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.align.multiple.util; 022 023import java.util.ArrayList; 024import java.util.List; 025 026import javax.vecmath.Matrix4d; 027 028import org.biojava.nbio.structure.Atom; 029import org.biojava.nbio.structure.Calc; 030import org.biojava.nbio.structure.SVDSuperimposer; 031import org.biojava.nbio.structure.StructureException; 032import org.biojava.nbio.structure.StructureTools; 033import org.biojava.nbio.structure.align.multiple.Block; 034import org.biojava.nbio.structure.align.multiple.BlockSet; 035import org.biojava.nbio.structure.align.multiple.MultipleAlignment; 036 037/** 038 * Superimposes each structure in a {@link MultipleAlignment} onto a reference 039 * structure. 040 * <p> 041 * Performs a global superposition of the MultipleAlignment in case 042 * there is only one {@link BlockSet}, and a superposition for every BlockSet 043 * in case there is more than one (flexible alignment). 044 * <p> 045 * This class uses the {@link SVDSuperimposer} algorithm. 046 * 047 * @author Spencer Bliven 048 * @author Aleix Lafita 049 * @since 4.1.0 050 * 051 */ 052public class ReferenceSuperimposer implements MultipleSuperimposer { 053 054 private int reference; 055 056 /** 057 * Default Constructor. 058 * Uses the first structure as the reference. 059 */ 060 public ReferenceSuperimposer() { 061 this(0); 062 } 063 064 /** 065 * Constructor using a specified structure as reference. 066 * 067 * @param reference Index of the structure to use as a reference 068 * (it has to be > 0) 069 */ 070 public ReferenceSuperimposer(int reference) { 071 if (reference<0) { 072 throw new IllegalArgumentException( 073 "reference index has to be positive, but was "+reference); 074 } 075 this.reference = reference; 076 } 077 078 @Override 079 public void superimpose(MultipleAlignment alignment) 080 throws StructureException { 081 082 //Check for inconsistencies in the alignment 083 if(alignment.getEnsemble() == null) { 084 throw new NullPointerException("No ensemble set for this alignment." 085 + " Structure information cannot be obtained."); 086 } 087 if (alignment.size() < 1) { 088 throw new IndexOutOfBoundsException( 089 "No aligned structures, alignment size == 0."); 090 } 091 if (alignment.getCoreLength() < 1){ 092 throw new IndexOutOfBoundsException( 093 "Alignment too short, core alignment length < 1."); 094 } 095 096 List<Atom[]> atomArrays = alignment.getAtomArrays(); 097 if (atomArrays.size() <= reference) { 098 throw new IndexOutOfBoundsException(String.format( 099 "Invalid reference structure: requested %d but " 100 + "only %d structures.", 101 reference,atomArrays.size())); 102 } 103 104 alignment.clear(); 105 106 //Calculate BlockSet transformations 107 for (BlockSet bs:alignment.getBlockSets()){ 108 109 //Block transformations 110 List<Matrix4d> transforms = 111 new ArrayList<Matrix4d>(atomArrays.size()); 112 113 //Loop through structures 114 for (int i=0; i<atomArrays.size(); i++){ 115 116 if( i == reference) { 117 //Identity operation 118 Matrix4d ident = new Matrix4d(); 119 ident.setIdentity(); 120 transforms.add(ident); 121 continue; 122 } 123 124 Atom[] ref = atomArrays.get(reference); 125 Atom[] curr = atomArrays.get(i); 126 127 List<Atom> atomSet1 = new ArrayList<Atom>(); 128 List<Atom> atomSet2 = new ArrayList<Atom>(); 129 130 for( Block blk : bs.getBlocks() ) { 131 if( blk.size() != atomArrays.size()) { 132 throw new IllegalStateException(String.format( 133 "Mismatched block length. Expected %d " 134 + "structures, found %d.", 135 atomArrays.size(),blk.size() )); 136 } 137 //Loop through all aligned residues 138 for (int j=0; j<blk.length(); j++){ 139 Integer pos1 = blk.getAlignRes().get(reference).get(j); 140 Integer pos2 = blk.getAlignRes().get(i).get(j); 141 142 if (pos1==null || pos2==null) continue; 143 atomSet1.add(ref[pos1]); 144 atomSet2.add(curr[pos2]); 145 } 146 } 147 Atom[] array1 = atomSet1.toArray(new Atom[atomSet1.size()]); 148 Atom[] array2 = atomSet2.toArray(new Atom[atomSet2.size()]); 149 150 array2 = StructureTools.cloneAtomArray(array2); 151 152 //From the superimposer we obtain the rotation and translation 153 SVDSuperimposer svd = new SVDSuperimposer(array1, array2); 154 Calc.transform(array2, svd.getTransformation()); 155 transforms.add(svd.getTransformation()); 156 } 157 //Set transformation of the BlockSet 158 bs.setTransformations(transforms); 159 } 160 } 161}