[Q&A] Represent Cis-Trans in SMILES Notation of Functional Groups in the Ring (No identifying bond type of ring) #4593
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I want to ask that is there any representation that can push SMILES support initial thought about functional group direction in ring. In particular, let's say that, Cyclo-hexane or benzene for example, and inserting functional groups (example: Methyl to be easy). In the SMILES Notation, I should expect it can somehow draw or represent partially the direction to be drawn even though the molecular fingerprint would be identical. Cyclo-hexane ( (Z)-1,2-Me2 == (E)-1,2-Me2 == ... Reference: Compresive Handbook of Bond Dissociation Energies of Yu Ran Luo (2007) --> Page 35, 36 |
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Hi, I hope I've understood the question correctly.
In this situation cis/trans isn't the correct terminology as far as the RDKit is concerned. Within the RDKit cis/trans applies to bonds, but here we're dealing with atomic stereochemistry: chirality
Are you asking how to distinguish between these two structures?