Greg, thx for answer > In the RDKit the chiral order is determined by the order of the atom's > bonds. Here's a bit of code showing how to get the neighboring atoms in the > correct order:
Your code tells that atom.GetBonds() return correct order, but the order is simple numerical order and chiralTag corresponds to the numerical order (not to chiral tag in smiles string). So the following code should give the same result: for atom in m.GetAtoms(): if atom.GetChiralTag() not in (Chem.CHI_TETRAHEDRAL_CCW,Chem.CHI_TETRAHEDRAL_CW): continue print( atom.GetChiralTag(), sorted([n.GetIdx() for n in atom.GetNeighbors()]) ) Is it correct? Best, Rafal _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
