Thanks for the fast answer.
Unfortunately, the solution wont work for me, as I need the atom ids
of the search-fragment in the molecule (what getSubgraphAtomsMap/s()
does/should do).
Cheers,
Martin
On Fri, May 15, 2009 at 3:46 PM, Egon Willighagen
<egon.willigha...@gmail.com> wrote:
> On Fri, May 15, 2009 at 2:25 PM, Martin Guetlein
> <martin.guetl...@googlemail.com> wrote:
>> However, if I change smilesSearch to "CC", the map is empty, and the output
>> is:
>> Atoms of search in molecule: ' '
>>
>> Looks like a bug to me. Does anyone know a workaround?
>
> Solution:
>
> for (IBond bond : molecule.bonds()) {
> if (bond.getAtomCount() == 2 &&
> "C".equals(bond.getAtom(0).getSymbol()) &&
> "C".equals(bond.getAtom(1).getSymbol())) {
> match = true;
> }
> }
>
> Interestingly enough, the CC smiles is an example in the JavaDoc:
>
> http://pele.farmbio.uu.se/nightly-1.2.x/api/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.html
>
> I will need to check if we have a unit test for it...
>
> Egon
>
> --
> Post-doc @ Uppsala University
> http://chem-bla-ics.blogspot.com/
>
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