Re: [Rdkit-discuss] Enumerate Torsion angles

[Ivan Tubert-Brohman]

Hi Rohit,

Could you attach a complete example? I took the script from the email you
refer to, only edited the line that says mol = Chem.MolFromSmiles('CC')
to make it say mol = Chem.MolFromSmiles('CC'), and when I run it I get nine
torsions:

(2, 0, 1, 5)
(2, 0, 1, 6)
(2, 0, 1, 7)
(3, 0, 1, 5)
(3, 0, 1, 6)
(3, 0, 1, 7)
(4, 0, 1, 5)
(4, 0, 1, 6)
(4, 0, 1, 7)

Ivan

On Wed, Oct 19, 2022 at 3:36 AM Rohit Modee 
wrote:

> Hi,
>
> I am using enumeratetorsion angle function from this post
> https://sourceforge.net/p/rdkit/mailman/message/34554615/
> Re: [Rdkit-discuss] detect dihedral angles in a conformation
> 
> Re: [Rdkit-discuss] detect dihedral angles in a conformation Open-Source
> Cheminformatics and Machine Learning
> sourceforge.net
>
>
> The problem is if we provide Ethane or propane, it misses a few dihedrals.
>
> below for ethane, it misses atoms 6 and 5. No dihedrals for them.
>
>
> Similarly, for propane, it misses atom 11 and 12 dihedrals.
>
> What I expect it to have is say 11-3-2-1 and 12-3-2-1.
>
>
> Is there a way to get those missing dihedrals.
>
> Regards,
> Rohit Modee
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> Rdkit-discuss mailing list
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>
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[Rdkit-discuss] Call for documentation writers

[Téletchéa Stéphane]

  
  
Dear all,

I had the chance to go to RDKIT UGM last week, and amongst various
discussions, 
I stepped up to provide and/or organize some documentation.

During the hackhathon I had the opportunity to set up a raw list of
wishes, nothing spectacular,
but with in mind the possibility of:
- setting up contribution rules for people willing to help in
documentation
- determine 2/3 topics that could illustrate non-trivial features
- allowing to assemble already discussed topics (but long time ago),
and/or provide other visuals for specific features (tables, images,
etc).

We worked on such a project 2 years ago, having in mind Google's
sponsored "Season Of Docs",
but unfortunately the project could not go further: 

https://docs.google.com/document/d/1GuhKrAb0biZD3sc1qZWYJXQGUFLFoMgjnoxEx_A6Cvw/edit

This is thus officially the new day 1 of documentation contribution
to this wonderful project.
I'll set up some preliminary data from the notes taken last week,
but don't hesitate to reply to this list,
and/or to me directly, I know some people have already stepped up,
kuddos to them.

All the best,

Stéphane

-- 
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
  


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[Rdkit-discuss] Enumerate Torsion angles

[Rohit Modee]

Hi,

I am using enumeratetorsion angle function from this post 
https://sourceforge.net/p/rdkit/mailman/message/34554615/
Re: [Rdkit-discuss] detect dihedral angles in a 
conformation
Re: [Rdkit-discuss] detect dihedral angles in a conformation Open-Source 
Cheminformatics and Machine Learning
sourceforge.net


The problem is if we provide Ethane or propane, it misses a few dihedrals.

below for ethane, it misses atoms 6 and 5. No dihedrals for them.

[cid:33854ad4-adfe-47b3-92e6-1c3849d46e04]

Similarly, for propane, it misses atom 11 and 12 dihedrals.

What I expect it to have is say 11-3-2-1 and 12-3-2-1.

[cid:8514f059-57cc-42e3-992d-40707ee6bbd6]

Is there a way to get those missing dihedrals.

Regards,
Rohit Modee
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