Hi Rocco,
Point taken. I don’t think you’d be able to get RDKit to spit such SMILES
strings out unless you tortured it pretty hard, however.
Dave
On Mon, 18 Nov 2019 at 16:36, Rocco Moretti <rmoretti...@gmail.com> wrote:
> Actually, it is possible to get arbitrary orders, if you (ab)use the '.'
> component ("zero order bond") directive and the numeric bonding ("ring
> closure") directives:
>
> >>> Chem.MolToSmiles( Chem.MolFromSmiles("O1.Cl2.C12" ) )
> 'OCCl'
>
> Whether you want to do things that way is another question.
>
> On Mon, Nov 18, 2019 at 10:24 AM David Cosgrove <
> davidacosgrov...@gmail.com> wrote:
>
>> Hi Rafal,
>> It is not always possible to preserve the atom ordering in the SMILES
>> string because there is an implied bond between contiguous symbols in the
>> SMILES. I think, for example, that the molecule with the SMILES OCCl
>> couldn’t have the order in the molecule object O first, Cl second, C third,
>> with bonds between 1 and 3 and 2 and 3 and get the SMILES in that order.
>>
>> I hope that made sense. Please ask again if not.
>>
>> Best regards,
>> Dave
>>
>>
>> On Mon, 18 Nov 2019 at 12:33, Rafal Roszak <rmrmg.c...@gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> Is there any way to preserve atom order from Mol object during
>>> exporting to smiles? I tried MolToSmiles with rootedAtAtom=0 and
>>> canonical=False options but it not always prevent oryginal order.
>>> I know I can use _smilesAtomOutputOrder to map old indices to new one
>>> in canonical smiles but maybe we have something more handy?
>>>
>>> Best,
>>>
>>> Rafał
>>>
>>>
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>> --
>> David Cosgrove
>> Freelance computational chemistry and chemoinformatics developer
>> http://cozchemix.co.uk
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
