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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