A little about Chirality, 3D, etc…
There is two importants information that you need to take into account.
Lot of the olfactive molecules are based or originally discovered in nature. Generally Nature is very economic so a little molecular modification can have a huge difference in term of Odor. This is basically due to the high interaction of a given molecule to a serie of olfactive receptors. In over words, this is not linear and really related to ligand protein interaction.
Two things that may help you:
- when we know totally 3D of a molecule. it’s written in the SMILES. Using RDKit tool you can have a canonical (unique) representation of this molecule, E/Z represent (encoded by those charaters /,) is very important in the 3D, another one called R/S is also represented in the SMILES and can be encoded in GCN. If, we can produce / purify this particular molecule and smell it. Then you will have one (but human response can vary time to time) olfactive sentence to describe it.
- when you cannot purify / separate / create a pure potentially chiral molecule. You may have in the best situation (if only one chirality center) two molecules in a mixture generally 50/50. in this conditions, you have the overlap of two olfactive descriptions (it’s not really linear cause the power of the two isomers can be also different!).
As you can see, we have like in pharmaceutical challenges and chemical databases a part of the molecules that are 3D unique and this part vary based on the target. Finally, in Pharma, between 30-50% of drugs are pure 3D molecules.