Thanks,
This is a useful initiative
On Tue, Mar 2, 2010 at 9:14 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> (Reposted from my blog following Greg's suggestion )
>
> Hello all,
>
> Right now, I'm adding stereo (i.e. double bond stereochemistry, and
> chirality) to the MDL Mol format in OpenBabel. There are three places
> where stereochemical information can be stored in these files: the
> coordinates, the atom parity (in the atom block), the bond stereo (in
> the bond block).
>
> My current understanding is that where 3D coordinates are present,
> there's no need to store stereochemical information in either the atom
> parity or the bond block. I think I'll probably set the atom parity
> anyway (since I've already written the code, and it helps when you
> look at the file to be able to easily identify the chiral centers).
>
>
The main problem is lack of information as to whether the geometry (2D or
3D) is definitive or arbitrary. It is impossible to construct a 3D model of
(say) alanine without a perceived stereochemistry at the Carbon. Similarly
most modern 2D graphic programs will draw a double bond as cis or trans (not
normally linear although this was common in typesetting). If the (arbitrary)
geometry is then transmitted without details of authoring, then the reader
may assume a definitive stereochemistry. Put another way, there is no way of
indicating by coordinates alone that stereochemistry is unknown. I thinks
it's very important not to use the geometry as definitive unless it is clear
that the author specified it (which normally only comes from crystal
structures or computational chemistry).
P.
> For 2D coordinates, there's no need to store the bond stereochemistry
> (as this can be worked out from the coordinates), but chirality needs
> to be stored explicitly. The normal way to store this is not using
> atom parity (but I'll set this anyway for the same reasons as above),
> but by setting one of the bonds on the tetrahedral center to up or
> down.
>
> 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.
> but
> the alternative is to just forget the stereochemistry, or else to
> store both cis/trans stereo *and* chirality in the bond block, which
> may just about be possible but is likely to be a real mess.
>
> Is it ambiguous or merely complicated? If the latter then we should use it
to remove ambiguity.
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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