How should a stereocenter with undefined configuration be interpreted?
No SMILES or OpenSMILES documentation explains this point. If it is not addressed, implementations will need to invent their own rules, which can cause data loss.
Options:
Either. One or the other descriptor is present, but which one is unknown.
Mixture. A mixture of configurations of unknown ration is present.
(1) or (2)
For its part, V2000 uses this interpretation: "It could be either of two stereoisomers, or a mixture of the two." In other words, (3).
Given the large number of V2K<->SMILES conversions being performed, and given no clear advantage to any option, (3) makes the most sense.
How should a stereocenter with undefined configuration be interpreted?
No SMILES or OpenSMILES documentation explains this point. If it is not addressed, implementations will need to invent their own rules, which can cause data loss.
Options:
For its part, V2000 uses this interpretation: "It could be either of two stereoisomers, or a mixture of the two." In other words, (3).
Given the large number of V2K<->SMILES conversions being performed, and given no clear advantage to any option, (3) makes the most sense.
See also the discussion here.