stereochemical labels

[nbehrnd]

En route to prepare a C2 symmetric box ligand, I wonder about the line

opts.addStereoAnnotation = True

(line 25) in the unchanged file depict_ligands.py. Was this installed to add a small (R) or (S) next to the corresponding center -- similar to the example to the left in RDKit's cookbook here?

The setup I use relies on Python 3.11.7 to use a virtual environment amended by pip install -r ./requirements.txt and hence RDKit 2023.09.4 (as checked within Python's CLI by print(rdkit.__version__)) while any RDKit related package provided by Linux Debian intentionally was removed ahead of time. An entry of

C[C@H]1COC2=[N]1*[N]1=C(C2)OC[C@@H]1C a box01

in a file submitted to depict_ligands.py only yields an illustration

without the labels in .png and .svg file format. Later, I equally would like to add for instance either one of the two BINOLs. This is why the presence of the small markers in the eventual preview by Avogadro might be helpful to identify the wanted isomer.

box01.cjson.zip

[ghutchis]

That was certainly my goal - to indicate stereo wherever it's specified.

Maybe the first thing to check is whether something with a well-defined stereo (e.g., camphor or an amino acid) works first?

I'll check this against my version of RDKit - certainly I know they've found some subtle bugs in the depiction code from time to time.

[ghutchis]

Looking at the cookbook, it might also need:

from rdkit.Chem import rdCIPLabeler
rdCIPLabeler.AssignCIPLabels(…)