Hi David and Geoff,
I ran the calculation again to reproduce the problem and realized that it
was my computer's memory that caused the program to abort not converting
all the compounds.
This time it converted all compounds. So no worries there. I still got
several following warnings though.
"*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule (6674)
with Atom Ids as follows: 7 9
Warning: Stereochemistry is wrong, using the distance geometry method
instead
"
The command I ran is
$ obabel 2D.sdf -O 3D.sdf --gen3d
But I still see 0.0000 for z-coordinates for several compounds. Do you
still want those compounds to test yourself?
Thanks,
Jubilant
On Wed, Oct 25, 2017 at 9:39 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > Are you able to provide files that show this? Or reduce it to single
> compounds that are being eliminated that can be shared?
>
> Even if it’s only a subset, that would be helpful.
>
> I’m working on a distance geometry method that should offer increased
> range. Either way, having examples is crucial.
>
> Thanks,
> -Geoff
>
>
>
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