#include <BALL/KERNEL/residue.h>

Inheritance diagram for BALL::Residue:

Public Types
Enums
enum	Property { PROPERTY__NON_STANDARD = Fragment::NUMBER_OF_PROPERTIES + 1, PROPERTY__AMINO_ACID, PROPERTY__WATER, PROPERTY__HAS_SSBOND, PROPERTY__C_TERMINAL, PROPERTY__N_TERMINAL, PROPERTY__CYCLIC, NUMBER_OF_PROPERTIES }

enum	FullNameType { NO_VARIANT_EXTENSIONS, ADD_VARIANT_EXTENSIONS, ADD_RESIDUE_ID, ADD_VARIANT_EXTENSIONS_AND_ID }

Public Types inherited from BALL::Fragment
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 Residue &residue) const

bool	operator!= (const Residue &residue) const

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

	Residue (const Residue &residue, bool deep=true)
	Copy constructor. More...

	Residue (const String &name, const String &id=BALL_RESIDUE_DEFAULT_ID, char insertion_code=BALL_RESIDUE_DEFAULT_INSERTION_CODE)
	Detailled constructor. More...

virtual	~Residue ()
	Destructor. More...

virtual void	clear ()
	Clears the contents of this instance. More...

virtual void	destroy ()
	Clears the contents of this instance and removes it from all composite structures. More...

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

void	persistentRead (PersistenceManager &pm)

Assignment
void	set (const Residue &residue, bool deep=true)

Residue &	operator= (const Residue &residue)

void	get (Residue &residue, bool deep=true) const

void	swap (Residue &residue)

Accessors
String	getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const

bool	hasTorsionPhi () const

Angle	getTorsionPhi () const

bool	hasTorsionPsi () const

Angle	getTorsionPsi () const

bool	hasTorsionOmega () const

Angle	getTorsionOmega () const

Protein *	getProtein ()

const Protein *	getProtein () const

Chain *	getChain ()

const Chain *	getChain () const

SecondaryStructure *	getSecondaryStructure ()

const SecondaryStructure *	getSecondaryStructure () const

PDBAtom *	getPDBAtom (Position position)

const PDBAtom *	getPDBAtom (Position position) const

void	setID (const String &id)

const String &	getID () const

void	setInsertionCode (char insertion_code)

char	getInsertionCode () const

Size	countPDBAtoms () const

void	prepend (PDBAtom &atom)

void	append (PDBAtom &atom)

void	insert (PDBAtom &atom)

void	insertBefore (PDBAtom &atom, Composite &before)

void	insertAfter (PDBAtom &atom, Composite &after)

bool	remove (PDBAtom &atom)

void	spliceBefore (Residue &residue)

void	spliceAfter (Residue &residue)

void	splice (Residue &residue)

Predicates
bool	isAminoAcid () const

bool	isTerminal () const

bool	isNTerminal () const

bool	isCTerminal () const

Type predicates
virtual bool	isResidue () const

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::Fragment
bool	operator== (const Fragment &fragment) const

bool	operator!= (const Fragment &fragment) const

	Fragment ()

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

	Fragment (const String &name)

virtual	~Fragment ()

Fragment &	operator= (const Fragment &fragment)

virtual bool	isFragment () 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
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	isMolecule () const

virtual bool	isProtein () 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

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

Residue class. This class is used to represent residues in proteins.

Definition at line 36 of file residue.h.

Member Enumeration Documentation

enum BALL::Residue::FullNameType

Enum used to describe the kind of name constructed by getFullName .

Enumerator
NO_VARIANT_EXTENSIONS	This returns the unmodified residue name only.
ADD_VARIANT_EXTENSIONS	Add the residue variant extensions (e.g. '-C' for C-terminal residues)
ADD_RESIDUE_ID
ADD_VARIANT_EXTENSIONS_AND_ID

Definition at line 76 of file residue.h.

enum BALL::Residue::Property

Enumerator
PROPERTY__NON_STANDARD
PROPERTY__AMINO_ACID
PROPERTY__WATER
PROPERTY__HAS_SSBOND
PROPERTY__C_TERMINAL
PROPERTY__N_TERMINAL
PROPERTY__CYCLIC	Property for cyclic peptides. This property is set by the build bonds processor, if an atom of the first and an atom of the last residue in a chain share a bond.
NUMBER_OF_PROPERTIES

Definition at line 48 of file residue.h.

Constructor & Destructor Documentation

BALL::Residue::Residue ( )

Default constructor.

BALL::Residue::Residue	(	const Residue &	residue,
		bool	deep = `true`
	)

Copy constructor.

BALL::Residue::Residue	(	const String &	name,
		const String &	id = `BALL_RESIDUE_DEFAULT_ID`,
		char	insertion_code = `BALL_RESIDUE_DEFAULT_INSERTION_CODE`
	)

Detailled constructor.

virtual BALL::Residue::~Residue ( )

virtual

Destructor.

Member Function Documentation

void BALL::Residue::append ( PDBAtom & atom )

Append a PDBAtom at the last position.

Parameters

atom	the PDBAtom to append

virtual void BALL::Residue::clear ( )

virtual

Clears the contents of this instance.

Reimplemented from BALL::AtomContainer.

Size BALL::Residue::countPDBAtoms ( ) const

Count the child PDBAtoms.

