gt; And I tried to use UFFAddTorsionConstraint for an example.
> https://gist.github.com/iwatobipen/42c325f2471166ff4084051381d0ef78
> By using these method I think you can keep the torsions.
> Thanks.
>
> Taka
>
> 2020年4月26日(日) 19:35 Bruce Milne :
>
>> Hi Taka,
>&g
rs with user defined
> cores.
>
> https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock
> http://rdkit.blogspot.com/2019/01/more-on-constrained-embedding.html
> Thanks,
>
> Taka
>
>
>
uce F. Milne
CFisUC
Department of Physics
University of Coimbra
Rua Larga
3004 - 516 Coimbra
Portugal
https://orcid.org/-0002-5522-4808
https://publons.com/researcher/2905148/bruce-milne/
https://www.linkedin.com/in/brucemilne
A/h = S/k
___
Rdkit-di
Hi,
Did you try setting the length of the fingerprint (fpSize) to a higher value
than the default 2048 to see if you can get one with 0's?
Cheers,
Bruce
>
> Message: 2
> Date: Thu, 1 Jun 2017 16:28:40 +0200
> From: Nils Weskamp
> To: Rdkit-discuss@lists.sourceforge.net
> Subject: [Rdkit-discus
Hi Greg,
Thanks, that makes sense. I see the table has only charged/protonated atom
types for nitrogen. Obvious once you look at it... ;)
Cheers,
Bruce
On 16 May 2017 at 06:53, Greg Landrum wrote:
> Hi Bruce,
>
>
>
> On Mon, May 15, 2017 at 3:46 PM, Bruce Milne wrote:
>
Hi,
I've noticed that if I define a molecule as neutral, positive and negative
(depending on protonation) the EState indices calculated by RDKit reflect
the changes as expected:
m = Chem.MolFromSmiles('CCO')
m_neg = Chem.MolFromSmiles('CC[O-]')
m_pos = Chem.MolFromSmiles('CC[OH2+]')
EState indi
:
AllChem.MMFFOptimizeMoleculeConfs(m, numThreads=0, mmffVariant='MMFF94',
confId=id)
print >>file('{0}{1}.mol'.format('conformer_', count),
'w+'),Chem.MolToPDBBlock(m,
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