[Cdk-user] IteratingMDLReader

[Om <omp...@gm...>]

Hi,

How do I read sdf file in a indexed way using CDK IteratingMDLReader?
Meaning: Suppose I have SDF file of 5 Molecules. I want to compare 2nd
Molecule with say 1st, 3rd and 5th Molecule. Some thing like 'ListIterator'
of the java.util

Is there any way pass to numerical index to next() object of
IteratingMDLReader [say like mol_query = (Molecule) myiter.next(int 5)];

Code Snippet of unsuccessful attempt :(
------------------------
sdfile= new BufferedReader (new FileReader(new File("test.sdf")));
IteratingMDLReader myiter = new IteratingMDLReader(sdfile,
DefaultChemObjectBuilder.getInstance());

Molecule mol_target = null;
Molecule mol_query = null;
HydrogenAdder ha = new HydrogenAdder();
Fingerprinter fprinter = new Fingerprinter(length, depth);
while (myiter.hasNext())
{
       mol_target = (Molecule) myiter.next();
   ha.addExplicitHydrogensToSatisfyValency(mol_target);
        fp_target = fprinter.getFingerprint(mol_target);

       for (index_query=1; myiter.hasNext(); ++index_query)
       {
       mol_query = (Molecule) myiter.next();
       ha.addExplicitHydrogensToSatisfyValency(mol_query);
       fp_query = fprinter.getFingerprint(mol_query);
       //
       }
}
-----------------------

Any help would be highly appreciated
Thanks


Om Prakash
Research Student,
Bioinformatics Center
University of Pune
Pune-411007
India