de.bioforscher.singa.structure.model.mmtf

Class MmtfAtom

java.lang.Object

de.bioforscher.singa.structure.model.mmtf.MmtfAtom

All Implemented Interfaces:

Atom

public class MmtfAtom
extends Object
implements Atom

The implementation of Atom for mmtf structures. Remembers the internal group index (parent reference), the group position index and the index for the atom data array.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
MmtfAtom(MmtfAtom mmtfAtom)

Method Summary

Modifier and Type	Method and Description
Integer	getAtomIdentifier() Returns the atom identifier, an integer greater or equal to 1.
String	getAtomName() Returns a short atom name.
Atom	getCopy()
Element	getElement() Returns the Element.
Vector3D	getPosition() Returns the position in three dimensional space.
void	setPosition(Vector3D position) Sets the position in three dimensional space.
String	toString()

Methods inherited from class java.lang.Object

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

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

flatToString

Constructor Detail

MmtfAtom

public MmtfAtom(MmtfAtom mmtfAtom)

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.

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.

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.

getCopy

public Atom getCopy()

Specified by:

getCopy in interface Atom

toString

public String toString()

Overrides:

toString in class Object