Hi,
This can be done with an isomorphism checker, for example the
UniversalIsomorphismTester. But, in general, if you have a method
like:
isIsomorphic(IAtomContainer a, IAtomContainer b)
then a way to do this is:
public void makeUnique(ArrayList<IAtomContainer> all) {
ArrayList<IAtomContainer> unique = new ArrayList<IAtomContainer>();
for (IAtomContainer a : all) {
if (isUnique(a, unique)) unique.add(a):
}
}
where the isUnique() method would be something like:
public boolean isUnique(IAtomContainer a, ArrayList<IAtomContainer> l) {
for (IAtomContainer b : l) {
if (isIsomorphic(a, b)) return false;
}
return true;
}
and, as I say isIsomorphic is probably just calls
UniversalIsomorphismTester.isIsomorphic(a, b) - for simple
applications, it is convenient to put the try{...} catch {...} block
in this part, and just ignore problems.
gilleain
On Thu, Jul 2, 2009 at 1:29 PM, suyog<[email protected]> wrote:
>
>
> hi... all
> I have one .sdf file with thousands of molecule in it...
> I want to identify duplicate molecules(having similar structure) from .sdf
> file using CDK...
>
> How do I do this????
> Which classes should i use??
> Or if you have any sample code please paste link....
>
> Any suggestion/ clue is appreciated....
>
>
> Thanks & Regards
> Suyog
> --
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>
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