/**
* 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;
}
@Test
public void testHasAminoAtoms() {
Atom CA = new AtomImpl();
CA.setName("CA");
CA.setElement(Element.C);
CA.setPDBserial(1);
Atom C = new AtomImpl();
C.setName("C");
C.setElement(Element.C);
C.setPDBserial(2);
Atom N = new AtomImpl();
N.setName("N");
N.setElement(Element.N);
N.setPDBserial(3);
Atom O = new AtomImpl();
O.setName("O");
O.setElement(Element.O);
O.setPDBserial(4);
Atom OXT = new AtomImpl();
OXT.setName("OXT");
OXT.setElement(Element.O);
OXT.setPDBserial(5);
Group g = new HetatomImpl();
g.addAtom(CA);
g.addAtom(C);
g.addAtom(N);
g.addAtom(O);
assertTrue(g.hasAminoAtoms());
g = new HetatomImpl();
g.addAtom(CA);
g.addAtom(C);
g.addAtom(N);
g.addAtom(O);
g.addAtom(OXT);
assertTrue(g.hasAminoAtoms());
g = new AminoAcidImpl();
g.addAtom(CA);
g.addAtom(C);
g.addAtom(N);
g.addAtom(O);
assertTrue(g.hasAminoAtoms());
g = new HetatomImpl();
g.addAtom(CA);
g.addAtom(C);
g.addAtom(N);
assertFalse(g.hasAminoAtoms());
g = new HetatomImpl();
g.addAtom(CA);
g.addAtom(C);
g.addAtom(N);
g.addAtom(OXT);
assertFalse(g.hasAminoAtoms());
}
