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 <baoille...@gmail.com> wrote:
> On 16 May 2012 16:28, Craig James <cja...@emolecules.com> wrote:
>
>> On Mon, May 14, 2012 at 3:46 AM, Noel O'Boyle <baoille...@gmail.com>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:
>>
>> >> So...should we retain them or not? I think what I'll do is add an
>> >> option to allow users to retain them exactly. However, the default
>> >> will be that the wedges/hashes in the output will be solely dependent
>> >> on the perceived stereochemistry. *Sigh* This applies to all 2D output
>> >> formats.
>> >
>> > Having the option to retain them exactly sounds sensible, but that
>> > means retaining all of the user-provided markings, right? This almost
>> > sounds to me like it's a read setting, not a write one. But then I'm
>> > not familiar with the internal flow for processing mols in OB.
>>
>> It seemed to me like the opposite (maybe Greg is following this now?).
>> At the end of this discussion, I was left with the understanding that
>> OpenBabel *would* keep the 0D stereo information, or at least optionally be
>> able to keep it.
>>
>> And in that same thread, Peter beat me in making all my key arguments.
>> In particular:
>>
>>
>> http://www.mail-archive.com/blueobelisk-discuss@lists.sourceforge.net/msg00666.html
>>
>> ... in which Peter argues that editors tend to draw zig-zag bonds by
>> default, so you can't rely on 2D coordinates to deduce whether an author
>> really meant cis or trans. And more to the point, Peter closes by saying:
>>
>> >> For 0D coordinates, there are no guidelines. I propose to store
>> >> cis/trans stereo using the bond stereo (you know, UP [or DOWN] at both
>> >> ends of a double bond means cis), and chirality using the atom parity.
>> >> The MDL spec states that atom parity should be ignored when read,
>> >
>> > I know this is the spec and I don't want to get into more arguments about
>> > whether it should be changed. At this stage I think it is useful if
>> > programs
>> > have the capability to read and interpret this field.
>>
>>
>> Exactly.
>>
>> To reiterate my earlier argument, I just can't see any reason not to
>> include cis/trans and chiral information in 0D SD Files. It's genuinely
>> useful, and it doesn't hurt anything. The fact that it stretches the
>> CTFile spec strikes me as uninteresting. Apps are free to ignore it.
>>
>> Craig
>>
>
> Ok - I'll add it back.
>
Can you tell me where we stand on this?
Thanks!
Craig
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