Hello Alfredo,
The tag "CHI_TETRAHEDRAL_CW" means clockwise and CCW means anti-clockwise (I have no idea why it is coded CCW rather than ACW, but whatever ;) ). These chiral tags are related but not corresponding to the absolute chirality (R/S) defined in organic chemistry. Look at the SMILES you provided and you will find that both of the chiral carbons are [C@@H]. According to the theory of Smiles in DayLight (https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html 3.3.3) > The symbol "@" indicates that the following neighbors are listed > anticlockwise (it is a "visual mnemonic" in that the symbol looks like an > anticlockwise spiral around a central circle). "@@" indicates that the > neighbors are listed clockwise (you guessed it, anti-anti-clockwise). Then you may have realized that the tags "CHI_TETRAHEDRAL_CW" are corresponding to your SMILES but not the real chirality. I suggest you read the chapter 3.3.3 to understand the meaning of "chiral tag", then you will understand why they are not the absolute chirality. Absolute chirality depends on the chiral tag as well as the CIPRanks of the neighbor atoms. That is why the chirality of the two carbons are different while their chiral tags are the same. I am not sure if Lukas had the same question? Best regards, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics On 10/29/2019 21:14，Alfredo Quevedo<maquevedo....@gmail.com> wrote： Good morning, I am trying to manually set/change the stereochemistry of a chiral center of a molecule, and I cant understand how to set the CHI_TETRAHEDRAL_CW/CHI_TETRAHEDRAL_CCW tag on a certain atom. So far my script does the following: ----- from rdkit import Chem from rdkit.Chem import AllChem molecule='C[C@@H](C(=O)COc1c(F)c(F)cc(F)c1F)n1cc([C@@H](NCc2ccc3c(c2)OCO3)c2ncc[nH]2)nn1' molecule_smiles=Chem.MolFromSmiles(molecule) chiralty=Chem.FindMolChiralCenters(molecule_smiles) centers=len(chiralty) for i in range(centers): current_center=chiralty[i][1] print(current_center) center_to_change=chiralty[i][0] print(center_to_change) for a in molecule_smiles.GetAtoms(): print(a.GetChiralTag()) ---- executing the above mentioned script I can see that the molecule has 2 chiral centers, the first one on index 1, which is S, and the second one, with index 19, which is R. Both chiral tags are set to: CHI_TETRAHEDRAL_CW. now, I want to manually change the configuration of index 19 to S, so I want to change its tag to CHI_TETRAHEDRAL_CCW. Which would be the command to set this tag and how is the index indicated? thanks in advance for the help, kind regards Alfredo
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