@Test
public void testMapAtomsOfAlignedStructures() throws Exception {

    String filenameMolOne = "data/mdl/murckoTest6_3d_2.mol";
    String filenameMolTwo = "data/mdl/murckoTest6_3d.mol";
    //String filenameMolTwo = "data/mdl/murckoTest6_3d_2.mol";
    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filenameMolOne);
    IAtomContainer molOne;
    IAtomContainer molTwo;
    Map<Integer, Integer> mappedAtoms = new HashMap<Integer, Integer>();
    MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
    molOne = reader.read(new AtomContainer());
    ins = this.getClass().getClassLoader().getResourceAsStream(filenameMolTwo);
    reader = new MDLV2000Reader(ins, Mode.STRICT);
    molTwo = reader.read(new AtomContainer());
    mappedAtoms = AtomMappingTools.mapAtomsOfAlignedStructures(molOne, molTwo, mappedAtoms);
    //logger.debug("mappedAtoms:"+mappedAtoms.toString());
    //logger.debug("***** ANGLE VARIATIONS *****");
    double AngleRMSD = GeometryTools.getAngleRMSD(molOne, molTwo, mappedAtoms);
    //logger.debug("The Angle RMSD between the first and the second structure is :"+AngleRMSD);
    //logger.debug("***** ALL ATOMS RMSD *****");
    Assert.assertEquals(0.2, AngleRMSD, 0.1);
    double AllRMSD = GeometryTools.getAllAtomRMSD(molOne, molTwo, mappedAtoms, true);
    //logger.debug("The RMSD between the first and the second structure is :"+AllRMSD);
    Assert.assertEquals(0.242, AllRMSD, 0.001);
    //logger.debug("***** BOND LENGTH RMSD *****");
    double BondLengthRMSD = GeometryTools.getBondLengthRMSD(molOne, molTwo, mappedAtoms, true);
    //logger.debug("The Bond length RMSD between the first and the second structure is :"+BondLengthRMSD);
    Assert.assertEquals(0.2, BondLengthRMSD, 0.1);
}