#include <BALL/KERNEL/chain.h>

Inheritance diagram for BALL::Chain:

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 Chain &chain) const
bool	operator!= (const Chain &chain) const
Constructors and Destructors
	Chain ()
	Default constrcutor.
	Chain (const Chain &chain, bool deep=true)
	Copy constructor.
	Chain (const String &name)
	Detailled constructor.
virtual	~Chain ()
	Destructor.
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const
void	persistentRead (PersistenceManager &pm)
Assignment
void	set (const Chain &chain, bool deep=true)
Chain &	operator= (const Chain &chain)
void	get (Chain &chain, bool deep=true) const
void	swap (Chain &chain)
Accessors
Protein *	getProtein ()
const Protein *	getProtein () const
SecondaryStructure *	getSecondaryStructure (Position position)
const SecondaryStructure *	getSecondaryStructure (Position position) const
Residue *	getResidue (Position position)
const Residue *	getResidue (Position position) const
Residue *	getNTerminal ()
const Residue *	getNTerminal () const
Residue *	getCTerminal ()
const Residue *	getCTerminal () const
PDBAtom *	getPDBAtom (Position position)
const PDBAtom *	getPDBAtom (Position position) const
Size	countSecondaryStructures () const
Size	countResidues () const
Size	countPDBAtoms () const
void	prepend (SecondaryStructure &secondary_structure)
void	append (SecondaryStructure &secondary_structure)
void	insert (SecondaryStructure &secondary_structure)
void	insertBefore (SecondaryStructure &secondary_structure, Composite &before)
void	insertAfter (SecondaryStructure &secondary_structure, Composite &after)
bool	remove (SecondaryStructure &secondary_structure)
void	prepend (Residue &residue)
void	append (Residue &residue)
void	insert (Residue &residue)
void	insertBefore (Residue &residue, Composite &before)
void	insertAfter (Residue &residue, Composite &after)
bool	remove (Residue &residue)
void	spliceBefore (Chain &chain)
void	spliceAfter (Chain &chain)
void	splice (Chain &chain)
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.

Private Member Functions
AtomContainer *	getAtomContainer (Position position)
const AtomContainer *	getAtomContainer (Position position) const
Atom *	getAtom (Position position)
const Atom *	getAtom (Position position) 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)

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

Protein chain class. This class represents a polypeptide chain within a Protein . Chains can contain SecondaryStructure s or Residue s.

Definition at line 30 of file chain.h.

Member Enumeration Documentation

enum BALL::Chain::Property

Enumerator:

NUMBER_OF_PROPERTIES

Definition at line 43 of file chain.h.

Constructor & Destructor Documentation

BALL::Chain::Chain ( )

Default constrcutor.

BALL::Chain::Chain	(	const Chain &	chain,
		bool	deep = `true`
	)

Copy constructor.

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

Detailled constructor.

virtual BALL::Chain::~Chain ( )

virtual

Destructor.

Member Function Documentation

void BALL::Chain::append ( SecondaryStructure & secondary_structure )

Append a SecondaryStructure after the last position.

Parameters

secondary_structure the SecondaryStructure to append

void BALL::Chain::append ( Residue & residue )

Append a Residue after the last position.

Parameters

residue the Residue to append

void BALL::Chain::append ( Atom & atom )

private

void BALL::Chain::append ( AtomContainer & atom_container )

private

Size BALL::Chain::countPDBAtoms ( ) const

Count the PDBAtoms

Returns: Size the number of PDBAtoms

Size BALL::Chain::countResidues ( ) const

Count the Residues

Returns: Size the number of residues

Size BALL::Chain::countSecondaryStructures ( ) const

Count the SecondaryStructures

Returns: Size the number of secondary structures

virtual void BALL::Chain::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.

void BALL::Chain::get	(	Chain &	chain,
		bool	deep = `true`
	)		const

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

Parameters

chain the chain to be assigned to

See Also: chain::set

Atom* BALL::Chain::getAtom ( Position position )

private

const Atom* BALL::Chain::getAtom ( Position position ) const

private

AtomContainer* BALL::Chain::getAtomContainer ( Position position )

private

const AtomContainer* BALL::Chain::getAtomContainer ( Position position ) const

private

Residue* BALL::Chain::getCTerminal ( )

Get a pointer to the C-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns: Residue* - mutable pointer to the C-terminal Residue

const Residue* BALL::Chain::getCTerminal ( ) const

Get a constant pointer to the C-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns: Residue* - constant pointer to the C-terminal Residue

Residue* BALL::Chain::getNTerminal ( )

Get a pointer to the N-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns: Residue* - mutable pointer to the N-terminal Residue

const Residue* BALL::Chain::getNTerminal ( ) const

Get a constant pointer to the N-terminal Residue. The pointer is 0 if this instance does not have a Residue with the property "PROPERTY__AMINO_ACID".

