@Test
public void testResolveOverlap4() throws Exception {

    double overlapScore = 0;
    logger.debug("Test case with atom clash");
    String filename = "data/cml/overlaptest.cml";
    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
    CMLReader reader = new CMLReader(ins);
    IChemFile chemFile = (IChemFile) reader.read(new ChemFile());
    IAtomContainer atomContainer = (IAtomContainer) ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
    //MoleculeViewer2D.display(new AtomContainer(atomContainer), false);
    OverlapResolver or = new OverlapResolver();
    overlapScore = or.resolveOverlap(atomContainer, null);
    //MoleculeViewer2D.display(new AtomContainer(atomContainer), false);
    Assert.assertEquals(0.0, overlapScore, 0.0001);
    logger.debug("End of test case with atom clash");
}