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Removing explicit hydrogrens on large PubChem compounds
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mpustelnik

Joined: 02 Jul 2002
Posts: 112

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Link to postPosted: Thu Jan 17, 2013 6:43 pmPost subject: Removing explicit hydrogrens on large PubChem compounds Reply with quote

Attached are two compounds from PubChem in which the standardizer api gets unresponsive when removing explicit hydrogens.  I have verified this through Standardizer tool, Marvin Sketch and Java API.  I noticed that the memory usage slowly increases, so there maybe a memory leak.  Would be nice to have a timeout option for standardizer.

I suspect that there is more in PubChem that Standardizer may have problems with but these are the first ones that I have encountered that have blocked data importing.




 Filename: pubchem-err.sdf    Filesize: 53.76 KB    Downloaded: 200 Time(s)
 Description:  

 Filename: PubChem.xml    Filesize: 384 Bytes    Downloaded: 222 Time(s)
 Description:  
Viktoria
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Joined: 27 Dec 2010
Posts: 135

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Link to postPosted: Mon Jan 21, 2013 9:33 amPost subject: Reply with quote

Thank you for reporting this poblem; we will investigate it.

Best regards,

Viktoria

Viktoria
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Joined: 27 Dec 2010
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Link to postPosted: Mon Jan 28, 2013 9:07 amPost subject: Reply with quote

Hi,

We found the problem. 
The fix will be available in version 5.12.x or 6.0.

Best regards,

Viktoria

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