My two cents:
OpenBabel implements Razinger's algorithm (J. Chem. In& Comput. Sci. 1993,
33, 812-825) in determining so-called true and para stereocenters.
"Atom 2" is an example of the former. "Atom 6" is an example of the latter.
Razinger's rules are quite elaborate but in short: the reason why atom 6 is
a para center is because of one substituent being chiral and being part of a
ring system with topological symmetry.
Keep in mind that only two distinct stereoisomers exist, although 2^2 is
theoretically the maximum number, given the number of stereogenic centers.
Some of the combinations of stereo parities are actually equivalent (also
stated in the article).
Therefore, people might be tempted to think the one true center generates
the two stereoisomers. Which is wrong if you follow the methodology of
Razinger.
Regards,
Nick
From: Pascal Muller [mailto:pascal.jm.mul...@gmail.com]
Sent: Tuesday, August 06, 2013 3:15 PM
To: babel
Subject: [Open Babel] Ring symetry / Chirality
Dear all,
For the molecule
CC(O)N1CC(O)C1
atoms 2 and 6 are considered as chiral by openbabel, but actually only atom
2 is chiral (using obchiral program or IsChiral()).
If atom 2 is not chiral, like in
CC(C)N1CC(O)C1
openbabel finds no chirality.
Is that something already known?
Best regards,
Pascal
------------------------------------------------------------------------------
Get your SQL database under version control now!
Version control is standard for application code, but databases havent
caught up. So what steps can you take to put your SQL databases under
version control? Why should you start doing it? Read more to find out.
http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
