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

[<nl...@us...>]

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