Esempio n. 1
0
  /** @cdk.bug 1535055 */
  @Test
  public void testBug1535055() throws Exception {
    SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
    IAtomContainer mol = sp.parseSmiles("COC(=O)c1ccc2c(c1)c1ccccc1[nH]2");
    CDKHueckelAromaticityDetector.detectAromaticity(mol);
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
    SmilesGenerator sg = new SmilesGenerator();
    sg.setUseAromaticityFlag(true);
    String s1 = sg.createSMILES(mol);

    String filename = "data/cml/bug1535055.cml";
    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
    CMLReader reader = new CMLReader(ins);
    IChemFile chemFile = (IChemFile) reader.read(new ChemFile());

    // test the resulting ChemFile content
    Assert.assertNotNull(chemFile);
    IAtomContainer mol2 = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
    CDKHueckelAromaticityDetector.detectAromaticity(mol2);
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
    String s2 = sg.createSMILES(mol2);

    Assert.assertTrue(s1.contains("[nH]"));
    Assert.assertTrue(s2.contains("[nH]"));
  }
 /**
  * Sets the given cml. Does not update other fields like for example smiles
  *
  * @param cml
  */
 public void setCML(String cml) {
   InputStream inputStream = new ByteArrayInputStream(cml.getBytes());
   CMLReader cmlReader = new CMLReader(inputStream);
   try {
     IChemFile readFile = (IChemFile) cmlReader.read(new ChemFile());
     setAtomContainer((AtomContainer) ChemFileManipulator.getAllAtomContainers(readFile).get(0));
   } catch (CDKException e) {
     throw new RuntimeException("failed to read atomContainer", e);
   }
 }
 public IAtomContainer getAtomContainer() {
   if (atomContainer == null) {
     InputStream in = FileStoreKeeper.FILE_STORE.retrieve(fileStoreKey);
     CMLReader cmlReader = new CMLReader(in);
     try {
       IChemFile readFile = (IChemFile) cmlReader.read(new ChemFile());
       setAtomContainer((AtomContainer) ChemFileManipulator.getAllAtomContainers(readFile).get(0));
     } catch (CDKException e) {
       throw new RuntimeException("failed to read atomContainer", e);
     }
   }
   return atomContainer;
 }
Esempio n. 4
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 /**
  * A unit test for JUnit
  *
  * @exception Exception Description of the Exception
  */
 @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);
   // MoleculeViewer2D.display(new AtomContainer(atomContainer), false);
   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");
 }
Esempio n. 5
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 /**
  * 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");
 }
Esempio n. 6
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  @Test
  public void testMDMoleculeCustomizationRoundtripping() throws Exception {
    StringWriter writer = new StringWriter();

    CMLWriter cmlWriter = new CMLWriter(writer);
    cmlWriter.registerCustomizer(new MDMoleculeCustomizer());
    MDMolecule molecule = makeMDBenzene();
    cmlWriter.write(molecule);

    String serializedMol = writer.toString();
    logger.debug("****************************** testMDMoleculeCustomizationRoundtripping()");
    logger.debug(serializedMol);
    logger.debug("******************************");
    logger.debug("****************************** testMDMoleculeCustomization Write first");
    logger.debug(serializedMol);
    logger.debug("******************************");

    CMLReader reader = new CMLReader(new ByteArrayInputStream(serializedMol.getBytes()));
    reader.registerConvention("md:mdMolecule", new MDMoleculeConvention(new ChemFile()));
    IChemFile file = (IChemFile) reader.read(new ChemFile());
    List containers = ChemFileManipulator.getAllAtomContainers(file);
    Assert.assertEquals(1, containers.size());

    Object molecule2 = containers.get(0);
    Assert.assertTrue(molecule2 instanceof MDMolecule);
    MDMolecule mdMol = (MDMolecule) molecule2;

    Assert.assertEquals(6, mdMol.getAtomCount());
    Assert.assertEquals(6, mdMol.getBondCount());

    List residues = mdMol.getResidues();
    Assert.assertEquals(2, residues.size());
    Assert.assertEquals(3, ((Residue) residues.get(0)).getAtomCount());
    Assert.assertEquals(3, ((Residue) residues.get(1)).getAtomCount());
    Assert.assertEquals("myResidue1", ((Residue) residues.get(0)).getName());
    Assert.assertEquals("myResidue2", ((Residue) residues.get(1)).getName());
    Assert.assertEquals(0, ((Residue) residues.get(0)).getNumber());
    Assert.assertEquals(1, ((Residue) residues.get(1)).getNumber());

    List chargeGroup = mdMol.getChargeGroups();
    Assert.assertEquals(2, chargeGroup.size());
    Assert.assertEquals(2, ((ChargeGroup) chargeGroup.get(0)).getAtomCount());
    Assert.assertEquals(4, ((ChargeGroup) chargeGroup.get(1)).getAtomCount());
    Assert.assertNotNull(((ChargeGroup) chargeGroup.get(0)).getSwitchingAtom());
    Assert.assertEquals("a2", ((ChargeGroup) chargeGroup.get(0)).getSwitchingAtom().getID());
    Assert.assertNotNull(((ChargeGroup) chargeGroup.get(1)).getSwitchingAtom());
    Assert.assertEquals("a5", ((ChargeGroup) chargeGroup.get(1)).getSwitchingAtom().getID());

    Assert.assertEquals(2, ((ChargeGroup) chargeGroup.get(0)).getNumber());
    Assert.assertEquals(3, ((ChargeGroup) chargeGroup.get(1)).getNumber());

    writer = new StringWriter();

    cmlWriter = new CMLWriter(writer);
    cmlWriter.registerCustomizer(new MDMoleculeCustomizer());
    cmlWriter.write(mdMol);

    String serializedMDMol = writer.toString();
    logger.debug("****************************** testMDMoleculeCustomizationRoundtripping()");
    logger.debug(serializedMol);
    logger.debug("******************************");
    logger.debug("****************************** testMDMoleculeCustomization Write second");
    logger.debug(serializedMDMol);
    logger.debug("******************************");

    Assert.assertEquals(serializedMol, serializedMDMol);
  }
Esempio n. 7
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 private IChemFile parseCMLString(String cmlString) throws Exception {
   IChemFile chemFile = null;
   CMLReader reader = new CMLReader(new ByteArrayInputStream(cmlString.getBytes()));
   chemFile = (IChemFile) reader.read(new org.openscience.cdk.ChemFile());
   return chemFile;
 }