I don't think I understand the question. The Conformer object is normally
attached to/associated with a mol object.
-greg
On Sun, Aug 6, 2017 at 11:41 AM, Per Jr. Greisen <pgrei...@gmail.com> wrote:
> Thanks - worked perfectly if I was to do this conformers is there an easy
> way to transform between conformer object and molecule object?
>
> On Sun, Aug 6, 2017 at 4:11 AM, Ling Chan <lingtrek...@gmail.com> wrote:
>
>> Hello Per,
>>
>> Apparently the default for FindMolChiralCenters is that only explicitly
>> specified chiral centers are output. Try the following.
>>
>> Chem.FindMolChiralCenters(mh, includeUnassigned=True)
>>
>> As for AssignAtomChiralTagsFromStructure , I think it detects chirality
>> from 3D structures. You need atomic coordinates for it to work.
>>
>> Ling
>>
>>
>> On Sat, Aug 5, 2017 at 11:35 AM, Per Jr. Greisen <pgrei...@gmail.com>
>> wrote:
>>
>>> Hi all,
>>>
>>> I have an issue to correctly assign chirality through RDkit so I have
>>> the following isomers around a phosphorus atom:
>>>
>>> smiles = 'CCOP(C)(=O)SCC[NH+](C(C)C)C(C)C'
>>> m = Chem.MolFromSmiles(vx_smiles)
>>> mh = Chem.AddHs(m)
>>>
>>> m_s = Chem.MolToSmiles(Chem.MolFromSmiles(smiles),isomericSmiles=True)
>>>
>>> Chem.FindMolChiralCenters(mh)
>>>
>>> # returns none
>>> None
>>>
>>> #
>>> Chem.AssignAtomChiralTagsFromStructure(vxm_h)
>>> None
>>>
>>>
>>> How to resolve this - I am just starting to use RDkit and it is seems
>>> very promissing
>>>
>>> Thanks
>>>
>>>
>>> --
>>> With kind regards
>>>
>>> Per
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>
>
> --
> With kind regards
>
> Per
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
