Thanks for the change.
> But since it does involve recursively fragmenting the initial set of
> fragments, if your molecule has long chains, it can take a long time
> to complete
>
for a straight and branch chain of length upto 8 it is doing very fast.
that is fine..
But one problem is there, it is generating a same fragments.
say for (pentane) fragmenter is generating 5 fragments
all of the population is consisting of only 2 Unique fragments.
eventhough this block of code (line NO: 83-37) is running.
// make sure we don't add the same fragment twice
for (IAtomContainer partContainer : parts) {
if (!fragmentExists(partContainer, fragments))
fragments.add(partContainer);
}
}
well i have not tested it for large set of molecule but i am doing it now
and i will let you know the results.
Cheers
On 8/29/07, Rajarshi Guha <[EMAIL PROTECTED]> wrote:
>
>
> On Aug 27, 2007, at 4:47 AM, sushil ronghe wrote:
>
> >
> > actually i was testing a sdffile with the rajarshi's fragmenter
> > link : http://cheminfo.informatics.indiana.edu/~rguha/code/java/
> > Fragmenter.java
> >
> > i found that for one of the molecule in the file the fragmenter is
> > taking too much time..
> > (1 hour after that i stop the build.)
> > then i took the file and cut paste the molecule data into the new
> > mol file and incorporate the error in the file.
>
> I've updated the code at http://cheminfo.informatics.indiana.edu/
> ~rguha/code/java/#frags
>
> - made a few optimizations to reduce the recursive calls to the
> fragmentation routine
> - don't split at terminal bonds
>
> But since it does involve recursively fragmenting the initial set of
> fragments, if your molecule has long chains, it can take a long time
> to complete
>
> But, it runs quite fast for your example molecule
>
> -------------------------------------------------------------------
> Rajarshi Guha <[EMAIL PROTECTED]>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
> -------------------------------------------------------------------
> All great ideas are controversial, or have been at one time.
>
>
>
--
********************************
sushil ronghe
*********************************
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