Yes, I have two instances of MarvinSketch JS - one configured to use official ChemAxon web services, the second one is configured to use Beaker so effectively RDkit. But this is just to provide illustration I check it manually as well with the function provided in original post and JChem.
On Tue, Sep 8, 2015 at 2:36 PM, John M <john.wilkinson...@gmail.com> wrote: > Noel pointed out I probably wasn't clear with the CCG comment. RDKit uses > this algorithm which is what I was referring to - > http://www.chemcomp.com/journal/chiral.htm > > Just to clarify - you're showing all images from MarvinSketch JS. How are > you putting the data in to the editor? > > John > > Regards, > John W May > john.wilkinson...@gmail.com > > On 8 September 2015 at 13:58, Michał Nowotka <mmm...@gmail.com> wrote: > >> As I'm not a chemistry expert, let me forward a message from my colleague, >> which shows another example, where RDkit seems to return incorrect results: >> >> >> MJ150720 >> >> 14 14 0 0 0 0 0 0 0 0999 V2000 >> -4.9107 0.2893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -5.6251 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -5.6251 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -4.9107 -1.3607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -4.1962 -0.9482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -4.1962 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -2.7675 0.8911 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 >> -2.7673 -0.1231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -3.3923 -0.7249 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >> -3.3701 -1.7178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -2.0528 0.2893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -3.8707 0.9392 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 >> -3.3925 0.2670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> -1.9262 -0.5010 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 >> 1 2 2 0 0 0 0 >> 2 3 1 0 0 0 0 >> 3 4 2 0 0 0 0 >> 4 5 1 0 0 0 0 >> 5 6 2 0 0 0 0 >> 6 1 1 0 0 0 0 >> 8 11 1 0 0 0 0 >> 6 13 1 0 0 0 0 >> 13 8 1 0 0 0 0 >> 13 7 1 1 0 0 0 >> 13 12 1 6 0 0 0 >> 8 14 1 1 0 0 0 >> 8 9 1 6 0 0 0 >> 9 10 1 0 0 0 0 >> M END >> >> Taking this example of (-)-ephedrine (1R,2S) and depicting it as shown in >> this webpage ( >> http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/sterism3.htm “Two >> or more chiral centres") - we can see that marvin gives the correct stereo >> centres. >> >> And after cleanup, it’s still the same: >> >> >> RDKit however, gives this (it’s mislabeled a hydrogen, lets clean it up) >> >> >> After cleanup, the stereo centres are still incorrect. >> >> >> >> >
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