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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