Given that the aromaticity detection ignores ring systems with more than 3
rings, I'm not sure that this molecule will be properly processed.
As for the time issue - I think this might be related to ring finding,
though I thought htat AllRingsFinder had a default timeout
On Tue, Nov 17, 2009 at 9:19 AM, Aziz Yasri <aya...@hotmail.fr> wrote:
> Dear Gwen,
>
> I am facing the same problem with the atomic descriptors in CDK. Partial
> charge calculations take a longtime for some molecules before it returns a
> value.
> I tried your molecule ( COC1=CC=C(c...@h]2n(C)C(=O)[...@h](C)NC(=O)[C@
> @H](C)NC(=O)[...@h]3cc4=cc=c(O)C(OC5=CC=C(C=C5)C(O)[...@h](N(C)C(=O)[...@h](C)NC2=O)C(=O)N3C)=C4)C=C1
> ) for partial charge calculations and it took me more than 15 minutes to
> return the partial charge values.
>
> I also noticed that polyaromatic molecules (fused aromatic rings) take more
> than 10 minutes. This has something to do with the aromaticity probably.
>
> I am really interested in comments on this behavior from CDK developers.
> Anyone experinced the same problem ? any relationships to the number of
> aromatic rings in the molecule ?
>
> I am looking forward hearing about this issues from people with experince
> in CDK toolkit.
>
> AYASRI
>
>
>
> > From: cdk-user-requ...@lists.sourceforge.net
> > Subject: Cdk-user Digest, Vol 42, Issue 10
> > To: cdk-user@lists.sourceforge.net
> > Date: Sat, 14 Nov 2009 12:02:51 +0000
> >
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> > Today's Topics:
> >
> > 1. 30 min for PEOE Partial Charge calculation (Gwenael Chev?)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 13 Nov 2009 19:03:57 +0100
> > From: Gwenael Chev? <gch...@novadecision.com>
> > Subject: [Cdk-user] 30 min for PEOE Partial Charge calculation
> > To: <cdk-user@lists.sourceforge.net>
> > Message-ID: <003001ca648b$abc86830$035938...@com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Dear all,
> >
> >
> >
> > I am using cdk-1.2.3 version and I want to calculate some descriptors.
> >
> > But when calculating the PEOE Partial Charge for some molecules (for
> example
> > :
> > COC1=CC=C(c...@h]2n(C)C(=O)[...@h](C)NC(=O)[C@@H](C)NC(=O)[...@h
> ]3CC4=CC=C(O)C(OC
> > 5=CC=C(C=C5)C(O)[...@h](N(C)C(=O)[...@h](C)NC2=O)C(=O)N3C)=C4)C=C1 ), it
> takes
> > more than 30 minutes.
> >
> > I also tried this molecule with other software, and it was as fast as for
> > other compounds (ie. Few seconds).
> >
> >
> >
> > Is somebody already had this problem ?
> >
> > How to fix it ?
> >
> > Is it possible to put a timeout duration ?
> >
> >
> >
> > Thanks for your help.
> >
> >
> >
> > Sincerely,
> >
> >
> >
> > Gwen
> >
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