On Wed, Mar 3, 2010 at 9:29 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> On 2 March 2010 11:23, Greg Landrum <greg.land...@gmail.com> wrote:
>
>
> Are some of the wedge/hash bonds in typical MOL files unrelated to
> stereochemistry? That is, are some purely for depiction? If I knew
> this for sure, I would not retain the wedge/hash bond designations in
> the input but just work them out from the perceived stereo.
>
> It is *posssible* to write wedge/hash bonds for any bond in a V2000 file.
The terms used in CTFILE are "bond stereo" and "wedge". So presumably all
such fields are related to "bond stereo". We wrote a CML2SDF writer
(sponsored by MDL and I think meeting with their unofficial approval) and
there are no special checks as to when such a field can be written.
The only other formal questions are (a) can the current version of ISIS Draw
or similar program write out a wedge bond unrelated to stereochemistry and
(b) can the current program read such a field (that does not make
stereochemical sense) without flagging an error. If the answerr to both of
these is "yes" then I suspect the answer is "yes, they can be purely for
depiction",
P.
> - Noel
>
--
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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