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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