org.biojava.bio.structure
Class SVDSuperimposer
java.lang.Object
org.biojava.bio.structure.SVDSuperimposer
public class SVDSuperimposer
- extends java.lang.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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SVDSuperimposer
public SVDSuperimposer(Atom[] atomSet1,
Atom[] atomSet2)
throws StructureException
- Throws:
StructureException
getRMS
public static double getRMS(Atom[] atomSet1,
Atom[] atomSet2)
throws StructureException
- calculate the RMS (root mean square) of two sets of atoms
- Parameters:
atomSet1
- atomSet2
-
- Returns:
- the RMS of two atom sets
- Throws:
StructureException
getRotation
public Matrix getRotation()
getTranslation
public Atom getTranslation()
printMatrix
public void printMatrix(Matrix m)