PDBAtom Class Reference
[Molecular Datastructures]

Atom class with additional attributes. More...

#include <PDBAtom.h>

Inheritance diagram for 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 }
	Possible values for the PDB remoteness indicator.
enum	Property { NUMBER_OF_PROPERTIES = Atom::NUMBER_OF_PROPERTIES }
	Properties of the PDBAtom. More...
Public Member Functions
Constructors and Destructors
	PDBAtom () throw ()
	Default constructor.
	PDBAtom (const PDBAtom &pdb_atom, bool deep=true) throw ()
	Copy constructor.
	PDBAtom (const String &name) throw ()
	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) throw ()
	Detailed constructor.
virtual	~PDBAtom () throw ()
	Destructor.
virtual void	destroy () throw ()
	Clears the contents of the atom and removes it from all composite structures.
Predicates
bool	operator== (const PDBAtom &pdb_atom) const throw ()
	Equality operator.
bool	operator!= (const PDBAtom &pdb_atom) const throw ()
	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) throw ()
	Assignment with cloning facility.
void	get (PDBAtom &pdb_atom, bool deep=true) const throw ()
	Copy this instance to {pdb_atom}.
PDBAtom &	operator= (const PDBAtom &pdb_atom) throw ()
	Assignment operator.
void	swap (PDBAtom &pdb_atom) throw ()
	Swapping of PDBAtoms.
virtual void	clear () throw ()
	Clear the contents of the atom.
Accessors
Protein *	getProtein () throw ()
	Get a pointer to the parent protein.
const Protein *	getProtein () const throw ()
	Get a pointer to the parent protein.
Chain *	getChain () throw ()
	Get a pointer to the parent chain.
const Chain *	getChain () const throw ()
	Get a pointer to the parent chain.
Residue *	getResidue () throw ()
	Get a pointer to the parent residue.
const Residue *	getResidue () const throw ()
	Get a pointer to the parent residue.
void	setBranchDesignator (char branch_designator) throw ()
	Set the branch designator.
char	getBranchDesignator () const throw ()
	Get the branch designator.
void	setRemotenessIndicator (char remoteness_indicator) throw ()
	Set the remoteness indicator.
char	getRemotenessIndicator () const throw ()
	Get the remoteness indicator.
void	setAlternateLocationIndicator (char alternate_location_indicator) throw ()
	Set the alternate location indicator.
char	getAlternateLocationIndicator () const throw ()
	Get the alternate location indicator.
void	setOccupancy (float occupancy) throw ()
	Set the occupancy.
float	getOccupancy () const throw ()
	Get the occupancy.
void	setTemperatureFactor (float temperature_factor) throw ()
	Set the temperature factor.
float	getTemperatureFactor () const throw ()
	Get the temperature factor.
Debugging and Diagnostics
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const throw ()
	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 Enumeration Documentation

enum PDBAtom::Property

Properties of the PDBAtom.

Reimplemented from Atom.

Member Function Documentation

virtual void PDBAtom::clear ( ) throw () [virtual]

Clear the contents of the atom.

Reimplemented from Atom.

virtual void PDBAtom::dump ( std::ostream & s = std::cout,

Size depth = 0

) const throw () [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 Atom.

void PDBAtom::get ( PDBAtom & pdb_atom,

bool deep = true

) const throw ()

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

pdb_atom the PDBAtom to be assigned to

char PDBAtom::getAlternateLocationIndicator ( ) const throw ()

Get the alternate location indicator.

Returns:
char the alternate location indicator

char PDBAtom::getBranchDesignator ( ) const throw ()

Get the branch designator.

Returns:
char the branch designator

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

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 Atom.

Chain* PDBAtom::getChain ( ) throw ()

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 Atom.

float PDBAtom::getOccupancy ( ) const throw ()

Get the occupancy.

Returns:
float occupancy the occupancy

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

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* PDBAtom::getProtein ( ) throw ()

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 PDBAtom::getRemotenessIndicator ( ) const throw ()

Get the remoteness indicator.

Returns:
char the remoteness indicator

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

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 Atom.

Residue* PDBAtom::getResidue ( ) throw ()

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 Atom.

float PDBAtom::getTemperatureFactor ( ) const throw ()

Get the temperature factor.

Returns:
float the temperature factor

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

Inequality operator.

See also:
operator ==

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

Assignment operator.
The assignment is deep.
Parameters:

pdb_atom the PDBAtom to be copied (cloned)

Returns:
pdb_atom& - the instance

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

Equality operator.

See also:
Object::operator ==

void PDBAtom::persistentRead ( PersistenceManager & pm ) throw (Exception::GeneralException) [virtual]

Reads a PDBAtom object from a persistent stream.

Parameters:

pm the persistence manager

Reimplemented from Atom.

void 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 Atom.

void PDBAtom::set ( const PDBAtom & pdb_atom,

bool deep = true

) throw ()

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 PDBAtom::setAlternateLocationIndicator ( char alternate_location_indicator ) throw ()

Set the alternate location indicator.

Parameters:

alternate_location_indicator the alternate location indicator

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

Set the branch designator.

Parameters:

branch_designator the branch designator

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

Set the occupancy.

Parameters:

occupancy the occupancy

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

Set the remoteness indicator.

Parameters:

remoteness_indicator the remoteness indicator

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

Set the temperature factor.

Parameters:

temperature_factor the temperature factor

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

Swapping of PDBAtoms.

Parameters:

pdb_atom the PDBAtom {*this} is being swapped with

PDBAtom Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Friends

Detailed Description

Member Enumeration Documentation

Member Function Documentation

PDBAtom Class Reference
[Molecular Datastructures]