Package org.biojava.nbio.structure.align

Class StructurePairAligner

  • public class StructurePairAligner
extends Object
    Perform a pairwise protein structure superimposition.

    The algorithm is a distance matrix based, rigid body protein structure superimposition. It is based on a variation of the PSC++ algorithm provided by Peter Lackner (Peter.Lackner@sbg.ac.at, personal communication) .

    Example

      public void run(){

                // first load two example structures
                InputStream inStream1 = this.getClass().getResourceAsStream("/files/5pti.pdb");
                InputStream inStream2 = this.getClass().getResourceAsStream("/files/1tap.pdb");

                Structure structure1 = null;
                Structure structure2 = null;

                PDBFileParser pdbpars = new PDBFileParser();
                structure1 = pdbpars.parsePDBFile(inStream1) ;
                structure2 = pdbpars.parsePDBFile(inStream2);


                // calculate structure superimposition for two complete structures
                StructurePairAligner aligner = new StructurePairAligner();


                        // align the full 2 structures with default parameters.
                        // see StructurePairAligner for more options and how to align
                        // any set of Atoms
                        aligner.align(structure1,structure2);

                        AlternativeAlignment[] aligs = aligner.getAlignments();
                        AlternativeAlignment a = aligs[0];
                        System.out.println(a);

                        //display the alignment in Jmol

                        // first get an artificial structure for the alignment
                        Structure artificial = a.getAlignedStructure(structure1, structure2);


                        // and then send it to Jmol (only will work if Jmol is in the Classpath)

                        BiojavaJmol jmol = new BiojavaJmol();
                        jmol.setTitle(artificial.getName());
                        jmol.setStructure(artificial);

                        // color the two structures


                        jmol.evalString("select *; backbone 0.4; wireframe off; spacefill off; " +
                                        "select not protein and not solvent; spacefill on;");
                        jmol.evalString("select *"+"/1 ; color red; model 1; ");


                        // now color the equivalent residues ...

                        String[] pdb1 = a.getPDBresnum1();
                        for (String res : pdb1 ){
                                jmol.evalString("select " + res + "/1 ; backbone 0.6; color white;");
                        }

                        jmol.evalString("select *"+"/2; color blue; model 2;");
                        String[] pdb2 = a.getPDBresnum2();
                        for (String res :pdb2 ){
                                jmol.evalString("select " + res + "/2 ; backbone 0.6; color yellow;");
                        }


                        // now show both models again.
                        jmol.evalString("model 0;");

        }
    Since:
    1.4
    Version:
    %I% %G%
    Author:
    Andreas Prlic, Peter Lackner