de.bioforscher.singa.structure.model.interfaces

Interface Atom

All Known Implementing Classes:

MmtfAtom, OakAtom

public interface Atom

An Atom is the physical instance of an atom in three dimensional space.

Author:

cl

Method Summary

Modifier and Type	Method and Description
default String	flatToString() Returns the flat String representation of this atom in the form:
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.

Method Detail

getAtomIdentifier

Integer getAtomIdentifier()

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.

Returns:

The atom identifier.

getPosition

Vector3D getPosition()

Returns the position in three dimensional space.

Returns:

The position.

setPosition

void setPosition(Vector3D position)

Sets the position in three dimensional space.

Parameters:

position - The position.

getElement

Element getElement()

Returns the Element.

Returns:

The Element.

getAtomName

String getAtomName()

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.

Returns:

A short atom name.

getCopy

Atom getCopy()

flatToString

default String flatToString()

Returns the flat String representation of this atom in the form:

     [AtomIdentifier]: [AtomName] ([xCoordinate], [yCoordinate], [zCoordinate])
 

For example:

     5444: CA (70.31099700927734, 35.60300064086914, -10.967000007629395)
     412: N2 (62.20399856567383, -8.505999565124512, 22.573999404907227)
 

Returns:

The flat String representation of this atom.