コード例 #1
0
 public String perceiveCDKAtomTypes(IMolecule mol)
             throws InvocationTargetException {
     
     ICDKMolecule cdkmol;
     
     try {
         cdkmol = cdk.asCDKMolecule(mol);
     } 
     catch ( BioclipseException e ) {
         e.printStackTrace();
         throw new InvocationTargetException(
                       e, "Error while creating a ICDKMolecule" );
     }
     
     IAtomContainer ac = cdkmol.getAtomContainer();
     CDKAtomTypeMatcher cdkMatcher 
         = CDKAtomTypeMatcher.getInstance(ac.getBuilder());
     
     StringBuffer result = new StringBuffer();
     int i = 1;
     for (IAtom atom : ac.atoms()) {
         IAtomType type = null;
         try {
             type = cdkMatcher.findMatchingAtomType(ac, atom);
         } 
         catch ( CDKException e ) {}
         result.append(i).append(':').append(
             type != null ? type.getAtomTypeName() : "null"
         ).append('\n'); // FIXME: should use NEWLINE here
         i++;
     }
     return result.toString();
 }
  @Test
  public void testSybylAtomTypePerceptionFromSMILES()
      throws FileNotFoundException, IOException, BioclipseException, CoreException,
          InvocationTargetException {

    ICDKMolecule mol = cdk.fromSMILES("C1CCCCC1CCOC");

    debug.perceiveSybylAtomTypes(mol);

    for (int i = 0; i < mol.getAtomContainer().getAtomCount(); i++) {
      IAtom a = mol.getAtomContainer().getAtom(i);
      System.out.println("Atom: " + a.getSymbol() + i + ", type=" + a.getAtomTypeName());
    }
  }
コード例 #3
0
  public DBMolecule(String name, ICDKMolecule cdkMolecule) throws BioclipseException {

    super();
    this.name = name;
    try {
      fingerPrint =
          cdkMolecule.getFingerprint(
              net.bioclipse.core.domain.IMolecule.Property.USE_CACHED_OR_CALCULATED);
    } catch (BioclipseException e) {
      logger.error("Could not create fingerprint for molecule", e);
    }
    persistedFingerPrint = makePersistedFingerPrint(fingerPrint);
    setAtomContainer(cdkMolecule.getAtomContainer());
    smiles = "";
    annotations = new ArrayList<Annotation>();
  }
  @Test
  public void testSybylAtomTypePerception()
      throws FileNotFoundException, IOException, BioclipseException, CoreException,
          InvocationTargetException {

    String path = getClass().getResource("/testFiles/atp.mol").getPath();
    ICDKMolecule mol = cdk.loadMolecule(new MockIFile(path));

    System.out.println("mol: " + mol.toString());

    debug.perceiveSybylAtomTypes(mol);

    for (int i = 0; i < mol.getAtomContainer().getAtomCount(); i++) {
      IAtom a = mol.getAtomContainer().getAtom(i);
      System.out.println("Atom: " + a.getSymbol() + i + ", type=" + a.getAtomTypeName());
    }
  }
  @Test
  public void testSybylAtomTypePerceptionBenzene()
      throws CDKException, FileNotFoundException, IOException, BioclipseException, CoreException,
          InvocationTargetException {

    IAtomContainer ac = MoleculeFactory.makeBenzene();

    ICDKMolecule mol = new CDKMolecule(ac);

    debug.perceiveSybylAtomTypes(mol);

    System.out.println("** BENZENE **");

    System.out.println(AtomContainerDiff.diff(ac, mol.getAtomContainer()));

    for (int i = 0; i < mol.getAtomContainer().getAtomCount(); i++) {
      IAtom a = mol.getAtomContainer().getAtom(i);
      System.out.println("Atom: " + a.getSymbol() + i + ", type=" + a.getAtomTypeName());
    }

    assertEquals("C.ar", mol.getAtomContainer().getAtom(0).getAtomTypeName());
    assertEquals("C.ar", mol.getAtomContainer().getAtom(1).getAtomTypeName());
    assertEquals("C.ar", mol.getAtomContainer().getAtom(2).getAtomTypeName());
    assertEquals("C.ar", mol.getAtomContainer().getAtom(3).getAtomTypeName());
    assertEquals("C.ar", mol.getAtomContainer().getAtom(4).getAtomTypeName());
    assertEquals("C.ar", mol.getAtomContainer().getAtom(5).getAtomTypeName());
  }
コード例 #6
0
ファイル: DSManager.java プロジェクト: bioclipse/bioclipse.ds
  public void runTest(
      String testID,
      IMolecule mol,
      IReturner<List<? extends ITestResult>> returner,
      IProgressMonitor monitor)
      throws BioclipseException {

    ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();

    IDSTest test = getTest(testID);
    List<? extends ITestResult> ret = null;
    try {

      // Preprocess the molecule
      ICDKMolecule cdkmol = cdk.asCDKMolecule(mol);

      // Clone the mol
      IAtomContainer clonedAC = null;
      try {
        clonedAC = (IAtomContainer) cdkmol.getAtomContainer().clone();
      } catch (CloneNotSupportedException e) {
        logger.error("Could not clone mol: " + cdkmol);
        return;
      }

      ICDKMolecule clonedMol = new CDKMolecule(clonedAC);
      ret = test.runWarningTest(clonedMol, monitor);

    } catch (Exception e) {
      // in case of error...
      LogUtils.debugTrace(logger, e);
      ITestResult er = new SimpleResult("Error: " + e.getMessage(), ITestResult.ERROR);
      er.setDetailedMessage(e.getMessage());
      List<ITestResult> trlist = new ArrayList<ITestResult>();
      trlist.add(er);
      monitor.done();
      returner.completeReturn(trlist);
      return;
    }

    monitor.done();
    returner.completeReturn(ret);
  }
コード例 #7
0
    public String perceiveSybylAtomTypes(IMolecule mol)
                        throws InvocationTargetException {
        
        ICDKMolecule cdkmol;
        
        try {
            cdkmol = cdk.asCDKMolecule(mol);
        } 
        catch (BioclipseException e) {
            System.out.println("Error converting cdk10 to cdk");
            e.printStackTrace();
            throw new InvocationTargetException(e);
        }
        
        IAtomContainer ac = cdkmol.getAtomContainer();
        CDKAtomTypeMatcher cdkMatcher 
            = CDKAtomTypeMatcher.getInstance(ac.getBuilder());
        AtomTypeMapper mapper 
            = AtomTypeMapper.getInstance(
                 "org/openscience/cdk/dict/data/cdk-sybyl-mappings.owl" );

        IAtomType[] sybylTypes = new IAtomType[ac.getAtomCount()];
        
        int atomCounter = 0;
        int a=0;
        for (IAtom atom : ac.atoms()) {
            IAtomType type;
            try {
                type = cdkMatcher.findMatchingAtomType(ac, atom);
            } 
            catch (CDKException e) {
                type = null;
            }
            if (type==null) {
//                logger.debug("AT null for atom: " + atom);
                type = atom.getBuilder().newAtomType(atom.getSymbol());
                type.setAtomTypeName("X");
            }
            AtomTypeManipulator.configure(atom, type);
            a++;
        }
        try {
            CDKHueckelAromaticityDetector.detectAromaticity(ac);
//            System.out.println("Arom: " 
//                + CDKHueckelAromaticityDetector.detectAromaticity(ac) );
		    } 
        catch (CDKException e) {
			    logger.debug("Failed to perceive aromaticity: " + e.getMessage());
		    }
        for (IAtom atom : ac.atoms()) {
            String mappedType = mapper.mapAtomType(atom.getAtomTypeName());
            if ("C.2".equals(mappedType)
                    && atom.getFlag(CDKConstants.ISAROMATIC)) {
                mappedType = "C.ar";
            } 
            else if ("N.pl3".equals(mappedType)
                    && atom.getFlag(CDKConstants.ISAROMATIC)) {
                mappedType = "N.ar";
            }
            try {
                sybylTypes[atomCounter] = factory.getAtomType(mappedType);
		        } 
            catch (NoSuchAtomTypeException e) {
                // yes, setting null's here is important
                sybylTypes[atomCounter] = null; 
			      }
            atomCounter++;
        }
        StringBuffer result = new StringBuffer();
        // now that full perception is finished, we can set atom type names:
        for (int i = 0; i < sybylTypes.length; i++) {
            if (sybylTypes[i] != null) {
                ac.getAtom(i).setAtomTypeName(sybylTypes[i].getAtomTypeName());
            } 
            else {
                ac.getAtom(i).setAtomTypeName("X");
            }
            
            result.append(i).append(':').append(ac.getAtom(i).getAtomTypeName())
                  /*.append("\n")*/;

        }
        return result.toString();
    }
コード例 #8
0
 public String debug(ICDKMolecule mol) {
     return mol.getAtomContainer().toString();
 }
コード例 #9
0
 public String diff(ICDKMolecule mol, ICDKMolecule mol2) {
     return AtomContainerDiff.diff(
         mol.getAtomContainer(), mol2.getAtomContainer()
     ); 
 }