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Home » DataWarrior » Bug Reports » Incorrect dearomatization of indazole structures (DataWarrior auto dearomatization of SDF indazole structures results in incorrect kekule form structures)
Incorrect dearomatization of indazole structures [message #1444] Tue, 30 November 2021 11:48 Go to next message
Andrievs is currently offline  Andrievs
Messages: 1
Registered: November 2021
Junior Member
I am having issues with SD files where the structure is an indazole superstructure.
I have attached a SD-file as examples with 3 structures.

The problem is that during the dearomatization process DataWarrior incorrectly places the double bonds resulting in a formation of s stereocenter.

See attached image for visual differences.
/forum/index.php?t=getfile&id=482&private=0

Is there a way to have the dearomatization be done correctly with out using additional software?

P.s. I am using DataWarrior version 5.5.0

Sincerely, Andrievs

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Re: Incorrect dearomatization of indazole structures [message #1445 is a reply to message #1444] Tue, 30 November 2021 14:53 Go to previous message
thomas is currently offline  thomas
Messages: 715
Registered: June 2014
Senior Member
Hi Andrievs,

Your SD-File includes a non-standard Marvin extension that is not understood by DataWarrior: MRV_IMPLICIT_H
Marvin uses that feature to define explicit hydrogen atoms, which usually is not needed, because molfiles
usually are in a kekulized form. If, however, molfiles just contain bonds marked to be aromatic, the Kekulizer needs more information, if multiple potentially protonated nitrogen atoms are present. Standard molfiles simply don't have a place to store that information. The only way to make your SD-files compatible would be to extend DataWarrior's molfile parser to support Marvin's non-standard extentions.

Hope this explains it, Thomas

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