Here's another problem case:

   [Cl].[Cl-].[Cl+]

There are six ways to write this SMILES, and the canonicalizer doesn't 
distinguish them:

   [Cl-].Cl.[Cl+]       
   Cl.[Cl-].[Cl+]       
   [Cl-].[Cl+].Cl       
   Cl.[Cl+].[Cl-]       
   [Cl+].[Cl-].Cl       
   [Cl+].Cl.[Cl-]

If you add another fragment, you get 24 choices, and so on (N! combinations, 
where N is the number of fragments).

Either the charge isn't being taken into account, or else fragments aren't 
being written in a canonical order.

Craig


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