package org.biojava.nbio.structure.align.quaternary;

/**
 * The parameter bean for the {@link QsAlign} algorithm.
 * 
 * @author Aleix Lafita
 * @since 5.0.0
 *
 */
public class QsAlignParameters {

	private double dCutoff = 10.0;

	/**
	 * 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;
	}

}

@@ -224,16 +224,112 @@
  = 10.0;
+%0A%09private double maxRmsd = 7.0;%0A%09private double minOrientationMetric = Math.PI / 8; // 45 degree
 %0A%0A%09/**%0A%09
@@ -701,10 +701,338 @@
 ff;%0A%09%7D%0A%0A
+%09%0A%09public double getMaxRmsd() %7B%0A%09%09return maxRmsd;%0A%09%7D%0A%0A%09public void setMaxRmsd(double maxRmsd) %7B%0A%09%09this.maxRmsd = maxRmsd;%0A%09%7D%0A%0A%09public double getMinOrientationMetric() %7B%0A%09%09return minOrientationMetric;%0A%09%7D%0A%0A%09public void setMinOrientationMetric(double minOrientationMetric) %7B%0A%09%09this.minOrientationMetric = minOrientationMetric;%0A%09%7D%0A%0A
 %7D%0A

Add more parameters for QsAlign