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tautomer canonicalization: conjugated either bonds
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Kenneth

Joined: 23 Mar 2012
Posts: 51

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Link to postPosted: Mon Feb 25, 2013 7:21 pmPost subject: tautomer canonicalization: conjugated either bonds Reply with quote

Hi,

After tautomer canonicalization the attached input molecue with conjugted either bonds converts to partially "either" bonds. For some reason the "either" flag for double bonds in molfile is converted to "either" of single bonds.

My settings:

plugin = new TautomerizationPlugin();

            plugin.setProtectAllTetrahedralStereoCenters(true);

            plugin.setProtectAromaticity(false);

            plugin.setProtectDoubleBondStereo(false);

            plugin.setProtectEsterGroups(true);

            plugin.setProtectLabeledTetrahedralStereoCenters(true);

            plugin.setExcludeAntiAromaticCompounds(false);

            plugin.setRationalTautomerGenerationMode(false);

            plugin.setMaxStructureCount(1000);

            plugin.setTakeCanonicalForm(true);

            plugin.setCleanResultStructures(true);

Jozsef
ChemAxon personnel
Joined: 25 May 2004
Posts: 568

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Link to postPosted: Thu Feb 28, 2013 7:35 pmPost subject: Reply with quote

Hi,

 

This is a bug.

The fix will be available in the 5.12 or in the 5.12.1.

Thanks for  testing!

 

Jozsi

Kenneth

Joined: 23 Mar 2012
Posts: 51

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Link to postPosted: Wed Mar 06, 2013 4:42 pmPost subject: Reply with quote

YEs, looks like fix is not in 5.12

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