private List order5(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[3]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC(C)CCC"), false); queries[1] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC(C)(C)CC"), false); queries[2] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CCC(C)CC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order5(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[3]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC(C)CCC"), false); queries[1] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC(C)(C)CC"), false); queries[2] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CCC(C)CC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order5(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[3]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("C1CCCC1"), false); queries[1] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC1CCC1"), false); queries[2] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC1CC1(C)"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order4(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[2]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("C1CCC1"), false); queries[1] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC1CC1"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order4(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[2]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("C1CCC1"), false); queries[1] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC1CC1"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List<List<Integer>> order3(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CCCC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order3(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("C(C)(C)(C)"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order5(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC(C)C(C)(C)"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order4(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC(C)CC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List<List<Integer>> order4(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CCCCC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List<List<Integer>> order7(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CCCCCCCC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List<List<Integer>> order2(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CCC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List<List<Integer>> order5(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CCCCCC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List<List<Integer>> order7(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CCCCCCCC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order4(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC(C)CC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order4(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator .createAnyAtomAnyBondContainer(sp.parseSmiles("C(C)(C)(C)(C)"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List order5(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CC(C)C(C)(C)"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private List<List<Integer>> order6(IAtomContainer atomContainer) { QueryAtomContainer[] queries = new QueryAtomContainer[1]; try { queries[0] = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(sp.parseSmiles("CCCCCCC"), false); } catch (InvalidSmilesException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } return ChiIndexUtils.getFragments(atomContainer, queries); }
private void addTemplateMol(IAtomContainer mol) { templates.add(mol); QueryAtomContainer query = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(mol, false); queries.add(query); for (int i = 0; i < mol.getAtomCount(); i++) { query.getAtom(i).setPoint3d(new Point3d(mol.getAtom(i).getPoint3d())); } patterns.add(Pattern.findSubstructure(query)); }
@Test public void testAnyAtomAnyBondCase() throws Exception { SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer target = sp.parseSmiles("O1C=CC=C1"); IAtomContainer queryac = sp.parseSmiles("C1CCCC1"); QueryAtomContainer query = QueryAtomContainerCreator.createAnyAtomAnyBondContainer(queryac, false); Assert.assertTrue("C1CCCC1 should be a subgraph of O1C=CC=C1", uiTester.isSubgraph(target, query)); Assert.assertTrue("C1CCCC1 should be a isomorph of O1C=CC=C1", uiTester.isIsomorph(target, query)); }