Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

hi,
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?

Also I am looking into the hibernate model for object -relation mapping and
potential betterment.


On Thu, Apr 25, 2013 at 1:31 PM, <nl...@us...> wrote:

> Hi Prateek,
>
> On Thursday 25 April 2013 12:17:59 Prateek Gupta wrote:
> > I also used the 2.2 version of the scaffolhunter software.I came across
> > multiple differences between the 1.7 to 2.2 version.
> > I understood my previous doubts after using the software more thoroughly.
> > But I want to what exactly is meant by
> > "calculation of fingerprints for effective filtering as well as a
> subgraph
> > isomorphism algorithm for validation, but lacks integration in the
> current
> > filtering framework" .
> > What are the discrepancies that are targetted.
>
> as you have seen, the current filtering framework is slightly different
> from
> the one used in the previous releases (v1.x). Another difference is that
> the
> new version uses Hibernate for object-relational mapping and is more
> independent of the database server used. However, this level of abstraction
> might prohibit some (MySQL-specific) database queries used in the previous
> version. For example, the filtering based on bit operations on the database
> site might be problematic. A good approach should be compatible with most
> database servers while still being as efficient as possible. This requires
> to
> investigate the operations supported by Hibernate and it might also help
> to do
> some test runs first to come up with feasible practical solution.
>
>
> Regards
>   Nils
>
>
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