Re: [Cdk-user] SMILES parsing takes forever

[Sun, Hongmei* <hon...@fd...>]

I experience same thing. The best solution is to fix that parser. 

Thanks.
 
Hongmei
 
 

-----Original Message-----
From: Nina Jeliazkova [mailto:ni...@ac...] 
Sent: Monday, June 26, 2006 9:33 AM
To: cdk...@li...
Cc: cdk...@li...
Subject: [Cdk-user] SMILES parsing takes forever

Hello all,

Is it be possible to set a timeout for SMILESparser? 

The problem is that it takes too long to parse the following SMILES 

"n(c(c(c(Nc(c(c(nc(c(c(Nc(c1c(cccc2)c2)c3)c3)c(cccc4)c4)c5)c5)c(cccc6)c6)c7)
c7)c(cccc8)c8)cc9)c19"

(don't know exactly how long, I've interrupted it after 10 minutes, which
IMHO
is already too much)

I was thinking that aromaticity detector timeout will manage it, but it
turns
out valencyChecker.saturate(molecule) is what hangs forever.
Has anybody experienced something similar?

Best regards,
Nina 

-- 
---------------------------------------------------------------
			      Dr. Nina Nikolova-Jeliazkova
       *      *               Institute for Parallel Processing
   *                *         Bulgarian Academy of Sciences
  *  IST Foundation    *      Acad. G. Bonchev St 25-A
   * The Bulgarian NREN *     1113 Sofia, Bulgaria
     *                 *      Tel: +359 886 802011
           *      *           ICQ: 10705013
     http://www.ist.bg        www: http://ambit.acad.bg/nina 	
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