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 do so. I will try to get to it 
in the next days and then write a short email to the mailing list when it is in.

Best,
Sereina


On 03 Mar 2017, at 00:15, Curt Fischer <curt.r.fisc...@gmail.com> wrote:

> 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 Hs
> AllChem.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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