/**
* creates a virtual C-beta atom. this might be needed when working with GLY
*
* <p>thanks to Peter Lackner for a python template of this method.
*
* @param amino the amino acid for which a "virtual" CB atom should be calculated
* @return a "virtual" CB atom
* @throws StructureException
*/
public static final Atom createVirtualCBAtom(AminoAcid amino) throws StructureException {
AminoAcid ala = StandardAminoAcid.getAminoAcid("ALA");
Atom aN = ala.getN();
Atom aCA = ala.getCA();
Atom aC = ala.getC();
Atom aCB = ala.getCB();
Atom[] arr1 = new Atom[3];
arr1[0] = aN;
arr1[1] = aCA;
arr1[2] = aC;
Atom[] arr2 = new Atom[3];
arr2[0] = amino.getN();
arr2[1] = amino.getCA();
arr2[2] = amino.getC();
// ok now we got the two arrays, do a SVD:
SVDSuperimposer svd = new SVDSuperimposer(arr2, arr1);
Matrix rotMatrix = svd.getRotation();
Atom tranMatrix = svd.getTranslation();
Calc.rotate(aCB, rotMatrix);
Atom virtualCB = Calc.add(aCB, tranMatrix);
virtualCB.setName("CB");
virtualCB.setFullName(" CB ");
return virtualCB;
}
