Going back through old mail I realized that I never did follow up on this
one.
It looks like these structures now embed (using the 2017.03.1 release). I
assume that the changes I made to fix #1240 (
https://github.com/rdkit/rdkit/issues/1240) - which make the code more
permissive in how the conformers are filtered - are responsible for that.
-greg
On Sat, Mar 4, 2017 at 7:39 AM, Greg Landrum <greg.land...@gmail.com> wrote:
> 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/Tryi
>> ng%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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>
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