Re: [Rdkit-discuss] difficulties with AllChem.EmbedMultipleConfs() on a macrocycle

Thanks Greg! This was the impetus I needed to upgrade to 2017.03. I now confirm that conformer generation happens very quickly. It's so nice to be able to visualize so nicely with py3dmol too. Curt On Sun, May 7, 2017 at 9:37 PM, Greg Landrum wrote: > Going back

Re: [Rdkit-discuss] difficulties with AllChem.EmbedMultipleConfs() on a macrocycle

Going back through old mail I realized that I never did follow up on this one. It looks like these structures now embed (using the 2017.03.1 release). I assume that the changes I made to fix #1240 ( https://github.com/rdkit/rdkit/issues/1240) - which make the code more permissive in how the

Re: [Rdkit-discuss] difficulties with AllChem.EmbedMultipleConfs() on a macrocycle

Hi Curt, Yes, I’m sorry, I used accidentally a modified version of mine where I played with a new feature to favour longer distances. With the standard RDKit version, I also get no conformation for the molecule without Hs. I indend to commit this feature as an option, but did not yet manage to

Re: [Rdkit-discuss] difficulties with AllChem.EmbedMultipleConfs() on a macrocycle

Thanks for the notebook Sereina! Unfortunately when I run it I get different results. In your version, the very first call to EmbedMolecule() returns 0, which presumably means that embedding went OK. *## Embed the molecule without HsAllChem.EmbedMolecule(m, useExpTorsionAnglePrefs=True,

[Rdkit-discuss] difficulties with AllChem.EmbedMultipleConfs() on a macrocycle

Hi all, I really like combination of rdkit and py3dmol and have been able to replicate e.g. Greg's notebook here: http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/blob/master/notebooks/Trying%20py3Dmol.ipynb But I can't seem to get AllChem.EmbedMultipleConfs() to generate any valid