#include <BALL/KERNEL/secondaryStructure.h>

Inheritance diagram for BALL::SecondaryStructure:

Public Types
Enums
enum	Type { HELIX, COIL, STRAND, TURN, UNKNOWN, NUMBER_OF_TYPES }

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

	SecondaryStructure (const SecondaryStructure &secondary_structure, bool deep=true)
	Copy constructor. More...

	SecondaryStructure (const String &name)

virtual	~SecondaryStructure ()
	Destructor. More...

virtual void	clear ()
	Clear the contents of the secondary structure. More...

virtual void	destroy ()
	Clear the contents of the secondary structure and remove it from all composite structures. More...

Predicates
bool	operator== (const SecondaryStructure &secondary_structure) const

bool	operator!= (const SecondaryStructure &secondary_structure) const

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

void	persistentRead (PersistenceManager &pm)

Assignment
void	set (const SecondaryStructure &secondary_structure, bool deep=true)

SecondaryStructure &	operator= (const SecondaryStructure &secondary_structure)

void	get (SecondaryStructure &secondary_structure, bool deep=true) const

void	swap (SecondaryStructure &secondary_structure)

Accessors
Type	getType () const
	Return the type of secondary structure. More...

void	setType (Type type)
	Set the type of secondary structure. More...

Protein *	getProtein ()

const Protein *	getProtein () const

Chain *	getChain ()

const Chain *	getChain () 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	countResidues () const

Size	countPDBAtoms () const

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 (SecondaryStructure &secondary_structure)

void	spliceAfter (SecondaryStructure &secondary_structure)

void	splice (SecondaryStructure &secondary_structure)

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::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

Protected Attributes
Type	type_
	The secondary structure type (helix, strand, coil, turn) More...

Private Member Functions
Fragment *	getFragment (Position position)

const Fragment *	getFragment (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)

Detailed Description

Secondary structure class. This class is used to represent secondary structure elements of protein chains.

Definition at line 29 of file secondaryStructure.h.

Member Enumeration Documentation

enum BALL::SecondaryStructure::Type

Secondary structure type

Enumerator
HELIX
COIL
STRAND
TURN
UNKNOWN
NUMBER_OF_TYPES

Definition at line 42 of file secondaryStructure.h.

Constructor & Destructor Documentation

BALL::SecondaryStructure::SecondaryStructure ( )

Default constructor.

BALL::SecondaryStructure::SecondaryStructure	(	const SecondaryStructure &	secondary_structure,
		bool	deep = `true`
	)

Copy constructor.

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

virtual BALL::SecondaryStructure::~SecondaryStructure ( )

virtual

Destructor.

Member Function Documentation

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

Append a Residue after the last position.

Parameters

residue the Residue to append

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

private

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

private

virtual void BALL::SecondaryStructure::clear ( )

virtual

Clear the contents of the secondary structure.

Reimplemented from BALL::AtomContainer.

Size BALL::SecondaryStructure::countPDBAtoms ( ) const

Count the PDBAtoms.

Returns: Size the number of PDBAtoms

Size BALL::SecondaryStructure::countResidues ( ) const

Count the Residues.

Returns: Size the number of residues

virtual void BALL::SecondaryStructure::destroy ( )

virtual

Clear the contents of the secondary structure and remove it from all composite structures.

Reimplemented from BALL::AtomContainer.

virtual void BALL::SecondaryStructure::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::AtomContainer.

void BALL::SecondaryStructure::get	(	SecondaryStructure &	secondary_structure,
		bool	deep = `true`
	)		const

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

Parameters

secondary_structure the SecondaryStructure to be assigned to

See Also: secondary_structure::set

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

private

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

private

Chain* BALL::SecondaryStructure::getChain ( )

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

Returns: Protein* - mutable pointer to the parent chain

const Chain* BALL::SecondaryStructure::getChain ( ) const

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

Returns: Protein* - constant pointer to the parent chain

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

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* - constant pointer to the C-terminal Residue

Fragment* BALL::SecondaryStructure::getFragment ( Position position )

private

const Fragment* BALL::SecondaryStructure::getFragment ( Position position ) const

private

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

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* - constant pointer to the N-terminal Residue

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

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

Parameters

position the position of the child PDBAtom

Returns: PDBAtom* - constant pointer to the child

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

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

Parameters

position the position of the child PDBAtom

Returns: PDBAtom* - mutable pointer to the child

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

Get a 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::SecondaryStructure::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 the given position.

Parameters

position the position of the child Residue

Returns: Residue* - mutable pointer to the child

const Residue* BALL::SecondaryStructure::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 the given position.

Parameters

position the position of the child Residue

Returns: Residue* - constant pointer to the child

Type BALL::SecondaryStructure::getType ( ) const

inline

Return the type of secondary structure.

Definition at line 150 of file secondaryStructure.h.

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

Insert a Residue after the last position.

Parameters

residue the Residue to insert

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

private

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

private

void BALL::SecondaryStructure::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 before

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

private

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

private

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

private

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

private

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

virtual

Internal state and consistency self-validation.

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

Reimplemented from BALL::AtomContainer.

bool BALL::SecondaryStructure::operator!= ( const SecondaryStructure & secondary_structure ) const

Inequality operator

See Also: operator ==

SecondaryStructure& BALL::SecondaryStructure::operator= ( const SecondaryStructure & secondary_structure )

Assignment operator.

Parameters

secondary_structure the SecondaryStructure to be copied (cloned)

Returns: Secondary_structure& - this instance

See Also: SecondaryStructure::set

bool BALL::SecondaryStructure::operator== ( const SecondaryStructure & secondary_structure ) const

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

See Also: Object::operator ==

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

virtual

Read a SecondaryStructure object from a persistent stream

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

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

virtual

Write a SecondaryStructure object to a persistent stream

Parameters

pm	the persistence manager

Reimplemented from BALL::AtomContainer.

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

Prepend a Residue at position 0.

Parameters

residue the Residue to prepend

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

private

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

private

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

Remove a Residue.

Parameters

residue the Residue to remove

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

private

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

private

void BALL::SecondaryStructure::set	(	const SecondaryStructure &	secondary_structure,
		bool	deep = `true`
	)

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

Parameters

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

void BALL::SecondaryStructure::setType ( Type type )

inline

Set the type of secondary structure.

Definition at line 153 of file secondaryStructure.h.

void BALL::SecondaryStructure::splice ( SecondaryStructure & secondary_structure )

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

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

private

void BALL::SecondaryStructure::spliceAfter ( SecondaryStructure & secondary_structure )

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

Parameters

secondary_structure the SecondaryStructure to access

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

private

void BALL::SecondaryStructure::spliceBefore ( SecondaryStructure & secondary_structure )

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

Parameters

secondary_structure the SecondaryStructure to access

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

private

void BALL::SecondaryStructure::swap ( SecondaryStructure & secondary_structure )

Swapping of two secondary structures.

Parameters

secondary_structure to swap with this instance

Member Data Documentation

Type BALL::SecondaryStructure::type_

protected

The secondary structure type (helix, strand, coil, turn)

Definition at line 323 of file secondaryStructure.h.

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation