org.wallerlab.yoink.molecular.domain

Class SimpleAtom

java.lang.Object

org.wallerlab.yoink.molecular.domain.SimpleAtom

All Implemented Interfaces:

Atom

public class SimpleAtom
extends java.lang.Object
implements Atom

the domain model of atom

Field Summary

Fields

Modifier and Type	Field and Description
protected Element	elementType
protected int	index

Constructor Summary

Constructors

Constructor and Description
SimpleAtom(int index, Element elementType, Coord coordinate)

Method Summary

Modifier and Type	Method and Description
Coord	getCoordinate() get the coordinate of the atom
Element	getElementType() get the element type of the atom
int	getIndex() get the atomic index in molecular system
RadialGrid	getRadialGrid() set the radial grid
double	getX3() get the x coordinate of the atom
double	getY3() get the y coordinate of the atom
double	getZ3() get the z coordinate of the atom
void	setRadialGrid(RadialGrid radial_grid) get the radial grid

Methods inherited from class java.lang.Object

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

Field Detail

index

protected final int index

elementType

protected final Element elementType

Constructor Detail

SimpleAtom

public SimpleAtom(int index,
                  Element elementType,
                  Coord coordinate)

Method Detail

getElementType

public Element getElementType()

get the element type of the atom

Specified by:

getElementType in interface Atom

Returns:

element of this atom, - Element

getIndex

public int getIndex()

get the atomic index in molecular system

Specified by:

getIndex in interface Atom

Returns:

atomic index in molecular system -Integer

getCoordinate

public Coord getCoordinate()

get the coordinate of the atom

Specified by:

getCoordinate in interface Atom

Returns:

Coord

getX3

public double getX3()

get the x coordinate of the atom

Specified by:

getX3 in interface Atom

Returns:

Double

getY3

public double getY3()

get the y coordinate of the atom

Specified by:

getY3 in interface Atom

Returns:

Double

getZ3

public double getZ3()

get the z coordinate of the atom

Specified by:

getZ3 in interface Atom

Returns:

Double

getRadialGrid

public RadialGrid getRadialGrid()

set the radial grid

Specified by:

getRadialGrid in interface Atom

Returns:

radial grids for density -RadialGrid

setRadialGrid

public void setRadialGrid(RadialGrid radial_grid)

get the radial grid

Specified by:

setRadialGrid in interface Atom

Parameters:

radial_grid - the grid to be used