Standardization of Guanidines

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Standardization of Guanidines
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Home -> Forums -> Support -> Structure manipulation: Canonicalization / standardization -> Standardization of Guanidines

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creisser
Joined: 26 Apr 2006
Posts: 81

Post subject: Standardization of Guanidines
Posted: Fri Jul 04, 2008 9:40 am

Hi, I think the 2 gunidines below are tautomers of each other. So I assumed, I would get the same unique molecule as output. However, I get 2 different ones using JChem 5.0.2.1 select jc_Standardize('CCN=C(N)N','sep=! config:tautomerize!outFormat:cxsmiles') from dual select jc_Standardize('CCNC(N)=N','sep=! config:tautomerize!outFormat:cxsmiles') from dual Thanks Catherine

Zsolt
Joined: 11 Jan 2006
Posts: 446
ChemAxon personnel

Post subject:
Posted: Fri Jul 04, 2008 8:18 pm

Hi, Yes, you are right, this is a bug. It will be fixed in JChem 5.0.7 / JChem 5.1. Regards, Zsolt

creisser
Joined: 26 Apr 2006
Posts: 81

Post subject:
Posted: Mon Jul 07, 2008 7:40 am

Thanks When is JChem 5.1 likley to come out? Catherine

Zsolt
Joined: 11 Jan 2006
Posts: 446
ChemAxon personnel

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Posted: Mon Jul 07, 2008 3:08 pm

It will come out in a week. Zsolt

creisser
Joined: 26 Apr 2006
Posts: 81

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Posted: Thu Jul 31, 2008 11:19 am

Hi I have downloaded version 5.0.07 and tried testing the above problem with it before upgrading the server. However, the issue is still present and both compounds are not standardized to the same molecule when using the Tautomerise option. Could you suggest any other way to find out tautomers and prevent users from adding the same compound twice? Thanks Catherine

Zsolt
Joined: 11 Jan 2006
Posts: 446
ChemAxon personnel

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Posted: Mon Aug 04, 2008 1:56 pm

creisser wrote:

I have downloaded version 5.0.07 and tried testing the above problem with it before upgrading the server.
However, the issue is still present and both compounds are not standardized to the same molecule when using the Tautomerise option.

This bug was fixed only in JChem 5.1. Sorry for the mistake, I misunderstood the developer who is working on tautomer generation.

My colleague will answer your other question soon.

Zsolt

Szabolcs
Joined: 03 Jun 2004
Posts: 956
ChemAxon personnel

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Posted: Mon Aug 04, 2008 1:57 pm

Hi Catherine,

creisser wrote:

Could you suggest any other way to find out tautomers and prevent users from adding the same compound twice?

From JChem 5.1, there will be a new JChem index option for efficient tautomer duplicate control. Until then you may try perfect search with tautomer option, however it may be very slow depending on the tautomer numbers.

Best regards,
Szabolcs

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