Sorry - I got things backward. It's storing the cis/trans stereochemistry
in a 0D format that's the problem. See the post and comments at
http://baoilleach.blogspot.com/2010/02/how-to-store-stereochemistry-in-mol.html
- Noel
On 12 May 2012 13:52, Noel O'Boyle <baoille...@gmail.com> wrote:
> It's intentional, rather than a bug. I originally had some code in there
> to support stereo in 0D SDF, but the format really doesn't support this
> officially - it's supposed to be either 2D or 3D. It's all very well for
> cis/trans, but it's not possible to store tet stereo without coordinates
> (which aren't present in 0D) or tet parities (which the spec explicitly
> says to ignore on reading).
>
> In short, we could support this, but Open Babel would be the only software
> to do so, and these 0D SDF files would not be handled correctly by others...
>
> In short, if you use --gen2d or --gen3d it will work fine.
>
> - Noel
>
> On 11 May 2012 23:48, Craig James <cja...@emolecules.com> wrote:
>
>> This looks bad:
>>
>> echo "C/C=C/C" | babel -i smi -o sdf | babel -i sdf -o can
>> CC=CC
>>
>> Notice the cis/trans bonds are lost. In OB 2.2.x, it works correctly:
>>
>> echo "C/C=C/C" | babel -i smi -o sdf | babel -i sdf -o can
>> C/C=C/C
>>
>> The problem seems to be here in 2.3.x:
>>
>> echo "C/C=C/C" | babel -i smi -o sdf
>>
>> OpenBabel05111215342D
>>
>> 4 3 0 0 0 0 0 0 0 0999 V2000
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 1 2 1 0 0 0 0
>> 2 3 2 0 0 0 0
>> 3 4 1 0 0 0 0
>> M END
>> $$$$
>>
>> Notice that the bond block has no stereo (cis/trans) markings. Do the
>> same thing in 2.2.x and the cis/trans bonds are properly marked:
>>
>> echo "C/C=C/C" | babel -i smi -o sdf
>>
>> OpenBabel05111215352D
>>
>> 4 3 0 0 0 0 0 0 0 0999 V2000
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0
>> 1 2 1 1 0 0
>> 2 3 2 3 0 0
>> 3 4 1 6 0 0
>> M END
>>
>> $$$$
>>
>> The bond block is correct here in this output from 2.2.x.
>>
>> Any ideas when this might have happened and if it was intentional?
>>
>> Thanks,
>> Craig
>>
>>
>>
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