org.biojava.nbio.structure

Class SVDSuperimposer

java.lang.Object

org.biojava.nbio.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:

                        // 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);

                

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

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.
static double	getTMScoreAlternate(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2) Calculate the TM-Score for the superposition.
javax.vecmath.Matrix4d	getTransformation()
Atom	getTranslation() Get the shift vector.

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. Atom sets must be pre-rotated.

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. Normalizes by the minimum-length structure (that is, min\{len1,len2\}). Atom sets must be pre-rotated.

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

getTMScoreAlternate

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

Calculate the TM-Score for the superposition. Normalizes by the maximum-length structure (that is, max\{len1,len2\}) rather than the minimum. Atom sets must be pre-rotated.

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

See Also:

#getTMScore(Atom[], Atom[], int, int)}, which normalizes by the minimum length

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

getTransformation

public javax.vecmath.Matrix4d getTransformation()