hi,
read the molecules first into a SetOfMolecules and than iterate over this:
for (int i=0; i<setOfMolecules.getAtomcontainerCount();i++){
if (i !=2 ){
compare;
}
}
this works fine if setOfMolecules <= 20000.
hope this helps
Christian
-------- Original-Nachricht --------
Datum: Thu, 13 Jul 2006 18:30:53 +0530
Von: Om <[EMAIL PROTECTED]>
An: cdk-user <[email protected]>
Betreff: [Cdk-user] IteratingMDLReader
> 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
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