The ability to determine CIP rules is a nice feature to have but not really
necessary for most cheminformatics applications. If someone donates this
code it would certainly be considered a valuable addition. I rewrote most
of the sterochemistry code for OB a few years ago and never got around to
implementing CIP since it has limited applications (i.e. naming). The
OpenBabel system was inspired by this paper:
M. Perdih, M. Razinger, Stereochemistry and sequence rules: a proposal for
modification of the Cahn-Ingold-Prelog system, Tetrahedron: Asymmetry,
1994, Volume 5, Issue 5, 835-861
On Wed, Dec 4, 2013 at 5:20 PM, Ana Teixeira <analinoteixe...@gmail.com>wrote:
> 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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