On Tue, Oct 26, 2010 at 2:33 PM, Rajarshi Guha <[email protected]>wrote:
> On Tue, Oct 26, 2010 at 8:26 AM, Tobias Girschick
> <[email protected]> wrote:
> >>> In fact, given the substructure you must perform a substructure search
> to
> >>> get the mapping of the target atoms to the substructure atoms and use
> that
> >>> mapping to remove the target atoms.
> >
> > Well, that's the thing I wanted to prevent...as I already have performed
> > some kind of substructure search. Is there a way to map the substructure
> on
> > on the molecule so that I can afterwards remove the overlapping atoms?
>
> Assuming you did the substructure search using the CDK,
Well...no. That is the tricky thing. I'd like to work with a setting where I
have a precalculated set of molecules and one substructure. (But maybe I am
going to/have to switch to CDK substructure search if the other way is not
possible.) Still brainstorming...
> you can find
> the atoms matching the query and then either mark those atoms for
> later removal, or remove them then and there
>
> See the Javadocs for SMARTSQueryTool for some example code that would
> let you identify the matching atoms
>
> --
> Rajarshi Guha
> NIH Chemical Genomics Center
>
--
Tobias Girschick
mailto: [email protected]
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