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, useBasicKnowledge=True)Out[7]: 0*


When I run your notebook, this same call returns -1.  Maybe my rdkit is
different than yours?  I'm using '2016.09.2' on Mac OSX 64-bit.



On Thu, Mar 2, 2017 at 12:00 PM, Sereina <sereina.rini...@gmail.com> wrote:

> Hi Curt,
>
> This is an interesting one. If you add the hydrogens before generating the
> conformer as in your example, then no conformation can be found. However,
> if you add them *after* the conformer generation, it works fine. Maybe that
> could serve as a work around for you. I attach a notebook as illustration.
> As this occurs with both DG and ETKDG, it may be due to the tests to ensure
> that the chiral centers are correct. I will have a closer look (hopefully
> with Greg’s help).
>
> Best,
> Sereina
>
>
>
>
>
> On 02 Mar 2017, at 19:34, 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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