#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
enum	StampType { MODIFICATION = 1 , SELECTION = 2 , BOTH = 3 }
typedef UnaryPredicate< Composite >	KernelPredicateType
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

Public Member Functions
Constructors and Destructors
	Residue ()
	Default constructor.
	Residue (const Residue &residue, bool deep=true)
	Copy constructor.
	Residue (const String &name, const String &id=BALL_RESIDUE_DEFAULT_ID, char insertion_code=BALL_RESIDUE_DEFAULT_INSERTION_CODE)
	Detailled constructor.
virtual	~Residue ()
	Destructor.
virtual void	clear ()
	Clears the contents of this instance.
virtual void	destroy ()
	Clears the contents of this instance and removes it from all composite structures.
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)
bool	operator== (const Residue &residue) const
bool	operator!= (const Residue &residue) const
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)
void	unsetInsertionCode ()
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
Public Member Functions inherited from BALL::Fragment
	Fragment ()
	Fragment (const Fragment &fragment, bool deep=true)
	Fragment (const String &name)
virtual	~Fragment ()
Fragment &	operator= (const Fragment &fragment)
bool	operator== (const Fragment &fragment) const
bool	operator!= (const Fragment &fragment) const
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.
bool	applyInterBond (UnaryProcessor< Bond > &processor)
	Apply to all bonds connected to atoms outside this AtomContainer.
Public Member Functions inherited from BALL::Composite
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)
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)
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 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.
bool	hasProperty (const std::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.
bool	isValid () const
void	dump (std::ostream &s=std::cout, Size depth=0) const

Debugging and Diagnostics
virtual bool	isValid () const
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const

Additional Inherited Members
static bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)
static Handle	getNextHandle ()
static Handle	getNewHandle ()
static void	clearLastPtr ()
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR
static KernelPredicateType	DEFAULT_UNARY_PREDICATE
	AutoDeletable ()
	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)
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

◆ FullNameType

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.

◆ Property

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

◆ Residue() [1/3]

BALL::Residue::Residue ( )

Default constructor.

◆ Residue() [2/3]

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

Copy constructor.

◆ Residue() [3/3]

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

Detailled constructor.

◆ ~Residue()

virtual BALL::Residue::~Residue ( )

virtual

Destructor.

Member Function Documentation

◆ append()

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

Append a PDBAtom at the last position.

Parameters

atom	the PDBAtom to append

◆ clear()

virtual void BALL::Residue::clear ( )

virtual

Clears the contents of this instance.

Reimplemented from BALL::AtomContainer.

◆ countPDBAtoms()

Size BALL::Residue::countPDBAtoms ( ) const

Count the child PDBAtoms.

Returns: Size the number of PDBAtoms

◆ destroy()

virtual void BALL::Residue::destroy ( )

virtual

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

Reimplemented from BALL::AtomContainer.

◆ dump()

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.

◆ get()

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

Assign a Residue object from another instance.

◆ getChain() [1/2]

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

◆ getChain() [2/2]

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

◆ getFullName()

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

◆ getID()

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

Retrieve the ID.

Returns: String the ID

◆ getInsertionCode()

char BALL::Residue::getInsertionCode ( ) const

Get the insertion code.

Returns: char the insertion code

◆ getPDBAtom() [1/2]

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

◆ getPDBAtom() [2/2]

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

◆ getProtein() [1/2]

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

◆ getProtein() [2/2]

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

◆ getSecondaryStructure() [1/2]

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

◆ getSecondaryStructure() [2/2]

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

◆ getTorsionOmega()

Angle BALL::Residue::getTorsionOmega ( ) const

Calculate the torsion angle psi.

Returns: Angle - the torsion angle phi

◆ getTorsionPhi()

Angle BALL::Residue::getTorsionPhi ( ) const

Calculate the torsion angle phi.

Returns: Angle - the torsion angle phi

◆ getTorsionPsi()

Angle BALL::Residue::getTorsionPsi ( ) const

Calculate the torsion angle psi.

Returns: Angle - the torsion angle phi

◆ hasTorsionOmega()

bool BALL::Residue::hasTorsionOmega ( ) const

Check whether the torsion angle omega is defined.

Returns: bool

◆ hasTorsionPhi()

bool BALL::Residue::hasTorsionPhi ( ) const

Check whether the torsion angle phi is defined.

Returns: bool

◆ hasTorsionPsi()

bool BALL::Residue::hasTorsionPsi ( ) const

Check whether the torsion angle psi is defined.

Returns: bool

◆ insert()

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

Insert a PDBAtom at the last position.

Parameters

atom	the PDBAtom to append

◆ insertAfter()

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

◆ insertBefore()

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

◆ isAminoAcid()

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

◆ isCTerminal()

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

◆ isNTerminal()

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

◆ isResidue()

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

inlinevirtual

Test if the Composite is a Residue

Reimplemented from BALL::Composite.

Definition at line 389 of file residue.h.

◆ isTerminal()

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

◆ isValid()

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.

◆ operator!=()

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

Inequality operator

See also: operator ==

◆ operator=()

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

Assignment operator

◆ 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 ==

◆ persistentRead()

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

virtual

Reads a Residue object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Fragment.

◆ persistentWrite()

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.

◆ prepend()

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

Prepend a PDBAtom at position 0.

Parameters

atom	the PDBAtom to prepend

◆ remove()

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

Remove a PDBAtom.

Parameters

atom	the PDBAtom to remove

◆ set()

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

◆ setID()

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

Set the ID.

Parameters

id	the new ID

◆ setInsertionCode()

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

Set the insertion code.

An insertion code is a visible ASCII character as well as the space character ' '.

Parameters

insertion_code the new insertion code

Exceptions

InvalidArgument if an unsupported insertion code has been specified.

◆ splice()

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

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

◆ spliceAfter()

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

◆ spliceBefore()

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

◆ swap()

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

Swap the contents of two Residue objects.

◆ unsetInsertionCode()

void BALL::Residue::unsetInsertionCode ( )

Unset the current insertion code.

This is equivalent to calling setInsertionCode(' ').

Public Types

Public Member Functions

Debugging and Diagnostics

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ FullNameType

◆ Property

Constructor & Destructor Documentation

◆ Residue() [1/3]

◆ Residue() [2/3]

◆ Residue() [3/3]

◆ ~Residue()

Member Function Documentation

◆ append()

◆ clear()

◆ countPDBAtoms()

◆ destroy()

◆ dump()

◆ get()

◆ getChain() [1/2]

◆ getChain() [2/2]

◆ getFullName()

◆ getID()

◆ getInsertionCode()

◆ getPDBAtom() [1/2]

◆ getPDBAtom() [2/2]

◆ getProtein() [1/2]

◆ getProtein() [2/2]

◆ getSecondaryStructure() [1/2]

◆ getSecondaryStructure() [2/2]

◆ getTorsionOmega()

◆ getTorsionPhi()

◆ getTorsionPsi()

◆ hasTorsionOmega()

◆ hasTorsionPhi()

◆ hasTorsionPsi()

◆ insert()

◆ insertAfter()

◆ insertBefore()

◆ isAminoAcid()

◆ isCTerminal()

◆ isNTerminal()

◆ isResidue()

◆ isTerminal()

◆ isValid()

◆ operator!=()

◆ operator=()

◆ operator==()

◆ persistentRead()

◆ persistentWrite()

◆ prepend()

◆ remove()

◆ set()

◆ setID()

◆ setInsertionCode()

◆ splice()

◆ spliceAfter()

◆ spliceBefore()

◆ swap()

◆ unsetInsertionCode()