thank you very much Hongbin for the detailed answer and for pointing the information. So, it is possible to manually change the tag from CW to CCW? kind regards
Alfredo Enviado desde BlueMail En 30 de octubre de 2019 01:32, en 01:32, Greg Landrum <greg.land...@gmail.com> escribió: >Hongbin has the answer here completely correct (thanks Hongbin!). > >And the reason it's CCW instead of ACW is that I say "counterclockwise" >and >not "anticlockwise" :-) > >-greg > >On Wed, Oct 30, 2019 at 3:07 AM Hongbin Yang <yanyangh...@163.com> >wrote: > >> 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> >> <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 >>> >>> >>> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>
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