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:
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> 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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