I have added a new constant in the cdkconstans called TOTAL_RING_BOND_COUNT.

In initialization code of smartquerytool i wrote
Iterator atomss = atomContainer.atoms();
            IAtom atom = (IAtom) atomss.next();
            List allatoms = atomContainer.getConnectedAtomsList(atom);
            int counter=0;
            IAtom any=null;
            for(int i=0;i<allatoms.size ();i++){
                any =(IAtom) allatoms.get(i);
            any.setProperty (CDKConstants.TOTAL_RING_BOND,new Integer(counter));counter=0;


every thing is fine upto here i have also checked the property it is set finely for all atoms.
Now i have another class whose method matches is called after the initialization code.

public boolean matches(IAtom atom) {
      Integer total_ring_bond = ((Integer)atom.getProperty( CDKConstants.TOTAL_RING_BOND)).intValue();
      if(Connection_Size == total_ring_bond)
          return true;
      return false;

but here the property is coming 0 for all atoms.

what might be the reason.

sushil ronghe
Center of Pharmacoinformatics