Access part of a molecule

MurckoChains.java

  private static IAtomContainer getChains(IAtomContainer mol) {
    IAtomContainer result = mol.getBuilder().newInstance(IAtomContainer.class);
    for (IAtom atom : mol.atoms())
      atom.setFlag(CDKConstants.VISITED, false);
    for (IBond bond : mol.bonds()) {
      if (!bond.isInRing()) {
        IAtom beg = bond.getAtom(0);
        IAtom end = bond.getAtom(1);
        if (!beg.getFlag(CDKConstants.VISITED)) {
          result.addAtom(beg);
          beg.setFlag(CDKConstants.VISITED, true);
        }
        if (!end.getFlag(CDKConstants.VISITED)) {
          result.addAtom(end);
          end.setFlag(CDKConstants.VISITED, true);
        }
        result.addBond(bond);
      }
    }
    return result;
  }

  public static void main(String[] args) throws CDKException {

    String smi = "COC1=C(O)C=C2C=CC=C(C3=CC(COC(=O)C4=CC5=C(NC=C5)C=C4)=CC(=C3)C(O)=O)C2=C1";

    IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
    SmilesParser smipar = new SmilesParser(bldr);
    SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Isomeric);

    IAtomContainer mol = smipar.parseSmiles(smi);
    Cycles.markRingAtomsAndBonds(mol);

    MurckoFragmenter fragmenter = new MurckoFragmenter();
    fragmenter.generateFragments(mol);
    for (IAtomContainer frag : fragmenter.getFrameworksAsContainers()) {
      String fragSmi = smigen.create(frag);
      String chainSmi = smigen.create(getChains(frag));
      System.err.println(fragSmi + " " + chainSmi);
    }
  }