Module pdb

Package de.grogra.ext.pdb.model

Class Atom

java.lang.Object

de.grogra.ext.pdb.model.Atom

public class Atom
extends Object

Author:

fdill, mdube This class models the pdb ATOM entry. atomName corresponds to the Atom name entry in the pdb file element is an identifier to which element the atom belongs to xCoord, yCoord, zCoord corresponds

Field Summary

Fields

Modifier and Type	Field	Description
static int	numberOfAtoms	a counter for statistics.

Constructor Summary

Constructors

Constructor	Description
Atom(String name, float x, float y, float z)	Creates an atom

Method Summary

Modifier and Type	Method	Description
String	getAtomName()
String	getElement()	The first character of the atom name indicates the element this atom belongs to
float	getXCoord()
float	getYCoord()
float	getZCoord()
void	setAtomName(String string)
void	setXCoord(float float1)
void	setYCoord(float float1)
void	setZCoord(float float1)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

numberOfAtoms

public static int numberOfAtoms

a counter for statistics. Is incremented with every creation.

Constructor Details

Atom

public Atom(String name,
 float x,
 float y,
 float z)

Creates an atom

Parameters:

name - - the name of the atom taken from the PDB entry

x - - the x coordinate

y - - the y coordinate

z - - the z coordinate

Method Details

getAtomName

public String getAtomName()

Returns:

the name of the atom

getElement

public String getElement()

The first character of the atom name indicates the element this atom belongs to

Returns:

the basic element

getXCoord

public float getXCoord()

Returns:

- the x coordinate

getYCoord

public float getYCoord()

Returns:

- the y coordinate

getZCoord

public float getZCoord()

Returns:

- the z coordinate

setAtomName

public void setAtomName(String string)

Parameters:

string -

setXCoord

public void setXCoord(float float1)

Parameters:

float1 -

setYCoord

public void setYCoord(float float1)

Parameters:

float1 -

setZCoord

public void setZCoord(float float1)

Parameters:

float1 -

toString

public String toString()

Overrides:

toString in class Object