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" | babe
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 a
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 wrote:
> It's intentional, rather t
Hi Noel,
Thanks for the pointer to your blog post ... it explains the issue well.
I'll address the topic here, but let me know if it would be better to post
on your blog for completeness or on the OB list for wider distribution.
My overall answer to this whole question is that it's always a mista
The issue is only regarding cis/trans stereo so I'll confine my comments to
that. (We do store tet stereo twice, as well as provide an option to read
the chirality flag if desired.)
You assume that there is a convention for storing cis/trans stereo in the
bond block, but that OB is not following i
See also this thread:
http://www.mail-archive.com/blueobelisk-discuss@lists.sourceforge.net/msg00665.html
where Greg Landrum dissuades me from including stereo in 0D Mol file.
- Noel
On 14 May 2012 11:32, Noel O'Boyle wrote:
> The issue is only regarding cis/trans stereo so I'll confine my
On Mon, May 14, 2012 at 3:46 AM, Noel O'Boyle wrote:
> See also this thread:
> http://www.mail-archive.com/blueobelisk-discuss@lists.sourceforge.net/msg00665.html
>
> where Greg Landrum dissuades me from including stereo in 0D Mol file.
>
Here's how that conversation ended. Greg wrote:
>> S
On 16 May 2012 16:28, Craig James wrote:
> On Mon, May 14, 2012 at 3:46 AM, Noel O'Boyle wrote:
>
>> See also this thread:
>> http://www.mail-archive.com/blueobelisk-discuss@lists.sourceforge.net/msg00665.html
>>
>> where Greg Landrum dissuades me from including stereo in 0D Mol file.
>>
>
>
Hi Noel,
I'm back from my vacation and caught up with the seemingly inevitable
backlog of stuff that build up... now back to reality!
On Sun, May 20, 2012 at 10:15 AM, Noel O'Boyle wrote:
> On 16 May 2012 16:28, Craig James wrote:
>
>> On Mon, May 14, 2012 at 3:46 AM, Noel O'Boyle wrote:
>>
>>
On 21 June 2012 16:13, Craig James wrote:
> Hi Noel,
>
> I'm back from my vacation and caught up with the seemingly inevitable
> backlog of stuff that build up... now back to reality!
>
> On Sun, May 20, 2012 at 10:15 AM, Noel O'Boyle wrote:
>>
>> On 16 May 2012 16:28, Craig James wrote:
>>>
>>>
Now added in r4898. Option "S" for read or write gives former 2.3.1 behaviour.
"obabel -:C/C=C/Cl -omol" still includes a warning message as follows:
*** Open Babel Warning in OpenBabel::MDLFormat::WriteMolecule
No 2D or 3D coordinates exist. Stereochemical information will be stored using
an
Hi Noel,
On Fri, Jun 22, 2012 at 4:01 AM, Noel O'Boyle wrote:
> Now added in r4898. Option "S" for read or write gives former 2.3.1
> behaviour.
>
> "obabel -:C/C=C/Cl -omol" still includes a warning message as follows:
>
> *** Open Babel Warning in OpenBabel::MDLFormat::WriteMolecule
> No 2D
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