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The protein structure modules of BioJava.

There is a newer version: 7.1.3

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.structure.symmetry.axis;

import javax.vecmath.Matrix3d;
import javax.vecmath.Matrix4d;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;

import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
import org.biojava.nbio.structure.symmetry.core.QuatSymmetrySubunits;

import java.util.List;

public abstract class AxisAligner {

	/**
	 * Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method)
	 * @param results symmetry results
	 * @return instance of AxisAligner
	 */
	public static AxisAligner getInstance(QuatSymmetryResults results) {
		String symmetry = results.getSymmetry();

		if ("H".equals(symmetry)) {
			return new HelixAxisAligner(results);
		} else {
			return new RotationAxisAligner(results);
		}
	}

	public abstract String getSymmetry();

	public abstract Matrix4d getTransformation();

	public abstract Matrix3d getRotationMatrix();

	public abstract Matrix4d getReverseTransformation();

	public abstract Vector3d getPrincipalRotationAxis();

	public abstract Vector3d getRotationReferenceAxis();

	public abstract Vector3d[] getPrincipalAxesOfInertia();

	public abstract Vector3d getDimension();

	/**
	 * Returns the radius for drawing polyhedra
	 * @return double radius
	 */
	public abstract double getRadius();

	/**
	 * Returns a transformation matrix transform polyhedra for Cn structures.
	 * The center in this matrix is the geometric center, rather then the centroid.
	 * In Cn structures those are usually not the same.
	 * @return
	 */
	public abstract Matrix4d getGeometicCenterTransformation();

	/**
	 * Returns the geometric center of polyhedron. In the case of the Cn
	 * point group, the centroid and geometric center are usually not
	 * identical.
	 * @return
	 */
	public abstract Point3d getGeometricCenter();

	public abstract Point3d getCentroid();

	public abstract QuatSymmetrySubunits getSubunits();

	public abstract List> getOrbits();

}