BALL::Fragment Class Reference

#include <BALL/KERNEL/fragment.h>

Inheritance diagram for BALL::Fragment:

Public Types
Enums
enum	Property { NUMBER_OF_PROPERTIES = AtomContainer::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 Fragment &fragment) const
bool	operator!= (const Fragment &fragment) const
Constructors and Destructors
	Fragment ()
	Fragment (const Fragment &fragment, bool deep=true)
	Fragment (const String &name)
virtual	~Fragment ()
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const
void	persistentRead (PersistenceManager &pm)
Assignment
Fragment &	operator= (const Fragment &fragment)
Debugging and Diagnostics
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
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
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.

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

Fragment class. Fragments are used to represent parts of molecules (for example functional groups, monomers in larger polymers).

Definition at line 20 of file fragment.h.

Member Enumeration Documentation

enum BALL::Fragment::Property

Enumerator:

NUMBER_OF_PROPERTIES

Definition at line 32 of file fragment.h.

Constructor & Destructor Documentation

BALL::Fragment::Fragment

(

)

Default constructor

BALL::Fragment::Fragment	(	const Fragment &	fragment,
		bool	deep = true
	)

Copy constructor

BALL::Fragment::Fragment

(

const String &

name

)

Constructor

virtual BALL::Fragment::~Fragment ( )

virtual

Destructor

Member Function Documentation

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

virtual

Internal state dump. Dump the current internal state to the output ostream s with dumping depth depth .

Parameters

s	- output stream where to output the internal state
depth	- the dumping depth

Reimplemented from BALL::AtomContainer.

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

bool BALL::Fragment::operator!=

(

const Fragment &

fragment

)

const

Inequality operator

See Also

operator ==

Fragment& BALL::Fragment::operator=

(

const Fragment &

fragment

)

Assignment operator.

Parameters

fragment

the Fragment to be copied (cloned)

Returns

Fragment& - this instance

bool BALL::Fragment::operator==

(

const Fragment &

fragment

)

const

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

See Also

Object::operator ==.

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

virtual

Reads a Fragment object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

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

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

virtual

Writes a Fragment object to a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

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