Egon Willighagen wrote:
> Hi all,
> the thread "SmilesParser extension" (on cdk-devel) lead to an interesti=
> The second option has existed longer, and the first was later.
> Now, IMHO, the second is wrong, because it assumes that the ordering of=
> in an AtomContainer is the same throughout it's lifetime. Which is, AFA=
> not true at all. So, using the second option, there is a good chance of=
> Now, the first option does not suffer from this situation because it=20
> explicitely defines the order which is not touched during the class' li=
> Now, I strongly believe we should remove the second option from the=20
I also think that an atom parity only makes sense in the context of a mol=
and it looks like we should keep the first concept.
We need to agree on a concept that we use for atom parities.
The Gasteiger handbook says on page 211 (volume 1) in 220.127.116.11: "The ligan=
the stereocenter are ordered such that the highest numbered atom points a=
from the observer. The parity (+1) is assigned if a traversal of the rema=
ligands by increasing atom numbers is clockwise". From the context, it be=
clear that here atom numbers do not mean atomic numbers but order of atom=
this special context (molecular file or data structure).
Priv. Doz. Dr. Christoph Steinbeck (c.steinbeck@...)
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.d=
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..