> Sounds like two different semantics of compare method; obviously both have
> reasons to exist.  The authors know better, but the current implementation
> seems to have in mind e.g. graph algorithms, where atoms are distinct graph
> nodes.  The other interpretation, comparing atoms themselves is useful, but a
> bit trickier - should it include equality of atom symbols only, or atom
> types, aromaticity flags, bond flags, 3D coordinates of atoms, etc?  IMHO
> matcher classes are better suited for this purpose.

So perhaps rename the method to clearly state that it is comparing identity?

-- 
// Jonathan

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