAcid.h.

Constructor & Destructor Documentation

BALL::NucleicAcid::NucleicAcid ( )

Default constructor.

BALL::NucleicAcid::NucleicAcid	(	const NucleicAcid &	nucleic_acid,
		bool	deep = `true`
	)

Copy constructor.

BALL::NucleicAcid::NucleicAcid	(	const String &	name,
		const String &	id = `BALL_NUCLEICACID_DEFAULT_ID`
	)

Detailed constructor.

virtual BALL::NucleicAcid::~NucleicAcid ( )

virtual

Destructor.

Member Function Documentation

virtual void BALL::NucleicAcid::clear ( )

virtual

Clear the contents of the nucleic acid.

Reimplemented from BALL::AtomContainer.

Size BALL::NucleicAcid::countNucleotides ( ) const

Return the number of Nucleotides contained in this instance NucleicAcid.

Returns: Size - number of Nucleotides

virtual void BALL::NucleicAcid::destroy ( )

virtual

Clear the contents of the nucleic acid and remove it from parent kernel objects.

Reimplemented from BALL::AtomContainer.

virtual void BALL::NucleicAcid::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::Molecule.

void BALL::NucleicAcid::get	(	NucleicAcid &	nucleic_acid,
		bool	deep = `true`
	)		const

Assign a NucleicAcid object from another.

Nucleotide* BALL::NucleicAcid::get3Prime ( )

Retrieve a pointer to the Nucleotide at the 3'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide.

Returns: Nucleotide* - mutable pointer to the first child Nucleotide

const Nucleotide* BALL::NucleicAcid::get3Prime ( ) const

Retrieve a const pointer to the nucleotide at the 3'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide.

Returns: Nucleotide* - constant pointer to the first child Nucleotide

Nucleotide* BALL::NucleicAcid::get5Prime ( )

Retrieve a pointer to the Nucleotide at the 5'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide.

Returns: Nucleotide* - mutable pointer to the last child Nucleotide

const Nucleotide* BALL::NucleicAcid::get5Prime ( ) const

Retrieve a const pointer to the Nucleotide at the 5'-end of this instance. The pointer is 0 if this instance does not have a Nucleotide.

Returns: Nucleotide* - constant pointer to the last child Nucleotide

const String& BALL::NucleicAcid::getID ( ) const

Retrieve the ID of the NucleicAcid.

Returns: String the ID

Nucleotide* BALL::NucleicAcid::getNucleotide ( Position position )

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

Parameters

position the position of the child Nucleotide

Returns: Nucleotide* - mutable pointer to the child Nucleotide at positon

const Nucleotide* BALL::NucleicAcid::getNucleotide ( Position position ) const

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

Parameters

position the position of the child Nucleotide

Returns: Nucleotide* - constant pointer to the child Nucleotide at positon

virtual bool BALL::NucleicAcid::isValid ( ) const

virtual

Internal state and consistency self-validation.

Returns: bool - true if the internal state of this instance atom is correct (self-validated) and consistent, false otherwise

Reimplemented from BALL::AtomContainer.

bool BALL::NucleicAcid::operator!= ( const NucleicAcid & nucleic_acid ) const

Inequality operator

See Also: operator ==

NucleicAcid& BALL::NucleicAcid::operator= ( const NucleicAcid & nucleic_acid )

Assignment operator.

bool BALL::NucleicAcid::operator== ( const NucleicAcid & nucleic_acid ) const

Equality operator. Two nucleic acids are equal if they have the same handle.

See Also: Object::operator ==.

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

virtual

Reads a NucleicAcid object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Molecule.

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

virtual

Writes a NucleicAcid object to a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Molecule.

void BALL::NucleicAcid::set	(	const NucleicAcid &	nucleic_acid,
		bool	deep = `true`
	)

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

Parameters

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

void BALL::NucleicAcid::setID ( const String & id )

Set the ID of the NucleicAcid.

Parameters

id	the new ID

void BALL::NucleicAcid::swap ( NucleicAcid & nucleic_acid )

Swap the contents of two NucleicAcid objects.

Member Data Documentation

String BALL::NucleicAcid::id_

private

Definition at line 231 of file nucleicAcid.h.

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation