/**
* A unit test for JUnit
*
* @exception Exception Description of the Exception
*/
@Test
public void testResolveOverlap5() throws Exception {
double overlapScore = 0;
logger.debug("Test case with atom clash");
IAtomContainer atomContainer =
new SmilesParser(DefaultChemObjectBuilder.getInstance())
.parseSmiles("OC4C(N2C1=C(C(=NC(=N1)SC)SC)C3=C2N=CN=C3N)OC(C4O)CO");
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(new AtomContainer(atomContainer));
sdg.generateCoordinates();
atomContainer = sdg.getMolecule();
OverlapResolver or = new OverlapResolver();
overlapScore = or.resolveOverlap(atomContainer, null);
// MoleculeViewer2D.display(new AtomContainer(atomContainer), true);
Assert.assertEquals(0.0, overlapScore, 0.0001);
logger.debug("End of test case with atom clash");
}
/**
* A unit test for JUnit
*
* @exception Exception Description of the Exception
*/
@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");
}
