Hi Tim,
I was able to convert the problematic molecule to a SDF file and reproduce
the error. Here's the test.sdf file. I used "obabel test.sdf -Otest.can".
OpenBabel05311714443D
7 4 0 0 0 0 0 0 0 0999 V2000
1.6789 -1.9571 0.9205 Cl 0 5 0 0 0 0 0 0 0 0 0 0
2.9546 -0.8420 0.3747 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7238 -0.0642 1.7843 Cl 0 0 0 0 0 0 0 0 0 0 0 0
4.2107 -1.8015 -0.4843 Cl 0 0 0 0 0 0 0 0 0 0 0 0
0.7232 1.4157 -0.6233 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.0756 1.0202 -0.3210 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5841 -0.0998 -0.3221 H 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
6 5 1 0 0 0 0
7 5 1 0 0 0 0
M CHG 1 1 -1
M END
$$$$
Best regards,
Xianghai
On Wed, May 31, 2017 at 8:09 AM, Tim Vandermeersch <
tim.vandermeer...@gmail.com> wrote:
> 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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