I am trying to generate InChIs (Codes as well as Keys) from Molecules. Now using the RDKit Node comes in very handy. But the node actually says that it requires an RDKit Column, but works perfectly fine with an SDF. Is it internally converting the SDF to an RDKit Molecule?
If so: how are Molecules represented in RDKit? Is the 2d/3d information, present in the SDF, kept somehow or is it a graph representation and the coordinates are calculated by RDKit itself?
I am asking this, because, as far as I know, InChI can infer stereochemistry from 3D molecules even if not labeled correctly. So for me it would be important to know if I have to delete the 3D information before generating InChIs to be certain that all molecules are treated similar independent of their 2D/3D depiction in the original SDF.
I know this probably in not a two sentence answer so:
Is there any documentation on the mol class and how molecule representations are treated when read in to RDKit as molecule and converted back to the original format? Then I’ll gladly read that and come back with more specific questions.
Looking forward to your answers,