BALL::PDBAtom Class Reference
[Molecular Datastructures]

#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 Member Functions
Constructors and Destructors

	PDBAtom ()
	Default constructor.
	PDBAtom (const PDBAtom &pdb_atom, bool deep=true)
	Copy constructor.
	PDBAtom (const String &name)
	Constructor.
	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	~PDBAtom ()
	Destructor.
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
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

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.

Reimplemented from BALL::Atom.

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]

Reimplemented from BALL::Atom.

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

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

Reimplemented from BALL::Atom.

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

Reimplemented from BALL::Atom.

float BALL::PDBAtom::getOccupancy ( ) const

Get the occupancy.

Returns:: float occupancy the occupancy

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

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

char BALL::PDBAtom::getRemotenessIndicator ( ) const

Get the remoteness indicator.

Returns:: char the remoteness indicator

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

Reimplemented from BALL::Atom.

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

Reimplemented from BALL::Atom.

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]

Reimplemented from BALL::Atom.

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.

BALL::PDBAtom Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

BALL::PDBAtom Class Reference
[Molecular Datastructures]