BALL::Molecule Class Reference

#include <BALL/KERNEL/molecule.h>

Inheritance diagram for BALL::Molecule:

Public Types
Enums
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 Molecule &molecule) const
bool	operator!= (const Molecule &molecule) const
Constructors and Destructors
	Molecule ()
	Molecule (const Molecule &molecule, bool deep=true)
	Molecule (const AtomContainer &atomContainer, bool deep=true)
	Molecule (const String &name)
virtual	~Molecule ()
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const
void	persistentRead (PersistenceManager &pm)
Assignment
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)
Accessors
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)
Type predicates
virtual bool	isMolecule () const
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. 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	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

Protected Member Functions
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 Member Functions inherited from BALL::AutoDeletable
	AutoDeletable ()
	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)

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 Attributes inherited from BALL::Selectable
bool	selected_

Detailed Description

Molecule class. Used to represent general molecules without specific properties.

Definition at line 29 of file molecule.h.

Member Enumeration Documentation

enum BALL::Molecule::Property

Properties

Enumerator
IS_SOLVENT
NUMBER_OF_PROPERTIES

Definition at line 42 of file molecule.h.

Constructor & Destructor Documentation

BALL::Molecule::Molecule

(

)

Default constructor.

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

Copy constructor.

BALL::Molecule::Molecule	(	const AtomContainer &	atomContainer,
		bool	deep = true
	)

Constructor using an AtomContainer.

BALL::Molecule::Molecule

(

const String &

name

)

Detailled constructor.

virtual BALL::Molecule::~Molecule ( )

virtual

Destructor.

Member Function Documentation

void BALL::Molecule::append

(

Atom &

atom

)

Insert an atom as the last child.

Parameters

atom	the atom to add

void BALL::Molecule::append

(

AtomContainer &

atom_container

)

Append an AtomContainer as the last child.

Parameters

atom_container

the AtomContainer to add

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

protected

virtual void BALL::Molecule::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::Protein, and BALL::NucleicAcid.

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

Assign to another Molecule.

Parameters

molecule	the Molecule to be assigned to
deep	make a deep (=true) or shallow (=false) copy

Molecule* BALL::Molecule::getMolecule ( )

protected

const Molecule* BALL::Molecule::getMolecule ( ) const

protected

AtomContainer* BALL::Molecule::getSuperAtomContainer ( )

protected

const AtomContainer* BALL::Molecule::getSuperAtomContainer ( ) const

protected

System* BALL::Molecule::getSystem

(

)

Access the parent System.

Returns

System* pointer to the parent System

const System* BALL::Molecule::getSystem

(

)

const

Get a const pointer to the parent System.

Returns

System* pointer to the parent System

void BALL::Molecule::insert

(

Atom &

atom

)

Insert an atom as the last child.

Parameters

atom	the atom to add

void BALL::Molecule::insert

(

AtomContainer &

atom_container

)

Insert an AtomContainer as the last child.

Parameters

atom_container

the AtomContainer to add

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

protected

void BALL::Molecule::insertAfter	(	Atom &	atom,
		Composite &	after
	)

Insert an atom after a Composite object.

Parameters

atom	the atom to insert
after	the Composite object to insert after

void BALL::Molecule::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::Molecule::insertAfter ( Molecule &  molecule, Composite &  composite  )

protected

void BALL::Molecule::insertBefore	(	Atom &	atom,
		Composite &	before
	)

Insert an atom before a Composite object.

Parameters

atom	the atom to insert
before	the Composite object to insert before

void BALL::Molecule::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

void BALL::Molecule::insertBefore ( Molecule &  molecule, Composite &  composite  )

protected

virtual bool BALL::Molecule::isMolecule ( ) const

inlinevirtual

Test if the Composite is a Molecule

Reimplemented from BALL::Composite.

Definition at line 216 of file molecule.h.

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

protected

bool BALL::Molecule::operator!=

(

const Molecule &

molecule

)

const

Inequality operator

See also

operator ==

Molecule& BALL::Molecule::operator=

(

const Molecule &

molecule

)

Assignment operator.

Parameters

molecule

the Molecule to assign from

bool BALL::Molecule::operator==

(

const Molecule &

molecule

)

const

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

See also

Object::operator ==.

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

virtual

Reads a Molecule object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::NucleicAcid, and BALL::Protein.

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

virtual

Writes a Molecule object to a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

Reimplemented in BALL::NucleicAcid, and BALL::Protein.

void BALL::Molecule::prepend

(

Atom &

atom

)

Insert an atom as the first child.

Parameters

atom	the atom to add

void BALL::Molecule::prepend

(

AtomContainer &

atom_container

)

Insert an AtomContainer as the first child.

Parameters

atom_container

the AtomContainer to add

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

protected

bool BALL::Molecule::remove

(

Atom &

atom

)

Remove an atom.

Parameters

atom	the atom to remove

bool BALL::Molecule::remove

(

AtomContainer &

atom_container

)

Remove an AtomContainer.

Parameters

atom_container

the AtomContainer to remove

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

protected

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

Assign from another Molecule.

Parameters

molecule	the Molecule object to assign from
deep	make a deep (=true) or shallow (=false) copy

void BALL::Molecule::splice

(

AtomContainer &

atom_container

)

Move the children of atom_container into this molecule. The children of atom_container are inserted at the position of atom_container if it is a child of this. Otherwise the children are inserted using spliceBefore .

void BALL::Molecule::spliceAfter

(

AtomContainer &

atom_container

)

Cut all children of atom_container and append them after the children of this molecule.

Parameters

atom_container

the AtomContainer to access

void BALL::Molecule::spliceBefore

(

AtomContainer &

atom_container

)

Cut all children of atom_container and prepend them before the children of this molecule.

Parameters

atom_container

the AtomContainer to access

void BALL::Molecule::swap

(

Molecule &

molecule

)

Swap the contents of two molecules.

Parameters

molecule

the Molecule to swap contents with