Hi!
Thank you for your reply. If we use "add hydrogens (make explicit)" we have
effectively all the hydrogens in the .mol file. In our example, hydrogen of the
stereocenter appear with hash bond (6) but the wedge bond (normaly 1) is not
specified (0). Do we have to change the SMILE descriptor?
Bests regards,
Jean-françois BERRIEN
Chimie Organique
Responsable pédagogique des EDs UE1 de PACES, UE9A et UE9B de DFGSP2
Bureau DH33 A & B - Bâtiment D3 - 5, rue J.B. Clément
92296 Châtenay-Malabry
06 66 54 83 23
----- Mail original -----
De: "Geoffrey Hutchison" <geoff.hutchi...@gmail.com>
À: "labovedilla" <jean-francois.berr...@u-psud.fr>
Cc: openbabel-discuss@lists.sourceforge.net
Envoyé: Mercredi 15 Mai 2019 21:35:23
Objet: Re: [Open Babel] making wedge & hashed bonds
> We are using Open Babel to convert smile files into mol file but for
> stereocenters it generate only one wedge or one hashed bond. We would prefer
> to have both wedge and hashed bonds like in Cram convention.
I'm not sure I understand what you're asking. If a molecule requires both types
of wedge/hash bond to properly depict the stereo centers, Open Babel will do
that. In general, like most programs, it will only show the wedge/hash notation
when needed and omit any implicit hydrogens.
Are you trying to make sure the implicit hydrogens are shown so that the Mol
file indicates both wedge/hash for a Cram diagram? In that case, you might try
adding hydrogens.
-Geoff
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