ChemicalFilters { public List<Integer> getSortedFragment() { return Collections.unmodifiableList(fragmentSize); } ChemicalFilters(List<Map<Integer, Integer>> allMCS, List<Map<IAtom, IAtom>> allAtomMCS,
            Map<Integer, Integer> firstSolution, Map<IAtom, IAtom> firstAtomMCS, IAtomContainer sourceMol,
            IAtomContainer targetMol); synchronized void sortResultsByStereoAndBondMatch(); synchronized void sortResultsByFragments(); synchronized void sortResultsByEnergies(); List<Double> getSortedEnergy(); List<Integer> getSortedFragment(); List<Double> getStereoMatches(); static IBond.Order convertOrder(double srcOrder); static int convertBondOrder(IBond bond); static int convertBondStereo(IBond bond); static IBond.Stereo convertStereo(int stereoValue);  }
@Test public void testGetSortedFragment() throws InvalidSmilesException, CDKException { SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C"); IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1"); Isomorphism smsd1 = new Isomorphism(Algorithm.DEFAULT, true); smsd1.init(queryac, target, true, true); smsd1.setChemFilters(false, true, false); Integer score = 2; assertEquals(score, smsd1.getFragmentSize(0)); }