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 through old mail I realized t
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 confor
Hi Curt,
I believe that the problem here is caused by the number of specified chiral
centers in a ring. I'm basing that guess on the fact that if I turn off the
option to enforce chirality I get an answer very quickly:
In [12]: ps = AllChem.ETKDG()
In [13]: ps.randomSeed = 0xf00d
In [14]: ps.en
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
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, useBa
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