001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.structure.symmetry.core; 022 023import javax.vecmath.Matrix3d; 024import javax.vecmath.Matrix4d; 025import javax.vecmath.Point3d; 026import javax.vecmath.Vector3d; 027import java.util.List; 028 029public abstract class AxisAligner { 030 031 /** 032 * Returns an instance of AxisAligner for differnt type of QuatSymmetryResults (factory method) 033 * @param results symmetry results 034 * @return instance of AxisAligner 035 */ 036 public static AxisAligner getInstance(QuatSymmetryResults results) { 037 String symmetry = results.getSymmetry(); 038 039 if (symmetry.equals("H")) { 040 return new HelixAxisAligner(results); 041 } else { 042 return new RotationAxisAligner(results); 043 } 044 } 045 046 public abstract String getSymmetry(); 047 048 public abstract Matrix4d getTransformation(); 049 050 public abstract Matrix3d getRotationMatrix(); 051 052 public abstract Matrix4d getReverseTransformation(); 053 054 public abstract Vector3d getPrincipalRotationAxis(); 055 056 public abstract Vector3d getRotationReferenceAxis(); 057 058 public abstract Vector3d[] getPrincipalAxesOfInertia(); 059 060 public abstract Vector3d getDimension(); 061 062 /** 063 * Returns the radius for drawing polyhedra 064 * @return double radius 065 */ 066 public abstract double getRadius(); 067 068 /** 069 * Returns a transformation matrix transform polyhedra for Cn structures. 070 * The center in this matrix is the geometric center, rather then the centroid. 071 * In Cn structures those are usually not the same. 072 * @return 073 */ 074 public abstract Matrix4d getGeometicCenterTransformation(); 075 076 /** 077 * Returns the geometric center of polyhedron. In the case of the Cn 078 * point group, the centroid and geometric center are usually not 079 * identical. 080 * @return 081 */ 082 public abstract Point3d getGeometricCenter(); 083 084 public abstract Point3d getCentroid(); 085 086 public abstract Subunits getSubunits(); 087 088 public abstract List<List<Integer>> getOrbits(); 089 090}