private int loadSmiles(final InputStream in) throws IOException { int count = 0; try (BufferedReader brdr = new BufferedReader(new InputStreamReader(in, StandardCharsets.UTF_8))) { String line; while ((line = brdr.readLine()) != null) { if (line.isEmpty() || line.charAt(0) == '#') continue; try { if (add(line)) count++; } catch (InvalidSmilesException e) { e.printStackTrace(); } } } return count; }
private IAtomContainer parseSmiles(String smiles, boolean isRxnPart) throws InvalidSmilesException { try { // create the Beam object from parsing the SMILES Set<String> warnings = new HashSet<>(); Graph g = Graph.parse(smiles, strict, warnings); for (String warning : warnings) logger.warn(warning); // convert the Beam object model to the CDK - note exception thrown // if a kekule structure could not be assigned. IAtomContainer mol = beamToCDK.toAtomContainer(kekulise ? g.kekule() : g, kekulise); if (!isRxnPart) { try { // CXSMILES layer parseMolCXSMILES(g.getTitle(), mol); } catch (Exception e) { e.printStackTrace(); throw new InvalidSmilesException("Error parsing CXSMILES:" + e.getMessage()); } } return mol; } catch (IOException e) { throw new InvalidSmilesException("could not parse '" + smiles + "', " + e.getMessage()); } catch (Exception e) { throw new InvalidSmilesException("could not parse '" + smiles + "'"); } }
@Test public void testInvalidSmilesException_String() { final String EXPLANATION = "No, CDK cannot compute the multidollar ligand you search for target X."; InvalidSmilesException exception = new InvalidSmilesException(EXPLANATION); Assert.assertNotNull(exception); Assert.assertEquals(EXPLANATION, exception.getMessage()); } }
private int loadSmiles(final InputStream in) throws IOException { int count = 0; try (BufferedReader brdr = new BufferedReader(new InputStreamReader(in, StandardCharsets.UTF_8))) { String line; while ((line = brdr.readLine()) != null) { if (line.isEmpty() || line.charAt(0) == '#') continue; try { if (add(line)) count++; } catch (InvalidSmilesException e) { e.printStackTrace(); } } } return count; }
throw new InvalidSmilesException("Not a reaction SMILES: " + smiles); throw new InvalidSmilesException("Invalid reaction SMILES:" + smiles); } catch (Exception e) { e.printStackTrace(); throw new InvalidSmilesException("Error parsing CXSMILES:" + e.getMessage());
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>> 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<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 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); }