Hi all, I was using the (relatively) new Chem.FindPotentialStereo() functionality and was wondering how to set chiral tags on atoms with the new descriptors. I couldn't find a function to do this, so I tried a workaround by using the 'old' SetChiralTag() function (see code below). However, the definitions of these two descriptors don't always match, leading to changes in stereochemistry. Is there a function to set chiral information with the new descriptors?
Any help would be appreciated! Cheers, Kas >>> import rdkit >>> from rdkit import Chem >>> print("rdkit version " + rdkit.__version__) rdkit version 2021.03.1 >>> mol1 = Chem.MolFromSmiles("C[C@@]12[C@](CCCC2)([H])CCCC1") >>> mol2 = Chem.MolFromSmiles("CC12C(CCCC2)CCCC1") >>> >>> si = Chem.FindPotentialStereo(mol1) >>> for element in si: ... print(f' Type: {element.type}, Which: {element.centeredOn}, Specified: {element.specified}, Descriptor: {element.descriptor} ') ... ... atom = mol2.GetAtomWithIdx(element.centeredOn) ... if element.descriptor == Chem.StereoDescriptor.Tet_CCW: ... atom.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CCW) ... elif element.descriptor == Chem.StereoDescriptor.Tet_CW: ... atom.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CW) ... Type: Atom_Tetrahedral, Which: 1, Specified: Specified, Descriptor: Tet_CCW Type: Atom_Tetrahedral, Which: 2, Specified: Specified, Descriptor: Tet_CW >>> print(Chem.MolToSmiles(mol1) + "\n" + Chem.MolToSmiles(mol2)) C[C@]12CCCC[C@@H]1CCCC2 C[C@]12CCCC[C@H]1CCCC2
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss