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Problem with CL Standardizer
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Richard

Joined: 12 Nov 2008
Posts: 9

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Link to postPosted: Sun Apr 26, 2009 10:55 pmPost subject: Problem with CL Standardizer Reply with quote

Hi,

When trying to standardize a set of SMILES strings from the command line, I'm getting the following type of error:

WARNING: Chiral center has wrong connectivity at atom 2 in smiles: O[C@H](C\C(=C/C=C/1\CCC[C@@](C)([C@@H](CC[C@H]([C@H](C)CCCC(O)(C)C)2)\1)2)\C(=C)[C@@H](O)C1)1
The chirality is ignored.

 

The command I ran from the command prompt is as follows:

standardize 2008LiData.smi -c flo-standard.xml -o 2008LiData_CL.smi >> 2008LiData_CLStand2.txt 2>&1

 

I am using JChem version 5.1.3,  Windows XP professional OS. I attach all relevant files.

 

I did not receive any errors when I copied this SMILES in to the Daylight depiction utility.

The only references I've found to this type of problem in this forum suggest that this was a bug in older versions of JChem.

Am I doing something wrong?

 

Many thanks for any assistance.

 

Richard Marchese




 Filename: 2008LiData.smi    Filesize: 30.05 KB    Downloaded: 547 Time(s)
 Description:  

 Filename: 2008LiData_CL.smi    Filesize: 25.28 KB    Downloaded: 715 Time(s)
 Description:  

 Filename: flo-standard.xml    Filesize: 847 Bytes    Downloaded: 395 Time(s)
 Description:  

 Filename: 2008LiData_CLStand2.txt    Filesize: 7.18 KB    Downloaded: 365 Time(s)
 Description:  
Volfi
ChemAxon personnel
Joined: 07 Jun 2004
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Link to postPosted: Mon Apr 27, 2009 5:53 pmPost subject: Reply with quote

Hi,

It seems to be a bug. We fix it asap.

 

Andras

Volfi
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Joined: 07 Jun 2004
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Link to postPosted: Mon Apr 27, 2009 7:11 pmPost subject: Reply with quote

Hi,

 

I have fixed the bug.

Thank you for the report.

The next version will contain the fix.

 

Andras

Richard

Joined: 12 Nov 2008
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Link to postPosted: Mon Apr 27, 2009 8:20 pmPost subject: Reply with quote

Thank you.

 

Are you in a position to say when the next release will be?

Akos
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Joined: 09 Mar 2007
Posts: 864

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Link to postPosted: Tue Apr 28, 2009 4:49 pmPost subject: Reply with quote

Hi,

The 5.2.2 version is planned to be released by the end of May.

Best regards,

Akos

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