Re: [Scaffoldhunter-devel] How can I use substructure implementation?

[Shamshad A. <sha...@gm...>]

Hi,

I have implemented this feature with option to select a matcher from
Simple, VF2, and Fast Matchers.

Matchers are not working if we create   pattern graph or host graph with
false value of configure parameter

Thanks,
Shamshad
On Jul 28, 2014 5:07 PM, <nl...@us...> wrote:

> Hi Shamshad,
>
> the following code performs substructure search (without filtering) using
> our
> implementation:
>
> IAtomContainer acQuery = null; // input
> Collection<IAtomContainer> database = null; // input
>
> MoleculeGraph mgQuery = new MoleculeGraph(acQuery);
> SearchPattern sp = new SearchPattern(mgQuery, false);
>
> for (IAtomContainer molData : database) {
>     MoleculeGraph mgData = new MoleculeGraph(molData);
>     Matcher m = new MatcherFast(sp, mgData);
>     if (m.match()) {
>         // process matching molecule
>     }
> }
>
> Note that it is assumed that the query structure and the database have been
> loaded into the CDK datastructure IAtomContainer.
>
>
> Regards,
>   Nils
>
>
> On Wednesday 23 July 2014 23:24:13 Shamshad Alam wrote:
> > Hi,
> >
> > I am implementing filter command which allows user to filter dataset,
> > subset, sdf and csv files. I've used SMARTSQueryTool (available in CDK)
> to
> > filter structure. Now I'm looking for the ways to use substructure search
> > implementation available in scaffold hunter. I am still not able to
> > identify the entry point to substructure search.
> >
> > So, Could anyone help me with some demo code (or steps) to use the
> > substructure search implementation.
> >
> > Thanks,
> > Shamshad
>