de.bioforscher.singa.structure.model.oak

Class OakAtom

java.lang.Object

de.bioforscher.singa.structure.model.oak.OakAtom

All Implemented Interfaces:

Atom

public class OakAtom
extends Object
implements Atom

Author:

cl

Constructor Summary

Constructors

Constructor and Description
OakAtom(int identifier, Element element, String atomName, Vector3D position) Creates a new atom with the given pdbIdentifier, element, name and position.
OakAtom(OakAtom atom) This is a copy constructor.

Method Summary

Modifier and Type	Method and Description
void	addNeighbour(OakAtom node)
boolean	equals(Object o)
Integer	getAtomIdentifier() Returns the atom identifier, an integer greater or equal to 1.
String	getAtomName() Returns a short atom name.
OakAtom	getCopy()
Element	getElement() Returns the Element.
Set<OakAtom>	getNeighbours()
Vector3D	getPosition() Returns the position in three dimensional space.
int	hashCode()
void	setPosition(Vector3D position) Sets the position in three dimensional space.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface de.bioforscher.singa.structure.model.interfaces.Atom

flatToString

Constructor Detail

OakAtom

public OakAtom(int identifier,
               Element element,
               String atomName,
               Vector3D position)

Creates a new atom with the given pdbIdentifier, element, name and position.

Parameters:

identifier - The pdbIdentifier.

element - The element.

atomName - The name (pdb).

position - The position.

OakAtom

public OakAtom(OakAtom atom)

This is a copy constructor. Creates a new atom with the same attributes as the given atom. The neighbours of this atom are NOT copied. Due to the nature of this operation it would be bad to keep a part of the relations to the lifecycle of the atom to copy. If you want to keep the neighbouring atoms, copy the superordinate substructure that contains this atom and it will also traverse and copy the neighbouring atoms.

Parameters:

atom - The atom to copy.

Method Detail

getAtomIdentifier

public Integer getAtomIdentifier()

Description copied from interface: Atom

Returns the atom identifier, an integer greater or equal to 1. The identifier of the atom is not unique. Depending on the structure format you are reading there might be different atom identifiers for the same pdb structure. This means, if you have parse the pdb file of a pdb structure or the mmtf file of the same structure, you cannot rely on the identity of atoms in both structures.

Specified by:

getAtomIdentifier in interface Atom

Returns:

The atom identifier.

getPosition

public Vector3D getPosition()

Description copied from interface: Atom

Returns the position in three dimensional space.

Specified by:

getPosition in interface Atom

Returns:

The position.

setPosition

public void setPosition(Vector3D position)

Description copied from interface: Atom

Sets the position in three dimensional space.

Specified by:

setPosition in interface Atom

Parameters:

position - The position.

getElement

public Element getElement()

Description copied from interface: Atom

Returns the Element.

Specified by:

getElement in interface Atom

Returns:

The Element.

getAtomName

public String getAtomName()

Description copied from interface: Atom

Returns a short atom name. For example "CA" for C-alpha atoms in amino acids. The atom names might not be universally the same. Atoms with the name "OP2" might be called "O2P" in other structures.

Specified by:

getAtomName in interface Atom

Returns:

A short atom name.

addNeighbour

public void addNeighbour(OakAtom node)

getNeighbours

public Set<OakAtom> getNeighbours()

getCopy

public OakAtom getCopy()

Specified by:

getCopy in interface Atom

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object