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 [email protected] On 8 September 2015 at 13:58, Michał Nowotka <[email protected]> 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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