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
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
