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The protein structure modules of BioJava.
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/*
 *                    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.geometry;

import javax.vecmath.Matrix3d;
import javax.vecmath.Point3d;
import java.util.Arrays;
import java.util.List;


public class Tetrahedron implements Polyhedron {
	private static double TETRAHEDRAL_ANGLE = Math.acos(-1.0/3.0);
	private static int[] lineLoop1 = {0,1,2,3,0,2};
	private static int[] lineLoop2 = {1,3};

	private double circumscribedRadius = 1.0;

	/**
	 * Returns the radius of a circumscribed sphere, that goes
	 * through all vertices
	 * @return the cirumscribedRadius
	 */
	@Override
	public double getCirumscribedRadius() {
		return circumscribedRadius;
	}

	/**
	 * Set the radius of a circumscribed sphere, that goes
	 * through all vertices
	 * @param cirumscribedRadius the cirumscribedRadius to set
	 */
	public void setCirumscribedRadius(double cirumscribedRadius) {
		this.circumscribedRadius = cirumscribedRadius;
	}
	/**
	 * Returns the radius of an inscribed sphere, that is tangent to each
	 * of the tetrahedrons's faces
	 * @return the inscribedRadius
	 */
	public double getInscribedRadius() {
		double side = getSideLengthFromCircumscribedRadius(circumscribedRadius);
		return getInscribedRadiusFromSideLength(side);
	}

	/**
	 * Sets the radius of an inscribed sphere, that is tangent to each
	 * of the tetrahedron's faces
	 * @param inscribedRadius the inscribedRadius to set
	 */
	public void setInscribedRadius(double radius) {
		double side = getSideLengthFromInscribedRadius(radius);
		this.circumscribedRadius = getCircumscribedRadiusFromSideLength(side);
	}

	/**
	 * Returns the radius of a sphere, that is tangent to each
	 * of the tetrahedron's edges
	 *
	 * @return the midRadius
	 */
	public double getMidRadius() {
		double side = getSideLengthFromCircumscribedRadius(circumscribedRadius);
		return getMiddleRadiusFromSideLength(side);
	}

	/**
	 * Sets the radius of radius of a sphere, that is tangent to each
	 * of the tetrahedron's edges
	 * @param midRadius the midRadius to set
	 */
	public void setMidRadius(double radius) {
		double side = getSideLengthFromMiddleRadius(radius);
		this.circumscribedRadius = getCircumscribedRadiusFromSideLength(side);
	}

	/**
	 * Returns the vertices of an n-fold polygon of given radius and center
	 * @param n
	 * @param radius
	 * @param center
	 * @return
	 */
	@Override
	public  Point3d[] getVertices() {
		double x = getSideLengthFromCircumscribedRadius(circumscribedRadius)/2;
		double z = x/Math.sqrt(2);
		Point3d[] tetrahedron = new Point3d[4];
		tetrahedron[0] = new Point3d(-x,  0, -z);
		tetrahedron[1] = new Point3d( x,  0, -z);
		tetrahedron[2] = new Point3d( 0, -x,  z);
		tetrahedron[3] = new Point3d( 0,  x,  z);
		Point3d centroid = SuperPosition.centroid(tetrahedron);

		// rotate tetrahedron to align one vertex with the +z axis
		Matrix3d m = new Matrix3d();
		m.rotX(0.5 * TETRAHEDRAL_ANGLE);
		for (Point3d p: tetrahedron) {
			p.sub(centroid);
			m.transform(p);
		}
		return tetrahedron;
	};

	@Override
	public List getLineLoops() {
		return Arrays.asList(lineLoop1, lineLoop2);
	}

	@Override
	public int getViewCount() {
		return 3;
	}

	@Override
	public String getViewName(int index) {
		String name;
		switch (index) {
		case 0:  name = "Front 3-fold axis vertex-centered";
		break;
		case 1:  name = "Back 3-fold axis face-centered";
		break;
		case 2:  name = "Side 2-fold axis edge-centered";
		break;
		default: throw new IllegalArgumentException("getViewMatrix: index out of range:" + index);
		}
		return name;
	}

	@Override
	public Matrix3d getViewMatrix(int index) {
		Matrix3d m = new Matrix3d();
		switch (index) {
		case 0:  m.setIdentity(); // front vertex-centered
		break;
		case 1:  m.rotX(Math.PI); // back face-centered
		break;
		case 2: double angle = Math.PI - 0.5 * TETRAHEDRAL_ANGLE; // Side edge-centered
		m.rotX(angle);
		break;
		default: throw new IllegalArgumentException("getViewMatrix: index out of range:" + index);
		}
		return m;
	}

	private static double getSideLengthFromInscribedRadius(double radius) {
		return radius * Math.sqrt(24);
	}

	private static double getInscribedRadiusFromSideLength(double sideLength) {
		return sideLength / Math.sqrt(24);
	}

	private static double getSideLengthFromMiddleRadius(double radius) {
		return radius * Math.sqrt(8);
	}

	private static double getMiddleRadiusFromSideLength(double sideLength) {
		return sideLength / Math.sqrt(8);
	}

	private static double getSideLengthFromCircumscribedRadius(double radius) {
		return radius / Math.sqrt(3.0/8.0);
	}

	private static double getCircumscribedRadiusFromSideLength(double sideLength) {
		return sideLength * Math.sqrt(3.0/8.0);
	}

}