I don't remember if the SDF output code you are using in that version of
2.2.x ever made it to a release (I don't think so). In any case, it's not
correct, and was subsequently fixed. The "3" for a double bond stereo is
used to indicate unknown stereo - this is not quite clear in the spec ("3 =
Cis or trans (either) double bond") and so originally I was using it to
indicate the opposite meaning.
Apart from the "3", OB 2.3.x isn't reading the cis/trans bond stereo from
the bond block - it's just using the coordinates. As previously discussed,
there is no convention for storing bond stereo in the bond block, but I'm
going to bring it back for 0D as there's no alternative.
- Noel
On 21 May 2012 18:35, Craig James <cja...@emolecules.com> wrote:
> Hi,
>
> Version 2.3.x is declaring lots of double bonds to not be cis or trans
> that version 2.2.x thought were. In many cases 2.3.x is actually correct:
> the cis/trans spec in the bond block didn't match the 2D coordinates or was
> just plain wrong (for example, two "down" bonds on the same atom), so the
> SMILES from version 2.2.x was wrong and 2.3.x is correct to ignore it.
>
> However, I'm finding a lot of cases like three molecules in the attached
> SDF. It has 2D coordinates that indicate a cis or trans configuration, and
> the two single bonds adjacent to the double bond are correctly marked in
> each case. Yet when the SMILES has no cis/trans information.
>
> Strangely, this doesn't happen all the time. Lots of SMILES come out with
> the proper cis/trans configuration.
>
> Thanks,
> Craig
>
> OB 2.2.x:
>
> $ babel no-dbstereo.sdf -o can
> OC/C=C\CO
> CC(=O)/C=C/c1ccccc1
> ClC/C=C\CCl
>
> OB 2.3.x:
>
> $ babel no-dbstereo.sdf -o can
> OCC=CCO
> CC(=O)C=Cc1ccccc1
> ClCC=CCCl
>
>
>
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