Ah, it is a bug (or I regard it as one). This is a difference in how
explicit hydrogens are handled, and is fixed by #1576 (
https://github.com/openbabel/openbabel/pull/1576).
For the moment, to get the same canonical smiles string in this case, you
need to remove the hydrogens using "-d".
ClCCl.[Cl-].O vs ClCCl.O.[Cl-]
(with #1576 they both give ClCCl.[Cl-].O)
There is still a "unimplemented feature", and I think this is what Geoff
was thinking of. The order within the individual dot-disconnected SMILES is
not canonical (if I remember correctly).
- Noel
On 31 May 2017 10:54 p.m., "xh s" <sxh....@gmail.com> wrote:
> 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
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> OpenBabel-discuss mailing list
>>>> OpenBabel-discuss@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>
>>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
