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 <omar8...@gmail.com>: > 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 <gustavo.sea...@gmail.com> > 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 >> 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 >
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