OverlapResolver { public double getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds) { double overlapScore = 0; overlapScore = getAtomOverlapScore(ac, overlappingAtoms); return overlapScore; } OverlapResolver(); double resolveOverlap(IAtomContainer ac, IRingSet sssr); double displace(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds); double getOverlapScore(IAtomContainer ac, Vector overlappingAtoms, Vector overlappingBonds); double getAtomOverlapScore(IAtomContainer ac, Vector overlappingAtoms); double getBondOverlapScore(IAtomContainer ac, Vector overlappingBonds); boolean areIntersected(IBond bond1, IBond bond2);  }
@Test public void testResolveOverlap2() throws Exception { logger.debug("Test case with neither bond nor atom overlap"); String filename = "data/cml/overlaptest2.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); double score = new OverlapResolver().getOverlapScore(atomContainer, new Vector(), new Vector()); Assert.assertEquals(0.0, score, 0.0001); logger.debug("End of test case with neither bond nor atom overlap"); }