Hi,
I can't reproduce this. The order of fragments should be canonical (the
algorithm takes this into account). What is the original source of the
OBMol that gives a different result?
For example, the following SMILES all convert to the same canonical form:
ClCCl.O.[Cl-]
O.ClCCl.[Cl-]
O.[Cl-].ClCCl
ClCCl.[Cl-].O
[Cl-].ClCCl.O
[Cl-].O.ClCCl
=> ClCCl.O.[Cl-]
Kind regards,
Tim
On Sat, May 27, 2017 at 4:50 PM, Geoff Hutchison <geoff.hutchi...@gmail.com>
wrote:
> 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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