tautomer canonicalization

User 162d60ff7f

15-02-2013 15:34:49

Please advise why I am not getting same canonical tautomer for the 2 molfiles of diazepine attached.

Settings are exactly the same as on my other topic in this forum.

User 851ac690a0

15-02-2013 17:26:55



The main problem is that the middle ring is anti-aromatic.

Anti-aromatic rings are not handled in every case by the  rational canonic tautomer generator.

Identical canonic tauotmers are generated if you set false value for these three falgs: 

the "rational" mode  plugin.setRationalTautomerGenerationMode(false);

the "exclude anti-aromatic compounds"  plugin.setExcludeAntiAromaticCompounds(false);

the "protect double bond stereo flags"  plugin.setProtectDoubleBondStereo(false);