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

[Curt F. <cur...@gm...>]

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