org.biojava.nbio.structure.align.quaternary

Class QsAlignParameters

java.lang.Object

org.biojava.nbio.structure.align.quaternary.QsAlignParameters

public class QsAlignParameters
extends Object

The parameter bean for the QsAlign algorithm.

Since:

5.0.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
QsAlignParameters()

Method Summary

Modifier and Type	Method and Description
double	getdCutoff() The maximum allowed distance between the centroids of two equivalent Subunits, in A.
double	getMaxOrientationAngle() The maximum orientation angle between two equivalent Subunits, in radians.
double	getMaxRmsd() The maximum allowed RMSD of the alignment, in A.
void	setdCutoff(double dCutoff) The maximum allowed distance between the centroids of two equivalent Subunits, in A.
void	setMaxOrientationAngle(double maxOrientationAngle) The maximum orientation angle between two equivalent Subunits, in radians.
void	setMaxRmsd(double maxRmsd) The maximum allowed RMSD of the alignment, in A.

Methods inherited from class java.lang.Object

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

Constructor Detail

QsAlignParameters

public QsAlignParameters()

Method Detail

getdCutoff

public double getdCutoff()

The maximum allowed distance between the centroids of two equivalent Subunits, in A.

Returns:

dCutoff

setdCutoff

public void setdCutoff(double dCutoff)

The maximum allowed distance between the centroids of two equivalent Subunits, in A.

Parameters:

dCutoff -

getMaxRmsd

public double getMaxRmsd()

The maximum allowed RMSD of the alignment, in A.

Returns:

maxRmsd

setMaxRmsd

public void setMaxRmsd(double maxRmsd)

The maximum allowed RMSD of the alignment, in A.

Parameters:

maxRmsd -

getMaxOrientationAngle

public double getMaxOrientationAngle()

The maximum orientation angle between two equivalent Subunits, in radians. Range [0, Pi].

Returns:

the maximum orientation angle

setMaxOrientationAngle

public void setMaxOrientationAngle(double maxOrientationAngle)

The maximum orientation angle between two equivalent Subunits, in radians. Range [0, Pi].

Parameters:

maxOrientationAngle - maximum orientation angle