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

[Sereina]

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  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  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  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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> 
> 

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[Rdkit-discuss] 6th RDKit UGM in Berlin

[Volkamer, Andrea]

Dear all,

this year's RDKit User Group Meeting will take place from 20-22 September in 
Berlin, Germany and is being co-hosted by Andrea Volkamer (Charité - 
Universitätsmedizin Berlin) and Gerhard Wolber (Freie Universität Berlin).

Registration for the RDKit UGM is free:
https://www.eventbrite.com/e/6th-rdkit-ugm-2017-tickets-32526309066

We've gotten positive feedback about what has become the standard format for 
the UGM, so we plan to stick with that for this year:
Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, and 
talktorials. For those who haven’t attended before, talktorials are somewhere 
between a talk and a tutorial, they cover something interesting done with the 
RDKit and include the code used to do the work. During the presentation you'll 
give an overview of what you did and also show the pieces of the code that are 
central to the work. The idea is to mix the science up with the tutorial 
aspects.
Day 3 will be a hackathon: those who choose to stay will spend an intense day 
working in small groups to produce useful artifacts: new bits of code, KNIME 
nodes, KNIME workflows, tutorials, documentation, IPython notebooks, etc. We 
will once again try to structure this a bit by collecting a bunch of ideas for 
things to work on in advance. Last year we also did extended tutorials on Day 3 
if there are volunteers to do tutorials and people interested in attending 
them, we'll repeat that this year as well.

There will also be, of course, social activities.
A more detailed announcement with additional information about place, hotels 
and logistics will follow soon.

We are looking for people who are willing to do presentations, talktorials or 
posters on the first two days. If you're interested in contributing, please 
send us an email.

Lighting talks don't need to be arranged too far in advance; we will start 
collecting the list of people interested in doing those shortly before the 
event.

Best Regards,
Greg, Gerhard and Andrea



Prof. Dr. Andrea Volkamer

In-silico Toxicology Group
Institute of Physiology, Charité Universitätsmedizin Berlin
https://physiologie-cbf.charite.de/en/institute/workgroups/team_volkamer/

Campus Mitte: Virchowweg 6, 10117 Berlin/ Philippstraße 13, Haus 18, 10115 
Berlin

Phone: +49 30 - 450 528 554 / 209 347 938
E-Mail: andrea.volka...@charite.de
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