Egon Willighagen wrote:
Hi all,
the thread "SmilesParser extension" (on cdk-devel) lead to an interesting
observation:
IAtomContainer.addAtomParity(IAtomParity)
versus
IAtom.setParity(int)
The second option has existed longer, and the first was later.
Now, IMHO, the second is wrong, because it assumes that the ordering of atoms
in an AtomContainer is the same throughout it's lifetime. Which is, AFAIK,
not true at all. So, using the second option, there is a good chance of
isomerisation!
Now, the first option does not suffer from this situation because it
explicitely defines the order which is not touched during the class' life.
Now, I strongly believe we should remove the second option from the
interfaces.
Opinions?
I also think that an atom parity only makes sense in the context of a molecule
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 6.4.5.1: "The ligands of
the stereocenter are ordered such that the highest numbered atom points away
from the observer. The parity (+1) is assigned if a traversal of the remaining
ligands by increasing atom numbers is clockwise". From the context, it becomes
clear that here atom numbers do not mean atomic numbers but order of atoms in
this special context (molecular file or data structure).
Cheers,
Chris
--
Priv. Doz. Dr. Christoph Steinbeck ([EMAIL PROTECTED])
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de)
Zülpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
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