Re: [Rdkit-discuss] Get conformers as independent mols?

[Taka S. <ser...@gm...>]

Dear Gustavo,

As Omar described, you can get each conformer with confId.
Here is an example for rendering multiple confromers with py3Dmol.
https://gist.github.com/iwatobipen/1fbf30ed6c21a4016ec4885c7fd614ed

I hope this will help you.

Thanks,

Taka

2021年1月8日(金) 8:48 Omar H94 <oma...@gm...>:

> Dear  Gustavo,
>
> The show_rdkit function has a "conf_id" keyword argument that takes the id
> of the conformer to display. You may see the documentation:
> http://nglviewer.org/nglview/latest/api.html#nglview.show_rdkit
>
> To get a conformer of a mol as an independent mol, you may use the
> following function which takes a mol and a conformer id then returns a new
> mol that has only the specified conformer:
>
> def ConfToMol(mol, conf_id):
>     conf = mol.GetConformer(conf_id)
>     new_mol = Chem.Mol(mol)
>     new_mol.RemoveAllConformers()
>     new_mol.AddConformer(Chem.Conformer(conf))
>     return new_mol
>
> I hope this works for you.
> Best regards,
> Omar
>
>
>
> On Fri, Jan 8, 2021 at 1:58 AM Gustavo Seabra <gus...@gm...>
> wrote:
>
>> Hi all,
>>
>> Could anyone please help me with ideas on how to visualize
>> molecule conformers inside a Jupyter notebook?
>>
>> I generate the conformers, for example, using:
>> AllChem.EmbedMultipleConfs(mol, numConfs=5)
>>
>> And would like to see them in 3D inside the notebook.
>>
>> I tried using NGLView(https://github.com/nglviewer/nglview), but it
>> only shows what I believe is the first conformer in the molecule. How can I
>> change the conformer shown? or maybe is there a way to convert the
>> conformers to Mol objects?
>>
>> Any idea would be greatly appreciated.
>>
>> Thank you!
>> --
>> Gustavo Seabra.
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>