de.bioforscher.singa.structure.algorithms.gyration

Class Gyration

java.lang.Object

de.bioforscher.singa.structure.algorithms.gyration.Gyration

public class Gyration
extends Object

An implementation of the gyration radius measurement for the compactness of molecules. The gyration uses atoms and can be applied on any AtomContainer. Calculation is performed according to:

     Stockwell, GR, Thornton, JM (2006). Conformational diversity of ligands bound to proteins.
     J. Mol. Biol., 356, 4:928-44.
 

Author:

fk

Method Summary

Modifier and Type	Method and Description
List<Atom>	getAtoms() Returns the atoms the gyration has been calculated from.
Vector3D	getCentroid() Returns the centroid of this gyration.
double	getRadius() Returns the radius of this gyration.
static Gyration	of(AtomContainer atomContainer) Calculates the gyration for the atoms in the container.

Methods inherited from class java.lang.Object

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

Method Detail

of

public static Gyration of(AtomContainer atomContainer)

Calculates the gyration for the atoms in the container.

Parameters:

atomContainer - The atom container.

Returns:

The Gyration.

getAtoms

public List<Atom> getAtoms()

Returns the atoms the gyration has been calculated from.

Returns:

The atoms the gyration has been calculated from.

getCentroid

public Vector3D getCentroid()

Returns the centroid of this gyration.

Returns:

The centroid of this gyration.

getRadius

public double getRadius()

Returns the radius of this gyration.

Returns:

The radius of this gyration.