#include <BALL/KERNEL/PDBAtom.h>

Inheritance diagram for BALL::PDBAtom:

Public Types
Enums
enum	RemotenessIndicator { REMOTENESS_INDICATOR__UNKNOWN = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, REMOTENESS_INDICATOR__ALPHA = 'A', REMOTENESS_INDICATOR__alpha = 'a', REMOTENESS_INDICATOR__BETA = 'B', REMOTENESS_INDICATOR__beta = 'b', REMOTENESS_INDICATOR__GAMMA = 'G', REMOTENESS_INDICATOR__gamma = 'g', REMOTENESS_INDICATOR__DELTA = 'D', REMOTENESS_INDICATOR__delta = 'd', REMOTENESS_INDICATOR__EPSILON = 'E', REMOTENESS_INDICATOR__epsilon = 'e', REMOTENESS_INDICATOR__ZETA = 'Z', REMOTENESS_INDICATOR__zeta = 'z', REMOTENESS_INDICATOR__ETA = 'H', REMOTENESS_INDICATOR__eta = 'h', NUMBER_OF_REMOTENESS_INDICATORS }

enum	Property { PROPERTY__HETATM = Atom::NUMBER_OF_PROPERTIES + 1, NUMBER_OF_PROPERTIES }

Public Types inherited from BALL::Atom
enum	{ UNKNOWN_TYPE = -1, ANY_TYPE = 0, MAX_NUMBER_OF_BONDS = 12 }

enum	Property { NUMBER_OF_PROPERTIES = 0 }

enum	FullNameType { NO_VARIANT_EXTENSIONS, ADD_VARIANT_EXTENSIONS, ADD_RESIDUE_ID, ADD_VARIANT_EXTENSIONS_AND_ID, ADD_CHAIN_RESIDUE_ID, ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID }

typedef std::list< Atom * >	AtomPtrList

typedef std::list< Position >	AtomIndexList

typedef short	Type

typedef Index	BondIteratorPosition

typedef RandomAccessIterator < Atom, Bond, BondIteratorPosition, BondIteratorTraits >	BondIterator

typedef ConstRandomAccessIterator < Atom, Bond, BondIteratorPosition, BondIteratorTraits >	BondConstIterator
	Constant random access iterator for bonds. More...

typedef std::reverse_iterator < BondIterator >	BondReverseIterator
	Reverse random access iterator for bonds. More...

typedef std::reverse_iterator < BondConstIterator >	BondConstReverseIterator
	Constant reverse random access iterator for bonds. 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
	PDBAtom ()
	Default constructor. More...

	PDBAtom (const PDBAtom &pdb_atom, bool deep=true)
	Copy constructor. More...

	PDBAtom (const String &name)
	Constructor. More...

	PDBAtom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Atom::Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, char branch_designator=BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR, char remoteness_indicator=BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, char alternate_location_indicator=BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR, float occupancy=BALL_PDBATOM_DEFAULT_OCCUPANCY, float temperature_factor=BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR)
	Detailed constructor. More...

virtual	~PDBAtom ()
	Destructor. More...

virtual void	destroy ()

Predicates
bool	operator== (const PDBAtom &pdb_atom) const

bool	operator!= (const PDBAtom &pdb_atom) const

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

void	persistentRead (PersistenceManager &pm)

Assignment
void	set (const PDBAtom &pdb_atom, bool deep=true)

void	get (PDBAtom &pdb_atom, bool deep=true) const

PDBAtom &	operator= (const PDBAtom &pdb_atom)

void	swap (PDBAtom &pdb_atom)

virtual void	clear ()

Accessors
Protein *	getProtein ()

const Protein *	getProtein () const

Chain *	getChain ()

const Chain *	getChain () const

Residue *	getResidue ()

const Residue *	getResidue () const

void	setBranchDesignator (char branch_designator)

char	getBranchDesignator () const

void	setRemotenessIndicator (char remoteness_indicator)

char	getRemotenessIndicator () const

void	setAlternateLocationIndicator (char alternate_location_indicator)

char	getAlternateLocationIndicator () const

void	setOccupancy (float occupancy)

float	getOccupancy () const

void	setTemperatureFactor (float temperature_factor)

float	getTemperatureFactor () const

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

Public Member Functions inherited from BALL::Atom
	Atom ()

