Class SVDSuperimposer

A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class... example usage:

                        // get some arbitrary amino acids from somewhere
                        String filename   =  "/Users/ap3/WORK/PDB/5pti.pdb" ;

                        PDBFileReader pdbreader = new PDBFileReader();
                        Structure struc = pdbreader.getStructure(filename);
                        Group g1 = (Group)struc.getChain(0).getGroup(21).clone();
                        Group g2 = (Group)struc.getChain(0).getGroup(53).clone();

                        if ( g1.getPDBName().equals("GLY")){
                                if ( g1 instanceof AminoAcid){
                                        Atom cb = Calc.createVirtualCBAtom((AminoAcid)g1);
                                        g1.addAtom(cb);
                                }
                        }

                        if ( g2.getPDBName().equals("GLY")){
                                if ( g2 instanceof AminoAcid){
                                        Atom cb = Calc.createVirtualCBAtom((AminoAcid)g2);
                                        g2.addAtom(cb);
                                }
                        }

                        Structure struc2 = new StructureImpl((Group)g2.clone());

                        System.out.println(g1);
                        System.out.println(g2);


                        Atom[] atoms1 = new Atom[3];
                        Atom[] atoms2 = new Atom[3];

                        atoms1[0] = g1.getAtom("N");
                        atoms1[1] = g1.getAtom("CA");
                        atoms1[2] = g1.getAtom("CB");


                        atoms2[0] = g2.getAtom("N");
                        atoms2[1] = g2.getAtom("CA");
                        atoms2[2] = g2.getAtom("CB");


                        SVDSuperimposer svds = new SVDSuperimposer(atoms1,atoms2);


                        Matrix rotMatrix = svds.getRotation();
                        Atom tranMatrix = svds.getTranslation();


                        // now we have all the info to perform the rotations ...

                        Calc.rotate(struc2,rotMatrix);

                        //          shift structure 2 onto structure one ...
                        Calc.shift(struc2,tranMatrix);

                        //
                        // write the whole thing to a file to view in a viewer

                        String outputfile = "/Users/ap3/WORK/PDB/rotated.pdb";

                        FileOutputStream out= new FileOutputStream(outputfile);
                        PrintStream p =  new PrintStream( out );

                        Structure newstruc = new StructureImpl();

                        Chain c1 = new ChainImpl();
                        c1.setName("A");
                        c1.addGroup(g1);
                        newstruc.addChain(c1);

                        Chain c2 = struc2.getChain(0);
                        c2.setName("B");
                        newstruc.addChain(c2);

                        // show where the group was originally ...
                        Chain c3 = new ChainImpl();
                        c3.setName("C");
                        //c3.addGroup(g1);
                        c3.addGroup(g2);

                        newstruc.addChain(c3);
                        p.println(newstruc.toPDB());

                        p.close();

                        System.out.println("wrote to file " + outputfile);