org.wallerlab.yoink.molecular.domain

Class SimpleMolecule

java.lang.Object

org.wallerlab.yoink.molecular.domain.SimpleMolecule

All Implemented Interfaces:

Molecule

public class SimpleMolecule
extends java.lang.Object
implements Molecule

the domain model for molecule.

Field Summary

Fields

Modifier and Type	Field and Description
protected Region.Name	name

Constructor Summary

Constructors

Constructor and Description
SimpleMolecule(int index, java.util.List<Atom> atoms)

Method Summary

Modifier and Type	Method and Description
java.util.List<Atom>	getAtoms() get atoms in molecule
Coord	getCenterOfMass() get the center of mass of this molecule.
int	getIndex() get molecular index in molecular system
Region.Name	getName() get the molecular name
void	setCenterOfMass(Coord centerOfMass) set the center of mass of this molecule.
void	setName(Region.Name value) set the molecular name

Methods inherited from class java.lang.Object

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

Field Detail

name

protected Region.Name name

Constructor Detail

SimpleMolecule

public SimpleMolecule(int index,
                      java.util.List<Atom> atoms)

Method Detail

getName

public Region.Name getName()

get the molecular name

Specified by:

getName in interface Molecule

Returns:

name, - Region.Name

setName

public void setName(Region.Name value)

set the molecular name

Specified by:

setName in interface Molecule

Parameters:

value - -indicates which the molecule is in, Region.Name

getAtoms

public java.util.List<Atom> getAtoms()

get atoms in molecule

Specified by:

getAtoms in interface Molecule

Returns:

a List of atoms, Atom

getIndex

public int getIndex()

get molecular index in molecular system

Specified by:

getIndex in interface Molecule

Returns:

molecular index, Integer

getCenterOfMass

public Coord getCenterOfMass()

Description copied from interface: Molecule

get the center of mass of this molecule.

Specified by:

getCenterOfMass in interface Molecule

Returns:

center of mass, - Coord

setCenterOfMass

public void setCenterOfMass(Coord centerOfMass)

Description copied from interface: Molecule

set the center of mass of this molecule.

Specified by:

setCenterOfMass in interface Molecule

Parameters:

centerOfMass - - Coord