package org.biojava.nbio.structure.align.quaternary;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.ce.CeMain;
/**
* The parameter bean for the {@link QsAlign} algorithm.
*
* @author Aleix Lafita
* @since 5.0.0
*
*/
public class QsAlignParameters {
private double dCutoff = 10.0;
private double maxRmsd = 10.0;
private double maxOrientationAngle = Math.PI / 6; // 30 degree
private StructureAlignment aligner = new CeMain();
/**
* The maximum allowed distance between the centroids of two equivalent
* Subunits, in A.
*
* @return dCutoff
*/
public double getdCutoff() {
return dCutoff;
}
/**
* The maximum allowed distance between the centroids of two equivalent
* Subunits, in A.
*
* @param dCutoff
*/
public void setdCutoff(double dCutoff) {
this.dCutoff = dCutoff;
}
/**
* The maximum allowed RMSD of the alignment, in A.
*
* @return maxRmsd
*/
public double getMaxRmsd() {
return maxRmsd;
}
/**
* The maximum allowed RMSD of the alignment, in A.
*
* @param maxRmsd
*/
public void setMaxRmsd(double maxRmsd) {
this.maxRmsd = maxRmsd;
}
/**
* The maximum orientation angle between two equivalent Subunits, in
* radians. Range [0, Pi].
*
* @return the maximum orientation angle
*/
public double getMaxOrientationAngle() {
return maxOrientationAngle;
}
/**
* The maximum orientation angle between two equivalent Subunits, in
* radians. Range [0, Pi].
*
* @param maxOrientationAngle
* maximum orientation angle
*/
public void setMaxOrientationAngle(double maxOrientationAngle) {
this.maxOrientationAngle = maxOrientationAngle;
}
/**
* The structural alignment algorithm used to compare the clusters of
* Subunits.
*
* @return aligner
*/
public StructureAlignment getAligner() {
return aligner;
}
/**
* The structural alignment algorithm used to compare the clusters of
* Subunits.
*
* @param aligner
*/
public void setAligner(StructureAlignment aligner) {
this.aligner = aligner;
}
}