Agreed. If you set the bond wedging explicitly it should be preserved.
Here's the issue, which includes links to the commits with the fix (that's
now checked in):
https://github.com/rdkit/rdkit/issues/611
-greg
On Mon, Sep 7, 2015 at 1:10 PM, Noel O'Boyle <[email protected]> wrote:
> Hey Greg,
>
> I hope you had a good meeting.
>
> I was wondering whether it is possible to set the location of depicted
> wedge/hashes in a MOL file output.
>
> Right now, it seems that I can call WedgeHashBonds and that tells me
> where the wedge or hashes are via GetBondDir() (although I am still a
> bit confused as to which direction they are supposed to be). And I can
> set the BondDir fine...
>
> However, when I subsequently write out a MOL file it seems that any
> changes to the location of the BondDirs are just ignored.
>
> This is not a biggie for me, but it would be nice to be able to always
> set the same bond as the stereobond in a set of amino acids, as this
> makes it obvious which are D- versus L-.
>
> Regards,
> Noel
>
>
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