BALL::SecondaryStructure Class Reference

#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.
	SecondaryStructure (const SecondaryStructure &secondary_structure, bool deep=true)
	Copy constructor.
	SecondaryStructure (const String &name)
virtual	~SecondaryStructure ()
	Destructor.
virtual void	clear ()
	Clear the contents of the secondary structure.
virtual void	destroy ()
	Clear the contents of the secondary structure and remove it from all composite structures.
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.
void	setType (Type type)
	Set the type of secondary structure.
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.
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.

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

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.