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prevent template layout changes in partial clean
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Hans-Juergen

Joined: 05 Nov 2010
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Link to postPosted: Wed Jun 15, 2016 7:37 amPost subject: prevent template layout changes in partial clean Reply with quote

Hi,



I use the chemaxon standardizer to perform 'partial' clean2d operations.

The aim is to 'straighten' non linear triple bonds such as in case of cyanides.

This works pretty well. In some cases I realized that beside of cleaning the coordinates of atoms/bonds inside the CN group, there are additional changes done to the molecule. This happens if certain templates are present in the molecule e.g. a bicyclic ring is present. The layout of this templates gets changed. I attached an example to this forum post.

 

Obviously there exists (in the chemaxon environment) a library of templates that standardizer tries to match when performing a clean operation, and if present, forces the layout of the mapped atoms/bonds  in the input molecule to follow the layout defined in the template.

Question: Is there a way to prevent that this happens?

Hope one can help.

Thanks for feedback in advance.

Best regards

Hans-Juergen

 




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Zsolt
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Joined: 11 Jan 2006
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Link to postPosted: Thu Jun 16, 2016 4:45 pmPost subject: Reply with quote

You can use the template based clean option in Clean 2D action to clean the parts of the structures (e.g. some ring systems) according to a predefined template. Templates have to be defined in this case.

Hans-Juergen

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Link to postPosted: Fri Jun 17, 2016 8:32 amPost subject: Reply with quote

Hi,

 

thanks for your reply.

My question was not how to clean templates. In the particular example I attached to the post, the question was how to PREVENT that a template clean happens even in case you use clean2d with the partial option. So what I want to achieve is that ONLY the CN group gets straightened, but the bicyclic ring is UNTOUCHED.

Is that possible?

Cheers

Hans-Juergen

Zsolt
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Link to postPosted: Fri Jun 17, 2016 9:46 amPost subject: Reply with quote

With Standardizer it's not possible currently. You can achieve the expected output with template based clean, by defining the bicyclic ring as template.

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