Does JUMBO understand aromaticity?
This is typical of a wide range of questions about the level of detail and the algorithmic support that JUMBO provides. Molecular science has many ways of representing concepts, some of which map onto each other and some that conflict. JUMBO does not try to provide a single ‘correct’ view, nor does it attempt to translate between different represenations. For example, aromaticity can be defined by alternating single/double bonds (Kekulé); by ‘aromatic’ bonds (e.g. -5 in CCDC files) or by ‘aromatic atoms’ (e.g. SMILES uses lowercase as in ‘c1ccccc1’ for benzene.) These are not always reconcilable either at the algorithmic or the human level. JUMBO does its best to display the information usefully. Ultimately this may mean translating some of these concepts into a JUMBO-centric approach. (Remember that CML does not specify how this type of information should be carried and allows individual freedom). It is unlikely that JUMBO, as a core tool, will convert from one representation to anoth
