Example #1
0
 /**
  * Selects an optimum edge for elimination in structures without N2 nodes.
  *
  * <p>This might be severely broken! Would have helped if there was an explanation of how this
  * algorithm worked.
  *
  * @param ring
  * @param molecule
  */
 private IBond checkEdges(IRing ring, IAtomContainer molecule) {
   IRing r1, r2;
   IRingSet ringSet = ring.getBuilder().newInstance(IRingSet.class);
   IBond bond;
   int minMaxSize = Integer.MAX_VALUE;
   int minMax = 0;
   logger.debug("Molecule: " + molecule);
   Iterator<IBond> bonds = ring.bonds().iterator();
   while (bonds.hasNext()) {
     bond = (IBond) bonds.next();
     molecule.removeElectronContainer(bond);
     r1 = getRing(bond.getAtom(0), molecule);
     r2 = getRing(bond.getAtom(1), molecule);
     logger.debug("checkEdges: " + bond);
     if (r1.getAtomCount() > r2.getAtomCount()) {
       ringSet.addAtomContainer(r1);
     } else {
       ringSet.addAtomContainer(r2);
     }
     molecule.addBond(bond);
   }
   for (int i = 0; i < ringSet.getAtomContainerCount(); i++) {
     if (((IRing) ringSet.getAtomContainer(i)).getBondCount() < minMaxSize) {
       minMaxSize = ((IRing) ringSet.getAtomContainer(i)).getBondCount();
       minMax = i;
     }
   }
   return (IBond) ring.getElectronContainer(minMax);
 }
Example #2
0
 /**
  * removes all bonds connected to the given atom leaving it with degree zero.
  *
  * @param atom The atom to be disconnecred
  * @param molecule The molecule containing the atom
  */
 private void trim(IAtom atom, IAtomContainer molecule) {
   List<IBond> bonds = molecule.getConnectedBondsList(atom);
   for (int i = 0; i < bonds.size(); i++) {
     molecule.removeElectronContainer((IBond) bonds.get(i));
   }
   // you are erased! Har, har, har.....  >8-)
 }
Example #3
0
 /**
  * Eliminates one bond of this atom from the molecule
  *
  * @param atom The atom one bond is eliminated of
  * @param molecule The molecule that contains the atom
  */
 private void breakBond(IAtom atom, IAtomContainer molecule) {
   Iterator<IBond> bonds = molecule.bonds().iterator();
   while (bonds.hasNext()) {
     IBond bond = (IBond) bonds.next();
     if (bond.contains(atom)) {
       molecule.removeElectronContainer(bond);
       break;
     }
   }
 }
Example #4
0
  /**
   * Finds the Smallest Set of Smallest Rings.
   *
   * @param mol the molecule to be searched for rings
   * @return a RingSet containing the rings in molecule
   */
  public IRingSet findSSSR(IAtomContainer mol) {
    IBond brokenBond = null;
    IChemObjectBuilder builder = mol.getBuilder();
    IRingSet sssr = builder.newInstance(IRingSet.class);
    IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
    molecule.add(mol);
    IAtom smallest;
    int smallestDegree, nodesToBreakCounter, degree;
    IAtom[] rememberNodes;
    IRing ring;

    // Two Vectors - as defined in the article. One to hold the
    // full set of atoms in the structure and on to store the numbers
    // of the nodes that have been trimmed away.
    // Furhter there is a Vector nodesN2 to store the number of N2 nodes
    List<IAtom> fullSet = new ArrayList<IAtom>();
    List<IAtom> trimSet = new ArrayList<IAtom>();
    List<IAtom> nodesN2 = new ArrayList<IAtom>();

    initPath(molecule);
    logger.debug("molecule.getAtomCount(): " + molecule.getAtomCount());
    // load fullSet with the numbers of our atoms
    for (int f = 0; f < molecule.getAtomCount(); f++) {
      fullSet.add(molecule.getAtom(f));
    }
    logger.debug("fullSet.size(): " + fullSet.size());

    do {
      // Add nodes of degree zero to trimset.
      // Also add nodes of degree 2 to nodesN2.
      // In the same run, check, which node has the lowest degree
      // greater than zero.
      smallestDegree = 7;
      smallest = null;
      nodesN2.clear();
      for (int f = 0; f < molecule.getAtomCount(); f++) {
        IAtom atom = molecule.getAtom(f);
        degree = molecule.getConnectedBondsCount(atom);
        if (degree == 0) {
          if (!trimSet.contains(atom)) {
            logger.debug("Atom of degree 0");
            trimSet.add(atom);
          }
        }
        if (degree == 2) {
          nodesN2.add(atom);
        }
        if (degree < smallestDegree && degree > 0) {
          smallest = atom;
          smallestDegree = degree;
        }
      }
      if (smallest == null) break;

      // If there are nodes of degree 1, trim them away
      if (smallestDegree == 1) {
        trimCounter++;
        trim(smallest, molecule);
        trimSet.add(smallest);
      }

      // if there are nodes of degree 2, find out of which rings
      // they are part of.
      else if (smallestDegree == 2) {
        rememberNodes = new IAtom[nodesN2.size()];
        nodesToBreakCounter = 0;
        for (int f = 0; f < nodesN2.size(); f++) {
          ring = getRing((IAtom) nodesN2.get(f), molecule);
          if (ring != null) {
            // check, if this ring already is in SSSR
            if (!RingSetManipulator.ringAlreadyInSet(ring, sssr)) {
              sssr.addAtomContainer(ring);
              rememberNodes[nodesToBreakCounter] = (IAtom) nodesN2.get(f);
              nodesToBreakCounter++;
            }
          }
        }
        if (nodesToBreakCounter == 0) {
          nodesToBreakCounter = 1;
          rememberNodes[0] = (IAtom) nodesN2.get(0);
        }
        for (int f = 0; f < nodesToBreakCounter; f++) {
          breakBond(rememberNodes[f], molecule);
        }
        if (brokenBond != null) {
          molecule.addBond(brokenBond);
          brokenBond = null;
        }
      }
      // if there are nodes of degree 3
      else if (smallestDegree == 3) {
        ring = getRing(smallest, molecule);
        if (ring != null) {

          // check, if this ring already is in SSSR
          if (!RingSetManipulator.ringAlreadyInSet(ring, sssr)) {
            sssr.addAtomContainer(ring);
          }
          brokenBond = checkEdges(ring, molecule);
          molecule.removeElectronContainer(brokenBond);
        }
      }
    } while (trimSet.size() < fullSet.size());
    logger.debug("fullSet.size(): " + fullSet.size());
    logger.debug("trimSet.size(): " + trimSet.size());
    logger.debug("trimCounter: " + trimCounter);
    //		molecule.setProperty(CDKConstants.SMALLEST_RINGS, sssr);
    return sssr;
  }