BALL::PDBAtom Class Reference
[Molecular Datastructures]

Atom class with additional attributes. More...

#include <PDBAtom.h>

Inheritance diagram for BALL::PDBAtom:

[legend]


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 }
	Possible values for the PDB remoteness indicator.
enum	Property { NUMBER_OF_PROPERTIES = Atom::NUMBER_OF_PROPERTIES }
	Properties of the PDBAtom.
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 ()
	Clears the contents of the atom and removes it from all composite structures.
Predicates
bool	operator== (const PDBAtom &pdb_atom) const
	Equality operator.
bool	operator!= (const PDBAtom &pdb_atom) const
	Inequality operator.
Persistence
void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Writes a PDBAtom object to a persistent stream.
void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Reads a PDBAtom object from a persistent stream.
Assignment
void	set (const PDBAtom &pdb_atom, bool deep=true)
	Assignment with cloning facility.
void	get (PDBAtom &pdb_atom, bool deep=true) const
	Copy this instance to {pdb_atom}.
PDBAtom &	operator= (const PDBAtom &pdb_atom)
	Assignment operator.
void	swap (PDBAtom &pdb_atom)
	Swapping of PDBAtoms.
virtual void	clear ()
	Clear the contents of the atom.
Accessors
Protein *	getProtein ()
	Get a pointer to the parent protein.
const Protein *	getProtein () const
	Get a pointer to the parent protein.
Chain *	getChain ()
	Get a pointer to the parent chain.
const Chain *	getChain () const
	Get a pointer to the parent chain.
Residue *	getResidue ()
	Get a pointer to the parent residue.
const Residue *	getResidue () const
	Get a pointer to the parent residue.
void	setBranchDesignator (char branch_designator)
	Set the branch designator.
char	getBranchDesignator () const
	Get the branch designator.
void	setRemotenessIndicator (char remoteness_indicator)
	Set the remoteness indicator.
char	getRemotenessIndicator () const
	Get the remoteness indicator.
void	setAlternateLocationIndicator (char alternate_location_indicator)
	Set the alternate location indicator.
char	getAlternateLocationIndicator () const
	Get the alternate location indicator.
void	setOccupancy (float occupancy)
	Set the occupancy.
float	getOccupancy () const
	Get the occupancy.
void	setTemperatureFactor (float temperature_factor)
	Set the temperature factor.
float	getTemperatureFactor () const
	Get the temperature factor.
Debugging and Diagnostics
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
	Internal state dump.
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

Member Function Documentation

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 ) throw (Exception::GeneralException) [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 throw (Exception::GeneralException) `[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

BALL::PDBAtom Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Friends

Detailed Description

Member Function Documentation

BALL::PDBAtom Class Reference
[Molecular Datastructures]