Returns: Size the number of PDBAtoms

virtual void BALL::Residue::destroy ( )

virtual

Clears the contents of this instance and removes it from all composite structures.

Reimplemented from BALL::AtomContainer.

virtual void BALL::Residue::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::Fragment.

void BALL::Residue::get	(	Residue &	residue,
		bool	deep = `true`
	)		const

Assign a Residue object from another instance.

Chain* BALL::Residue::getChain ( )

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

Returns: Chain* - mutable pointer to the parent chain

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

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

Returns: Chain* - constant pointer to the parent chain

String BALL::Residue::getFullName ( FullNameType type = ADD_VARIANT_EXTENSIONS ) const

Return the fully qualified name. Residue names are modified as follows:

-N is added for N terminal residues
-C is added for C terminal residue
[-]S is added for CYS involved in a disulphide bridge
-M is added for individual amino acids (C and N terminal)

Parameters

type	if type is set to `NO_VARIANT_EXTENSIONS`, the variant extension (`-XX`) is omitted.

Returns: String the full fragment name

const String& BALL::Residue::getID ( ) const

Retrieve the ID.

Returns: String the ID

char BALL::Residue::getInsertionCode ( ) const

Get the insertion code.

Returns: char the insertion code

PDBAtom* BALL::Residue::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

const PDBAtom* BALL::Residue::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

Protein* BALL::Residue::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::Residue::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

SecondaryStructure* BALL::Residue::getSecondaryStructure ( )

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

Returns: SecondaryStructure* - mutable pointer to the parent chain

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

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

Returns: SecondaryStructure* - mutable pointer to the parent chain

Angle BALL::Residue::getTorsionOmega ( ) const

Calculate the torsion angle psi.

Returns: Angle - the torsion angle phi

Angle BALL::Residue::getTorsionPhi ( ) const

Calculate the torsion angle phi.

Returns: Angle - the torsion angle phi

Angle BALL::Residue::getTorsionPsi ( ) const

Calculate the torsion angle psi.

Returns: Angle - the torsion angle phi

bool BALL::Residue::hasTorsionOmega ( ) const

Check whether the torsion angle omega is defined.

Returns: bool

bool BALL::Residue::hasTorsionPhi ( ) const

Check whether the torsion angle phi is defined.

Returns: bool

bool BALL::Residue::hasTorsionPsi ( ) const

Check whether the torsion angle psi is defined.

Returns: bool

void BALL::Residue::insert ( PDBAtom & atom )

Insert a PDBAtom at the last position.

Parameters

atom	the PDBAtom to append

void BALL::Residue::insertAfter	(	PDBAtom &	atom,
		Composite &	after
	)

Insert a PDBAtom after a given Composite object.

Parameters

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

void BALL::Residue::insertBefore	(	PDBAtom &	atom,
		Composite &	before
	)

Insert a PDBAtom before a given Composite object.

Parameters

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

bool BALL::Residue::isAminoAcid ( ) const

Test if this residue is an amino acid. Returns true, if this instance has the property "PROPERTY__AMINO_ACID".

Returns: bool

bool BALL::Residue::isCTerminal ( ) const

Test if this residue is C-terminal. Returns true, if this instance has the property "PROPERTY__AMINO_ACID" and is the last amino acid residue in its parent chain.

Returns: bool

bool BALL::Residue::isNTerminal ( ) const

Test if this residue is N-terminal. Returns true, if this instance has the property "PROPERTY__AMINO_ACID" and is the first amino acid residue in its parent chain.

Returns: bool

virtual bool BALL::Residue::isResidue ( ) const

inlinevirtual

Test if the Composite is a Residue

Reimplemented from BALL::Composite.

Definition at line 376 of file residue.h.

bool BALL::Residue::isTerminal ( ) const

Test if this residue is terminal. Returns true, if this instance has the property "PROPERTY__AMINO_ACID" and is the first or last amino acid residue in its parent chain.

Returns: bool

virtual bool BALL::Residue::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::Residue::operator!= ( const Residue & residue ) const

Inequality operator

See also: operator ==

Residue& BALL::Residue::operator= ( const Residue & residue )

Assignment operator

bool BALL::Residue::operator== ( const Residue & residue ) const

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

See also: Object::operator ==

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

virtual

Reads a Residue object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Fragment.

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

virtual

Writes a Residue object to a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Fragment.

void BALL::Residue::prepend ( PDBAtom & atom )

Prepend a PDBAtom at position 0.

Parameters

atom	the PDBAtom to prepend

bool BALL::Residue::remove ( PDBAtom & atom )

Remove a PDBAtom.

Parameters

atom	the PDBAtom to remove

void BALL::Residue::set	(	const Residue &	residue,
		bool	deep = `true`
	)

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

Parameters

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

void BALL::Residue::setID ( const String & id )

Set the ID.

Parameters

id	the new ID

void BALL::Residue::setInsertionCode ( char insertion_code )

Set the insertion code.

Parameters

insertion_code the new insertion code

void BALL::Residue::splice ( Residue & residue )

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

void BALL::Residue::spliceAfter ( Residue & residue )

Cut all children of residue and append them after the children of this instance.

Parameters

residue the residue to access

void BALL::Residue::spliceBefore ( Residue & residue )

Cut all children of residue and prepend them before the children of this instance.

Parameters

residue the residue to access

void BALL::Residue::swap ( Residue & residue )

Swap the contents of two Residue objects.

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation