Hi all,
Interesting discussion. I have been facing this problem recently and I did
not know that RDKit could do it.
I developed an algorithm to classify stereocenters as R/S and double bonds
as E/Z using CIP rules and the information provided by openbabel. There is
only one CIP rule that for now is not implemented: cases where only
configurational differences between ligands are detected, due to the
ambiguity of this rule, which was also described by Paulina Mata (already
mentioned by Yoel).
In summary, to determine the chirality according to the R-S notation the
steps are: (1) identify the stereocenters, (2) number the atoms in the
molecule skeleton, (3) assign the priority of each ligand according to the
CIP rules, (4) map the ligands into the skeleton groups which results in a
permutation and finally (5) determine the parity of the permutation and
compare it to the initial sense of rotation given by openbabel (clockwise
or anticlockwise) which allows the classification of the stereocenter(s) in
R or S.
The algorithm is described in detail in the following technical report:
http://docs.di.fc.ul.pt/jspui/bitstream/10455/6894/1/TR_stereo.pdf
and was implemented in a webtool: http://nams.lasige.di.fc.ul.pt/tools.php
source code (in python): https://pypi.python.org/pypi/NAMS/0.9.2
Ana Teixeira
On Wed, Dec 4, 2013 at 3:44 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:
> On 2013-12-03 22:28, Geoffrey Hutchison wrote:
>
> > Craig's point is not that CIP is impossible, but rather from a
> practical implementation side, it's easier to use other local stereo
> designations. I might be wrong, but the codes that I can think of with
> CIP implementations are all commercial, and as part of structure -> name
> features. Both CIP and IUPAC name generation are really painful.
>
> Painful or not, RDKit has CIP. From software dependencies POV I'd prefer
> to not have to use 2 different kits, but until you guys convince your
> peers CIP is sooo last century and everybody changes their data models,
> I'll take what works.
>
> OE has it too, apparently, but they won't let me check their code out
> because I'm in .edu and not a PI. (Plus we're a public database, they
> seem to have an issue with those.)
>
> Dima
>
>
>
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