No, this is a known bug with disconnected fragments. The canonical algorithm
does not canonicalize the fragments.
Geoff
> On May 27, 2017, at 4:20 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
>
> Should be the same. Can you provide the files?
>
>> On 27 May 2017 12:51 a.m., "xh s" <sxh....@gmail.com> wrote:
>> In my program I convert the molecule ClCCl.O.[Cl-] (from both SMILES and
>> OBMol) to canonical SMILES but get two different answers, ClCCl.O.[Cl-] and
>> ClCCl.[Cl-].O
>>
>> My question is, is the order of disconnected parts controlled by the
>> algorithm so that there is only one unique way?
>>
>> Thanks!
>> Xianghai
>>
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