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How does partial clean works?
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Alena

Joined: 29 Sep 2011
Posts: 57

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Link to postPosted: Tue Feb 17, 2015 2:47 pmPost subject: How does partial clean works? Reply with quote

Hi all,

I'm trying to apply partial clean to some structures and cannot find any difference from initial structure. 

So the question is for what structures it works?

here is the code I'm using (we have JChem Cartridge only):

 

select jc_standardize(c.structure,

        'config:clean')
        from chem_structs c;

 

Environment:

Oracle environment: 

Oracle Database 11g Enterprise Edition Release 11.2.0.4.0 - 64bit Production
PL/SQL Release 11.2.0.4.0 - Production
CORE 11.2.0.4.0 Production
TNS for Linux: Version 11.2.0.4.0 - Production
NLSRTL Version 11.2.0.4.0 - Production


JChem owner: JCHEM_GG_EDITORIAL


JChem Server environment: 
Java VM vendor: Oracle Corporation
Java version: 1.7.0_67
Java VM version: 24.65-b04
JChem version: 15.1.12.0
JChem Index version: 14102000
JDBC driver version: 11.2.0.3.0

Thanks,

Alena

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
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Link to postPosted: Tue Feb 17, 2015 4:29 pmPost subject: Reply with quote

Hi Alena,

Partial clean did not work properly in JChem 15.1.12.0, see history of changes. Please upgrade to version 15.2.2.0 or later to fix this issue.

We can provide some examples to demonstrate the difference between full and partial 2D clean, if needed.  

Alena

Joined: 29 Sep 2011
Posts: 57

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Link to postPosted: Tue Feb 17, 2015 5:45 pmPost subject: Reply with quote

Thanks a lot for your answer!

Actually I wouldn't mind getting some examples because unfortunately upgrade is not a very quick procedure (here I mean not upgrade itself, but coordinating everything) and I'd like to have an idea of difference between partial and full clean.

Zsolt
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Link to postPosted: Thu Feb 19, 2015 10:44 amPost subject: Reply with quote

Partial clean: non-invasive 2D clean, rearranges only the parts of the molecule with wrong bond angles and lengths. Fallbacks to full clean in case of failure.
Full clean: assigns new 2D coordinates to each atom in the molecule. 

I have attached an example.




 Filename: full_clean_vs_partial_clean.png    Filesize: 51.31 KB    Viewed: 18216 Time(s)
 Description:  
full_clean_vs_partial_clean.png
Alena

Joined: 29 Sep 2011
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Link to postPosted: Thu Feb 19, 2015 3:40 pmPost subject: Reply with quote

thanks a lot for explanation and examples

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