	Atom (const Atom &atom, bool deep=true)

	Atom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, Index formal_charge=BALL_ATOM_DEFAULT_FORMAL_CHARGE)

virtual	~Atom ()

void	set (const Atom &atom, bool deep=true)

void	get (Atom &atom, bool deep=true) const

Atom &	operator= (const Atom &atom)

void	swap (Atom &atom)

bool	operator== (const Atom &atom) const

bool	operator!= (const Atom &atom) const

void	setElement (const Element &element)
	Assign the atom's element. More...

const Element &	getElement () const
	Return the atom's element. More...

void	setCharge (float charge)

float	getCharge () const

void	setFormalCharge (Index formal_charge)
	Set the atom's formal charge. More...

Index	getFormalCharge () const
	Return the atom's formal charge. More...

const Molecule *	getMolecule () const

Molecule *	getMolecule ()
	Return the molecule the atom is contained in (mutable) More...

const Fragment *	getFragment () const

Fragment *	getFragment ()
	Return the fragment the atom is contained in (mutable) More...

const Residue *	getResidue () const

Residue *	getResidue ()
	Return the residue the atom is contained in (mutable) More...

const SecondaryStructure *	getSecondaryStructure () const

SecondaryStructure *	getSecondaryStructure ()
	Return the secondary structure the atom is contained in (mutable) More...

const Chain *	getChain () const

Chain *	getChain ()
	Return the chain the atom is contained in (mutable) More...

void	setName (const String &name)
	Set the atom name. More...

const String &	getName () const
	Return the atom name. More...

String	getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const

void	setPosition (const Vector3 &position)

Vector3 &	getPosition ()
	Return the atom coordinates (mutable) More...

const Vector3 &	getPosition () const
	Return the atom coordinates (const) More...

void	setRadius (float radius)

float	getRadius () const
	Return the atom radius. More...

void	setType (Type atom_type)
	Assign the numerical atom type. More...

Type	getType () const
	Return the (numerical) atom type. More...

String	getTypeName () const
	Return the atom type name. More...

void	setTypeName (const String &name)
	Assign the atom type name. More...

void	setVelocity (const Vector3 &velocity)

Vector3 &	getVelocity ()

const Vector3 &	getVelocity () const

void	setForce (const Vector3 &force)

const Vector3 &	getForce () const
	Return the atom's force vector (const) More...

Vector3 &	getForce ()
	Return the atom's force vector (mutable) More...

Size	countBonds () const
	Return the number of bonds. More...

Bond *	getBond (Position index)

const Bond *	getBond (Position index) const

Bond *	getBond (const Atom &atom)

const Bond *	getBond (const Atom &atom) const

Bond *	createBond (Atom &atom)

Bond *	createBond (Bond &bond, Atom &atom)

Bond *	cloneBond (Bond &bond, Atom &atom)

bool	destroyBond (const Atom &atom)

void	destroyBonds ()

Atom *	getPartnerAtom (Position i)

const Atom *	getPartnerAtom (Position i) const

float	getDistance (const Atom &a) const

bool	hasBond (const Bond &bond) const

bool	isBoundTo (const Atom &atom) const

bool	isBound () const

bool	isGeminal (const Atom &atom) const

bool	isVicinal (const Atom &atom) const

virtual bool	isValid () const

bool	applyBonds (UnaryProcessor< Bond > &processor)

BondIterator	beginBond ()
	Return a bond iterator pointing to the first bond of the atom. More...

BondIterator	endBond ()
	Return a past-the-end bond iterator. More...

BondConstIterator	beginBond () const
	Return a constant bond iterator pointing to the first bond. More...

BondConstIterator	endBond () const
	Return a constant past-the-end bond iterator. More...

BondReverseIterator	rbeginBond ()
	Return a reverse bond iterator pointing to the last bond. More...

BondReverseIterator	rendBond ()
	Return a past-the-end bond iterator for reverse traversal. More...

BondConstReverseIterator	rbeginBond () const
	Return a constant reverse bond iterator pointing to the first atom. More...

