public class SVDSuperimposer
extends java.lang.Object
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(); }
Constructor and Description |
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SVDSuperimposer(Atom[] atomSet1,
Atom[] atomSet2)
Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.
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Modifier and Type | Method and Description |
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static double |
getRMS(Atom[] atomSet1,
Atom[] atomSet2)
Calculate the RMS (root mean square) deviation of two sets of atoms.
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Matrix |
getRotation()
Get the Rotation matrix that is required to superimpose the two atom sets.
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Atom |
getTranslation()
Get the shift vector.
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void |
printMatrix(Matrix m)
Simple debug method to print a Matrix object on System.out.
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public SVDSuperimposer(Atom[] atomSet1, Atom[] atomSet2) throws StructureException
atomSet1
- Atom array 1atomSet2
- Atom array 2StructureException
public static double getRMS(Atom[] atomSet1, Atom[] atomSet2) throws StructureException
atomSet1
- atom array 1atomSet2
- atom array 2StructureException
public Matrix getRotation()
public Atom getTranslation()
public void printMatrix(Matrix m)
m
- a Matrix