Re: [Scaffoldhunter-users] query

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

Hi Prateek,

On Thursday 25 April 2013 14:09:05 Prateek Gupta wrote:
> well currently I have prepared an algorithm for embedding JChemPaint as
> structure editor for the query.
> but I need to ask that JChemPaint saves and loads the editor structure in
> CML and MDL mol format but only loads sdf format.
> So I am employing a converter agent "obabel" so as to convert from CML to
> sdf format.This sdf file can be used as dataset for the query.
> Is there any discrepancy with this logic?

OpenBabel is written in C++ and using it for a cross-platform Java application 
like Scaffold Hunter has several disadvantages. Moreover, there should be no 
need to introduce additional dependencies. JChemPaint is based on CDK and it 
is straightforward to load MDL mol files with CDK using the class MDLReader 
(see 
edu.udo.scaffoldhunter.model.datacalculation.DBMoleculeToCDKMoleculeTransform 
for example code). Basically SDF is a container format for MDL mol files.


Regards,
  Nils