I was just wondering if there is a way to convert isomeric SMILES to canonical SMILES? Is it okay to use the RDKit Canon SMILES nodes to generate canonical SMILES after using isomeric Smiles to generate the molecule structure?
Does it make a difference which type of SMILES I use to generate 2D descriptors?
In short: RDKit’s canonicalisation node will not remove the isomeric features of the molecule, however, it might change the SMILES string itself (e.g.: F/C=C/F and F\C=C\F will be canonicalised to F/C=C/F and F/C=C\F or F\C=C/F to F/C=C\F ).
I am not sure what 2D descriptors do you want to use, and how are they implemented, therefore I can not guarantee you anything. However, in general, I would suggest to standardise - canonicalise - your molecules as much as your use-case allows you in order to avoid surprises arising from the representation of the molecule.
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