| Re: Incorrect dearomatization of indazole structures [message #1445 is a reply to message #1444] |
Tue, 30 November 2021 14:53  |
thomas
Messages: 655
Registered: June 2014
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Senior Member |
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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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