Hi guys,
I got completely puzzled by stereochemistry and the way to set it in rdkit. Among others we use rdkit to get 2D depictions. What I do in my code is that I construct molecule from scratch and set chiral tags to CHI_TETRAHEDRAL_CW for R, CHI_TETRAHEDRAL_CCW for S (this is the metadata we have for each atom, where applicable), otherwise CHI_UNSPECIFIED. Then I run sanitization on the molecule and generate images. That seems to be working incorrectly even for simple cases: e.g.: https://pdbe.org/chem/004 When constructing the molecule I set the stereocenter for the CA atom to CHI_TETRAHEDRAL_CCW (S), but when I then try to perceive the R/S by FindMolChiralCenters(force=false) it says ‘R’, so as the image. This is wrong. I can also directly set _CIPCODE for each atom where applicable to S/R directly (along with the chiral tags). Then the chiral atom is perceived as S by FindMolChiralCenters(force=false), but then again the image still says R. When I set neither the chiral tag nor the _CIPCODe and run AssignAtomChiralTagsFromStructure() and AssignStereochemistry() on the mol the atom under question gets atom tag CHI_TETRAHEDRAL_CW (I assume incorrectly), the _CIPCODE is correct (S) and the image is correct (why????) as well (attached). So my question is, how do I set stereochemistry on individual atoms, so that it is perceived by rdkit and is not overwritten in any subsequent step. I hope the above mentioned description makes at least some sense. If not, I’ll try to distill a code sample for constructing this molecule from raw data. I also reproduced the same steps on the http://pdbe.org/chem/THR, which also gives wrong results when I set chiral tags manually (bond wedging should not be on methyl group I assume. Interestingly here the setting chiral atoms from the structure by rdkit gives incorrect results as well (attached). For rdkit set tags I get CA - CHI_TETRAHEDRAL_CCW (S) – (correct) CB - CHI_TETRAHEDRAL_CCW (R) – (incorrect should be TETRAHEDRAL_CW - R) I’d be grateful for any piece of advice. Because I have no idea what I have been doing wrong the whole time. My settings: Rdkit: 2019.09.1/2019.03.2 Conda: 4.7.12 Python 3.7.4 os mac 10.15 Best, Lukas
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