BondConstReverseIterator	rendBond () const
	Return a constant past-the-end bond iterator for reverse traversal. 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

Private Member Functions
void	clear_ ()

Private Attributes
char	branch_designator_

char	remoteness_indicator_

char	alternate_location_indicator_

float	occupancy_

float	temperature_factor_

Friends
class	Bond

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::Atom
String	name_

String	type_name_

const Element *	element_

float	radius_

Type	type_

unsigned char	number_of_bonds_

Bond *	bond_ [MAX_NUMBER_OF_BONDS]

Index	formal_charge_

Vector3	position_

float	charge_

Vector3	velocity_

Vector3	force_

Protected Attributes inherited from BALL::Selectable
bool	selected_

Static Protected Attributes inherited from BALL::Atom
static AtomIndexList	free_list_

Detailed Description

Atom class with additional attributes. This class represents atoms read from PDB files. It contains additional attributes to hold the crystallographic properties of atoms from a PDB file (e.g., temperature factor, occupancy). For details on the PDB format and the detailed meaning of those fields, please refer to the PDB documentation at http://www.rcsb.org

See Also: PDBFile

Definition at line 38 of file PDBAtom.h.

Member Enumeration Documentation

enum BALL::PDBAtom::Property

Properties of the PDBAtom.

Enumerator
PROPERTY__HETATM	Property which indicates whether the current atom is a HETATM.
NUMBER_OF_PROPERTIES	The number of properties in PDBAtom.

Definition at line 76 of file PDBAtom.h.

enum BALL::PDBAtom::RemotenessIndicator

Possible values for the PDB remoteness indicator

Enumerator
REMOTENESS_INDICATOR__UNKNOWN
REMOTENESS_INDICATOR__ALPHA
REMOTENESS_INDICATOR__alpha
REMOTENESS_INDICATOR__BETA
REMOTENESS_INDICATOR__beta
REMOTENESS_INDICATOR__GAMMA
REMOTENESS_INDICATOR__gamma
REMOTENESS_INDICATOR__DELTA
REMOTENESS_INDICATOR__delta
REMOTENESS_INDICATOR__EPSILON
REMOTENESS_INDICATOR__epsilon
REMOTENESS_INDICATOR__ZETA
REMOTENESS_INDICATOR__zeta
REMOTENESS_INDICATOR__ETA
REMOTENESS_INDICATOR__eta
NUMBER_OF_REMOTENESS_INDICATORS

Definition at line 53 of file PDBAtom.h.

Constructor & Destructor Documentation

BALL::PDBAtom::PDBAtom ( )

Default constructor.

BALL::PDBAtom::PDBAtom	(	const PDBAtom &	pdb_atom,
		bool	deep = `true`
	)

Copy constructor.

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

Constructor.

BALL::PDBAtom::PDBAtom	(	Element &	element,
		const String &	name,
		const String &	type_name = `BALL_ATOM_DEFAULT_TYPE_NAME`,
		Atom::Type	atom_type = `BALL_ATOM_DEFAULT_TYPE`,
		const Vector3 &	position = `Vector3(BALL_ATOM_DEFAULT_POSITION)`,
		const Vector3 &	velocity = `Vector3(BALL_ATOM_DEFAULT_VELOCITY)`,
		const Vector3 &	force = `Vector3(BALL_ATOM_DEFAULT_FORCE)`,
		float	charge = `BALL_ATOM_DEFAULT_CHARGE`,
		float	radius = `BALL_ATOM_DEFAULT_RADIUS`,
		char	branch_designator = `BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR`,
		char	remoteness_indicator = `BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR`,
		char	alternate_location_indicator = `BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR`,
		float	occupancy = `BALL_PDBATOM_DEFAULT_OCCUPANCY`,
		float	temperature_factor = `BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR`
	)

Detailed constructor.

virtual BALL::PDBAtom::~PDBAtom ( )

virtual

Destructor.

Member Function Documentation

virtual void BALL::PDBAtom::clear ( )

virtual

Clear the contents of the atom.

Reimplemented from BALL::Atom.

void BALL::PDBAtom::clear_ ( )

private

virtual void BALL::PDBAtom::destroy ( )

virtual

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

Reimplemented from BALL::Atom.

virtual void BALL::PDBAtom::dump	(	std::ostream &	s = `std::cout`,
		Size	depth = `0`
	)		const

virtual

Internal state dump. Dump the current internal state of {*this} to the output ostream s with dumping depth depth .

