@Test
public void testEquals() {

    PharmacophoreAtom patom1 = new PharmacophoreAtom("[CX2]N", "Amine", new Point3d(0, 0, 0));
    patom1.setMatchingAtoms(new int[]{1, 4, 5});
    PharmacophoreAtom patom2 = new PharmacophoreAtom("[CX2]N", "Amine", new Point3d(0, 0, 0));
    patom2.setMatchingAtoms(new int[]{1, 4, 5});
    PharmacophoreAtom patom3 = new PharmacophoreAtom("[CX2]N", "Amine", new Point3d(0, 1, 0));
    patom3.setMatchingAtoms(new int[]{1, 4, 5});
    PharmacophoreAtom patom4 = new PharmacophoreAtom("[CX2]N", "Amine", new Point3d(0, 0, 0));
    patom4.setMatchingAtoms(new int[]{1, 4, 6});
    Assert.assertEquals(patom2, patom1);
    Assert.assertNotSame(patom3, patom1);
    Assert.assertNotSame(patom4, patom1);
}