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Avoiding automatic aromatization in version 4.0.3
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Jason

Joined: 04 Mar 2015
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Link to postPosted: Mon Apr 13, 2015 12:06 pmPost subject: Avoiding automatic aromatization in version 4.0.3 Reply with quote

Hi everyone,

I need to replicate some results that were calculated on version 4.0.3 and I'm having some issues. Hopefully someone is around that worked with the software back in the early 2000's! I'm using the majorms plugin to predict the major microspecies from smiles inputs. I've moved from using the existing software (which worked great) to the 4.0.3 version which aromatizes the smiles by default. Dearomatization of the output isn't acceptable because I need the identical structure as an output (apart from the ionisation changes). Is there a way to maintain the input kekule structure with this plugin?

Thanks,

Jason

László
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Joined: 14 Jan 2011
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Link to postPosted: Fri May 15, 2015 3:50 pmPost subject: Reply with quote

Hi Jason,

Could you send us a code example (with an input molecule) which shows the mentioned behavior?

Best regards,

Laszlo

Jason

Joined: 04 Mar 2015
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Link to postPosted: Mon May 18, 2015 12:50 amPost subject: Reply with quote

Thanks for responding Laszlo,

 

I managed to sort the issue out. I was attempting to dearomatise from the smiles string (which is ambiguous). I just needed to set the non aromatic flag when I was exporting to smiles in the first place.

Thanks, 

Jason

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