I can't seem to get a consistent canonical smiles for some structures. sdf -> cansmi -> cansmi should give the same value for both cansmi, no? Here's an example where it doesn't (I have more from pubchem). They ALL have dot-separated structures? Should one expect a canonical order of fragments?
$ babel pubchem6202.sdf -ocan pubchem6202.can 1 molecule converted 19 audit log messages $ more pubchem6202.can OCCc1sc[n+](c1C)Cc1cnc(nc1N)C.[Cl-].Cl 6202 $ babel pubchem6202.can -ocan - OCCc1sc[n+](c1C)Cc1cnc(nc1N)C.Cl.[Cl-] 6202 1 molecule converted 28 audit log messages
pubchem6202.sdf
Description: Binary data
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