Returns: Residue* - constant pointer to the N-terminal Residue

PDBAtom* BALL::Chain::getPDBAtom ( Position position )

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

Parameters

position the position of the child PDBAtom

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

const PDBAtom* BALL::Chain::getPDBAtom ( Position position ) const

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

Parameters

position the position of the child PDBAtom

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

Protein* BALL::Chain::getProtein ( )

Get a pointer to the parent protein. The pointer is 0 if this instance does not have a parent protein.

Returns: Protein* - mutable pointer to the parent protein

const Protein* BALL::Chain::getProtein ( ) const

Get a constant pointer to the parent protein. The pointer is 0 if this instance does not have a parent protein.

Returns: Protein* - constant pointer to the parent protein

Residue* BALL::Chain::getResidue ( Position position )

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

Parameters

position the position of the child Residue

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

const Residue* BALL::Chain::getResidue ( Position position ) const

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

Parameters

position the position of the child Residue

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

SecondaryStructure* BALL::Chain::getSecondaryStructure ( Position position )

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

Parameters

position the position of the child SecondaryStructure

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

const SecondaryStructure* BALL::Chain::getSecondaryStructure ( Position position ) const

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

Parameters

position the position of the child SecondaryStructure

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

void BALL::Chain::insert ( SecondaryStructure & secondary_structure )

Insert a SecondaryStructure after the last position.

Parameters

secondary_structure the SecondaryStructure to insert

void BALL::Chain::insert ( Residue & residue )

Insert a Residue after the last position.

Parameters

residue the Residue to insert

void BALL::Chain::insert ( Atom & atom )

private

void BALL::Chain::insert ( AtomContainer & atom_container )

private

void BALL::Chain::insertAfter	(	SecondaryStructure &	secondary_structure,
		Composite &	after
	)

Insert a SecondaryStructure after a given Composite object.

Parameters

secondary_structure	the SecondaryStructure to insert
after	the Composite object to insert after

void BALL::Chain::insertAfter	(	Residue &	residue,
		Composite &	after
	)

Insert a Residue after a given Composite object.

Parameters

residue	the Residue to insert
after	the Composite object to insert after

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

private

void BALL::Chain::insertAfter	(	AtomContainer &	atom_container,
		Composite &	after
	)

private

void BALL::Chain::insertBefore	(	SecondaryStructure &	secondary_structure,
		Composite &	before
	)

Insert a SecondaryStructure before a given Composite object.

Parameters

secondary_structure	the SecondaryStructure to insert
before	the Composite object to insert before

void BALL::Chain::insertBefore	(	Residue &	residue,
		Composite &	before
	)

Insert a Residue before a given Composite object.

Parameters

residue	the Residue to insert
before	the Composite object to insert before

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

private

void BALL::Chain::insertBefore	(	AtomContainer &	atom_container,
		Composite &	before
	)

private

bool BALL::Chain::operator!= ( const Chain & chain ) const

Inequality operator

See Also: operator ==

Chain& BALL::Chain::operator= ( const Chain & chain )

Assignment operator. The assignment is deep.

Parameters

chain the chain to be copied (cloned)

Returns: chain& - this instance.

See Also: chain::set

bool BALL::Chain::operator== ( const Chain & chain ) const

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

See Also: Object::operator ==

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

virtual

Reads a Chain object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

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

virtual

Writes a Chain object to a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

void BALL::Chain::prepend ( SecondaryStructure & secondary_structure )

Prepend a SecondaryStructure at position 0.

Parameters

secondary_structure the SecondaryStructure to prepend

void BALL::Chain::prepend ( Residue & residue )

Prepend a Residue at position 0.

Parameters

residue the Residue to prepend

void BALL::Chain::prepend ( Atom & atom )

private

void BALL::Chain::prepend ( AtomContainer & atom_container )

private

bool BALL::Chain::remove ( SecondaryStructure & secondary_structure )

Remove a SecondaryStructure

Parameters

secondary_structure the SecondaryStructure to remove

bool BALL::Chain::remove ( Residue & residue )

Remove a Residue.

Parameters

residue the Residue to remove

bool BALL::Chain::remove ( Atom & atom )

private

bool BALL::Chain::remove ( AtomContainer & atom_container )

private

void BALL::Chain::set	(	const Chain &	chain,
		bool	deep = `true`
	)

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

Parameters

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

void BALL::Chain::splice ( Chain & chain )

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

void BALL::Chain::splice ( AtomContainer & atom_container )

private

void BALL::Chain::spliceAfter ( Chain & chain )

Cut all children of chain and append them after the children of this chain.

Parameters

chain the chain to access

void BALL::Chain::spliceAfter ( AtomContainer & atom_container )

private

void BALL::Chain::spliceBefore ( Chain & chain )

Cut all children of chain and prepend them before the children of this chain.

Parameters

chain the chain to access

void BALL::Chain::spliceBefore ( AtomContainer & atom_container )

private

void BALL::Chain::swap ( Chain & chain )

Swapping of chains.

Parameters

chain the chain this instance is being swapped with

Public Types

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation