Thanks, I got confused by the function description found here: http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html <http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html>
In the description it says: rdkit.Chem.rdmolops.AssignStereochemistry((Mol)mol[, (bool)cleanIt=False[, (bool)force=False[, (bool)flagPossibleStereoCenters=False]]]) → None : <http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.AssignStereochemistry> Does the CIP stereochemistry assignment for the molecule’s atoms (R/S) and double bond (Z/E). Chiral atoms will have a property ‘_CIPCode’ indicating their chiral code. ARGUMENTS: mol: the molecule to use cleanIt: (optional) if provided, atoms with a chiral specifier that aren’t actually chiral (e.g. atoms with duplicate substituents or only 2 substituents, etc.) will have their chiral code set to CHI_UNSPECIFIED. Bonds with STEREOCIS/STEREOTRANS specified that have duplicate substituents based upon the CIP atom ranks will be marked STEREONONE. force: (optional) causes the calculation to be repeated, even if it has already been done flagPossibleStereoCenters (optional) set the _ChiralityPossible property on atoms that are possible stereocenters C++ signature : void AssignStereochemistry(RDKit::ROMol {lvalue} [,bool=False [,bool=False [,bool=False]]]) Just to be on the safe side the above function does n ot do the CIP stereochemistry assignment? Best, Zoltan On 27 Sep 2019, at 21:59, Dan Nealschneider <dan.nealschnei...@schrodinger.com> wrote: RDKit stores absolute configuration around atoms using parity (which is based on atom index), not CIP codes. This has oodles of benefits, for instance you can represent absolute configuration of atoms in achiral structures like 1,4-dimethylcyclohexane. So, yeah - AssignStereochemistry is intended to produce different results with different atom sequences. If you need Cahn/Ingold/Prelog-style R or S for display, maybe try: from rdkit import Chem print(Chem.FindMolChiralCenters(mol)) https://github.com/rdkit/rdkit/blob/2d8bb6c1687a2fa78f66fc61966544e5f44f157c/rdkit/Chem/__init__.py#L80 <https://github.com/rdkit/rdkit/blob/2d8bb6c1687a2fa78f66fc61966544e5f44f157c/rdkit/Chem/__init__.py#L80> dan nealschneider | senior developer <https://www.schrodinger.com/> On Wed, Sep 25, 2019 at 2:35 PM Zoltan Takacs <zozo...@gmail.com <mailto:zozo...@gmail.com>> wrote: Dear RDkitters, I am playing around with the assignstereochemistry function and I am getting confused. If I change the numbering of the atoms but not their coordinates (for example switch to canonical numbering) I get a different answer. In fact it only seems to work right when I switch to canonical numbering with openbabel. What rules does the function follow? Is there any role played by the numbering of atoms? Do they have to be numbered in any special way for example the groups need to follow each other when assigning CIP priority? Thanks _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net <mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
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