Stefan Kuhn <[EMAIL PROTECTED]> wrote:
> On Monday 11 June 2007 15:34, Rajarshi Guha wrote:
> > On Jun 11, 2007, at 9:20 AM, sushil ronghe wrote:
> > > Therefore a fast bistring comparision to rule out most
> > > structures (e.g. has it got an aromatic ring represented in the
> > > bitstring) before the more deep substructure matching would be very
> > > beneficial.
> > >
> > > This is absolutely fantastic idea.
> > > But what would be the benefit of that kind of search.
Speedup.
This is exactly how Ambit does substructure and similarity search. You could
try online or download http://ambit.acad.bg/ambit
Regards,
Nina
> > > If some one really want to use the information of the atoms given
> > > in MOL
> > > file we can use the atomtype class.
> > >
> > > Also if we are using the fingerprinting CDK need to Process the
> > > molecule.
> > > and same for substructure search. SO i don't think there will be
> > > any great difference
> > > i think!
> >
> > I think the idea is to have the bit strings precalculated for a set
> > of molecules. Then rather than doing a substructure search over all
> > the molecules, you can do a fast bit comparison, and get a smaller
> > number of molecules to perform the substructure search on.
> Indeed. This is the way to go. I can say that a bitsearch on the
precalculated
>
> fingeprints of the 20000 structures in NMRShiftDB is below a second, whereas
> the substructure search takes that on just a few structures. So it really
> helps.
> >
> > That is the way we do it in our databases here - definitely saves time!
> >
> > -------------------------------------------------------------------
> > Rajarshi Guha <[EMAIL PROTECTED]>
> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
> > -------------------------------------------------------------------
> > There is no truth to the allegation that statisticians are mean.
> > They are just your standard normal deviates.
> >
> >
> >
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