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

Reply via email to