I think it is but prove me wrong. According to this: http://chemwiki.ucdavis.edu/Organic_Chemistry/Chirality/Absolute_Configuration,_R-S_Sequence_Rules 'R' is clockwise and 'S' is counterclockwise.
On Tue, Sep 8, 2015 at 3:08 PM, Noel O'Boyle <[email protected]> wrote: > You are assuming that CHI_TETRAHEDRAL_CW means "R" and v.v. for "S". I > don't think that's correct. > > On 8 September 2015 at 12:58, Michał Nowotka <[email protected]> wrote: >> Hi, >> >> I'm comparing stereo centers assigned by ChemAxon JChem and RDKit. >> >> The code would be: >> >> #---------------------------------------------------------------------------------------------------------------------- >> >> from rdkit import Chem >> >> def getStereoInfo(smiles): >> ret = [] >> mol = Chem.MolFromSmiles(smiles) >> Chem.AssignStereochemistry(mol, flagPossibleStereoCenters=True, >> force=True) >> for atom in mol.GetAtoms(): >> stereo = str(atom.GetChiralTag()) >> atomIndex = atom.GetIdx() >> if str(atom.GetChiralTag()) != "CHI_UNSPECIFIED": >> if stereo == "CHI_TETRAHEDRAL_CW": >> chirality = "R" >> elif stereo == "CHI_TETRAHEDRAL_CCW": >> chirality = "S" >> else: >> chirality = "R/S" >> ret.append({"atomIndex":atomIndex,"chirality":chirality}) >> return ret >> >> #------------------------------------------------------------------------------------------------------------------- >> >> Now for (1R,2S,3S)-1,2,3-trichlorocyclopentane >> (Cl[C@H]1CC[C@@H](Cl)[C@H]1Cl), both RDKit and JChem give the same >> results: >> https://dl.dropboxusercontent.com/u/10967207/a.png >> >> But for ephedrine (O[C@H](c1ccccc1)[C@@H](NC)C) stereo centers are >> reversed. RDKit gives: >> https://dl.dropboxusercontent.com/u/10967207/b.png >> >> and JChem gives: >> https://dl.dropboxusercontent.com/u/10967207/c.png >> >> The same is shown by pseudo-ephedrine (O[C@@H](c1ccccc1)[C@@H](NC)C) >> which returns both stereo centers as 'R'. >> >> Is that a bug or an expected behavior? Are there any parameters in >> RDKit that can be set to get results similar to JChem? >> >> Regards, >> >> Michał Nowotka >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
