Atom Class Reference

An atom is defined by this class. More...

#include <Atom.h>

List of all members.

Public Member Functions
	Atom ()
	Constructor.
	Atom (int _atomNumber, string _atomName, char _confID, string _residueName, char _chainID, int _residueNumber, Point3< float > _coord, float _charge, float _radius, string _segName)
	Overloaded constructor.
void	print ()
	Prints out all atom information.
Point3< float >	getCoord ()
	Returns the coordinates of the atom.
float	getRadius ()
	Returns the radius of the atom.
int	getResidueNumber ()
	Returns the residue number the atom is assigned to.
string	getResidueName ()
	Returns the residue name the atom is assigned to.
void	setResidueName (string _residueName)
	Sets the residue name.
char	getChainID ()
	Returns the chain ID the atom is assigned to.
string	getAtomName ()
	Returns the atom name the atom is assigned to.
void	setCharge (float _charge)
	Sets the atom charge.
float	getCharge ()
	Returns the chare of the atom.
int	getAtomNumber ()
	Returns the atom ID.
string	pqrLine ()
	Prints out the atom information as a line in the PQR file.
Private Attributes
int	atomNumber
	ID of current Atom.
string	atomName
	Name of current Atom.
char	confID
	ID of conformation.
string	residueName
	Name of residue where current atom belongs to.
char	chainID
	ID of chain where current atom belongs to.
int	residueNumber
	Number of residue where current atom belongs to.
Point3< float >	coord
	Coordinate of current atom.
float	charge
	Charge of current atom in Coulomb.
float	radius
	Van-der-Waals radius of current atom in Angstroems.
string	segName
	Name of segment where current atom belongs to.

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Detailed Description

An atom is defined by this class.

An atom has an atom number, a name, is assigned to a conformation, a residue with a residue number, it has a charge, a van-der-Waals radius and is assigned to a specific segment. Although not all informations are necessary, they are provided.

Author:

Ilkay Sakalli

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Constructor & Destructor Documentation

Atom::Atom

(

)

[inline]

Constructor.

Atom::Atom	(	int	_atomNumber,
		string	_atomName,
		char	_confID,
		string	_residueName,
		char	_chainID,
		int	_residueNumber,
		Point3< float >	_coord,
		float	_charge,
		float	_radius,
		string	_segName
	)		[inline]

Overloaded constructor.

All information of an atom can be assigned via construction.

Parameters:

int	Atom number
string	Atom name
char	Conformation ID
string	Residue name
char	Chain ID
int	Residue ID
Point3	Coordinates of atom
float	Charge
float	Van-der-Waals (vdW) radius
string	Segment name

---

Member Function Documentation

string Atom::getAtomName

(

)

[inline]

Returns the atom name the atom is assigned to.

Returns:

string Returns the atom name the atom is assigned to.

int Atom::getAtomNumber

(

)

[inline]

Returns the atom ID.

Returns:

int Returns the atom ID.

char Atom::getChainID

(

)

[inline]

Returns the chain ID the atom is assigned to.

Returns:

string Returns the chain ID the atom is assigned to.

float Atom::getCharge

(

)

[inline]

Returns the chare of the atom.

Returns:

float Returns the charge of the atom.

Point3<float> Atom::getCoord

(

)

[inline]

Returns the coordinates of the atom.

Returns:

Point3<float> Returns x-, y-, z-coordinates of the current atom.

float Atom::getRadius

(

)

[inline]

Returns the radius of the atom.

Returns:

float Radius of atom in Angstroems.

string Atom::getResidueName

(

)

[inline]

Returns the residue name the atom is assigned to.

Returns:

string Returns the residue name the atom is assigned to.

int Atom::getResidueNumber

(

)

[inline]

Returns the residue number the atom is assigned to.

Returns:

int Returns the residue number.

string Atom::pqrLine

(

)

[inline]

Prints out the atom information as a line in the PQR file.

Returns:

string Formatted PQR line representation of the current atom.

void Atom::print

(

)

[inline]

Prints out all atom information.

Returns:

Void.

void Atom::setCharge

(

float

_charge

)

[inline]

Sets the atom charge.

Parameters:

string

Charge which should be assigned to the atom.

Returns:

Void.

void Atom::setResidueName

(

string

_residueName

)

[inline]

Sets the residue name.

Parameters:

string

Residue name the atom should be assigned to.

Returns:

Void.

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Member Data Documentation

string Atom::atomName [private]

Name of current Atom.

int Atom::atomNumber [private]

ID of current Atom.

char Atom::chainID [private]

ID of chain where current atom belongs to.

float Atom::charge [private]

Charge of current atom in Coulomb.

char Atom::confID [private]

ID of conformation.

Point3<float> Atom::coord [private]

Coordinate of current atom.

float Atom::radius [private]

Van-der-Waals radius of current atom in Angstroems.

string Atom::residueName [private]

Name of residue where current atom belongs to.

int Atom::residueNumber [private]

Number of residue where current atom belongs to.

string Atom::segName [private]

Name of segment where current atom belongs to.

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The documentation for this class was generated from the following file:

• Atom.h