org.biojava.bio.structure

Class SVDSuperimposer

java.lang.Object

org.biojava.bio.structure.SVDSuperimposer

public class SVDSuperimposer
extends Object

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

 try{

            // 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);

        } catch (Exception e){
            e.printStackTrace();
        }
        

Since:

1.5

Version:

%I% %G%

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
SVDSuperimposer(Atom[] atomSet1, Atom[] atomSet2) Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.

Method Summary

Methods

Modifier and Type	Method and Description
static double	getRMS(Atom[] atomSet1, Atom[] atomSet2) Calculate the RMS (root mean square) deviation of two sets of atoms.
Matrix	getRotation() Get the Rotation matrix that is required to superimpose the two atom sets.
static double	getTMScore(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2) Calculate the TM-Score for the superposition.
Atom	getTranslation() Get the shift vector.
void	printMatrix(Matrix m) Simple debug method to print a Matrix object on System.out.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SVDSuperimposer

public SVDSuperimposer(Atom[] atomSet1,
               Atom[] atomSet2)
                throws StructureException

Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.

Parameters:

atomSet1 - Atom array 1

atomSet2 - Atom array 2

Throws:

StructureException

Method Detail

getRMS

public static double getRMS(Atom[] atomSet1,
            Atom[] atomSet2)
                     throws StructureException

Calculate the RMS (root mean square) deviation of two sets of atoms.

Parameters:

atomSet1 - atom array 1

atomSet2 - atom array 2

Returns:

the RMS of two atom sets

Throws:

StructureException

getTMScore

public static double getTMScore(Atom[] atomSet1,
                Atom[] atomSet2,
                int len1,
                int len2)
                         throws StructureException

Calculate the TM-Score for the superposition.

Citation:
Zhang Y and Skolnick J (2004). "Scoring function for automated assessment of protein structure template quality". Proteins 57: 702 - 710.

Parameters:

atomSet1 - atom array 1

atomSet2 - atom array 2

len1 - The full length of the protein supplying atomSet1

len2 - The full length of the protein supplying atomSet2

Returns:

The TM-Score

Throws:

StructureException

getRotation

public Matrix getRotation()

Get the Rotation matrix that is required to superimpose the two atom sets.

Returns:

a rotation matrix.

getTranslation

public Atom getTranslation()

Get the shift vector.

Returns:

the shift vector

printMatrix

public void printMatrix(Matrix m)

Simple debug method to print a Matrix object on System.out.

Parameters:

m - a Matrix