Parameters

s	output stream where to output the internal state of the instance
depth	the dumping depth

Reimplemented from BALL::Atom.

void BALL::PDBAtom::get	(	PDBAtom &	pdb_atom,
		bool	deep = `true`
	)		const

Copy this instance to {pdb_atom}. The assignment is either deep or shallow (default).

Parameters

pdb_atom the PDBAtom to be assigned to

char BALL::PDBAtom::getAlternateLocationIndicator ( ) const

Get the alternate location indicator.

Returns: char the alternate location indicator

char BALL::PDBAtom::getBranchDesignator ( ) const

Get the branch designator.

Returns: char the branch designator

Chain* BALL::PDBAtom::getChain ( )

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

Returns: Chain* - mutable pointer to the parent chain

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

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

Returns: Chain* - constant pointer to the parent chain

float BALL::PDBAtom::getOccupancy ( ) const

Get the occupancy.

Returns: float occupancy the occupancy

Protein* BALL::PDBAtom::getProtein ( )

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

Returns: Protein* - mutable pointer to the parent protein

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

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

Returns: Protein* - constant pointer to the parent protein

char BALL::PDBAtom::getRemotenessIndicator ( ) const

Get the remoteness indicator.

Returns: char the remoteness indicator

Residue* BALL::PDBAtom::getResidue ( )

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

Returns: Residue* - mutable pointer to the parent residue

const Residue* BALL::PDBAtom::getResidue ( ) const

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

Returns: Residue* - constant pointer to the parent residue

float BALL::PDBAtom::getTemperatureFactor ( ) const

Get the temperature factor.

Returns: float the temperature factor

bool BALL::PDBAtom::operator!= ( const PDBAtom & pdb_atom ) const

Inequality operator

See Also: operator ==

PDBAtom& BALL::PDBAtom::operator= ( const PDBAtom & pdb_atom )

Assignment operator. The assignment is deep.

Parameters

pdb_atom the PDBAtom to be copied (cloned)

Returns: pdb_atom& - the instance

bool BALL::PDBAtom::operator== ( const PDBAtom & pdb_atom ) const

Equality operator.

See Also: Object::operator ==

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

virtual

Reads a PDBAtom object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Atom.

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

virtual

Writes a PDBAtom object to a persistent stream.

Parameters

pm	the persistence manager
name	the instance name

Reimplemented from BALL::Atom.

void BALL::PDBAtom::set	(	const PDBAtom &	pdb_atom,
		bool	deep = `true`
	)

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

Parameters

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

void BALL::PDBAtom::setAlternateLocationIndicator ( char alternate_location_indicator )

Set the alternate location indicator.

Parameters

alternate_location_indicator the alternate location indicator

void BALL::PDBAtom::setBranchDesignator ( char branch_designator )

Set the branch designator.

Parameters

branch_designator the branch designator

void BALL::PDBAtom::setOccupancy ( float occupancy )

Set the occupancy.

Parameters

occupancy the occupancy

void BALL::PDBAtom::setRemotenessIndicator ( char remoteness_indicator )

Set the remoteness indicator.

Parameters

remoteness_indicator the remoteness indicator

void BALL::PDBAtom::setTemperatureFactor ( float temperature_factor )

Set the temperature factor.

Parameters

temperature_factor the temperature factor

void BALL::PDBAtom::swap ( PDBAtom & pdb_atom )

Swapping of PDBAtoms.

Parameters

pdb_atom the PDBAtom {*this} is being swapped with

Friends And Related Function Documentation

friend class Bond

friend

Definition at line 43 of file PDBAtom.h.

Member Data Documentation

char BALL::PDBAtom::alternate_location_indicator_

private

Definition at line 308 of file PDBAtom.h.

char BALL::PDBAtom::branch_designator_

private

Definition at line 300 of file PDBAtom.h.

float BALL::PDBAtom::occupancy_

private

Definition at line 312 of file PDBAtom.h.

char BALL::PDBAtom::remoteness_indicator_

private

Definition at line 304 of file PDBAtom.h.

float BALL::PDBAtom::temperature_factor_

private

Definition at line 316 of file PDBAtom.h.

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation