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.enforceChirality=False

In [15]: AllChem.EmbedMolecule(mh,ps)
Out[15]: 0


but if I go back to the defaults I get the same lack of results that you
were seeing:

In [16]: ps.enforceChirality=True

In [17]: AllChem.EmbedMolecule(mh,ps)
Out[17]: -1



I'm not sure that there's a straightforward solution to this problem
without code changes, but I'll do a bit of looking to see if I can figure
something out.

-greg



On Thu, Mar 2, 2017 at 7:34 PM, Curt Fischer <curt.r.fisc...@gmail.com>
wrote:

> 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 conformers for a macrotriolide, macrosphelide A.
>
> *macrosphelide_a_smiles =
> 'C[C@H]1CC(O[C@H](C)[C@H](O)/C=C/C(O[C@@H](C)[C@@H](O)/C=C/C(O1)=O)=O)=O'*
> *m = Chem.MolFromSmiles(macrosphelide_a_smiles)*
> *mh = Chem.AddHs(m)*
> *AllChem.EmbedMultipleConfs(mh, useExpTorsionAnglePrefs=True,
> useBasicKnowledge=True)*
> *mb = Chem.MolToMolBlock(mh)*
>
> The EmbedMultipleConfs() call never terminates for me.  If I use a
> non-zero value for *maxAttempts*, the call does terminate, but when I
> look at *mb*, the coordinates for all atoms are zero.
>
> I've tried playing around with a few of the other options, without luck.
> Either all atom coordinates are still zero after *EmbedMultipleConfs()*,
> or the function call never terminates.
>
> Any chance someone knows how to coax this function into yielding a useful
> conformation for my molecule?
>
> Curt
>
>
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