On 16 November 2012 13:18, <ralf@ark.in-berlin.de> wrote:
John, Egon, and me seem to have come to an optimal solution
regarding a long-standing issue, i.e., why the user has to
call isConnected (doing an unnecessary graph walk) and then
partitionIntoMolecules() to separate parts of a Smiles molecule,
when the parts could be easily gotten from the parser itself.
There will soon be an additional accessor to the parser returning
an AtomContainerSet. This will also make it easy to enable
display disconnected Smiles in JCP. (It wasn't difficult before,
it just wasn't implemented)

Since this also concerns a user's request, I have set Cc accordingly.

If the suggestion is for the SMILES parser to return AtomContainerSet instead of a single molecule, I believe it is not the right approach. It might be useful for visualisation purposes, but not for calculations (yes, there are prediction algorithms who take a 'disconnected' salt). 

Best regards,

Ralf Stephan

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