Issue with oddt.toolkit

[Muela, Gerardo D]

To whom may concern, 

My name is Gerardo Muela. I am using ODDT to learn how it works and for research at the University of Texas at El Paso. I am running a Python Notebook that is inthis GitHub repository (https://github.com/oddt/jcheminf/blob/master/Snippet_2.ipynb) to see how ODDT works. I am reading ligand and protein files from a database to test the models with different data. It is reading the files correctly but, it is giving me an index error that is coming from the ob.py file from the oddt.toolkit package. In this email I attached some pictures of the code and the stack trace of the error. I would please like to know how can I solve this problem?

Sincerely, 

Gerardo Muela

[Maciek Wójcikowski]

Hi Gerardo,

Thanks for interest in ODDT. There has been a change in a limit and treatment of neighbors recently in 0.4 version. I've pushed yet another change today, to do it gracefully. What you see in these notebooks is the ligands in general set contain molecules that have atoms with connectivity > 6. I've run similar example and there are few organometallic compounds, mainly Rh,Rb etc. It doesn't hurt to skip the excessive bonds, since in most application there is no use for them. Current git master issues a warning when such atom is encountered and continues on. Please try to install recent git version of ODDT for your Notebook.

To update execute:

pip install -U --no-deps git+https://github.com/oddt/oddt.git

 

You need to have git installed for the command to execute (you can install it via conda). 

I've also noticed that the sample Notebooks are out of date (and not Python 3 ready). I'll update them and ping you back here.

I hope ODDT will turn out to be useful for your project.

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

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[Muela, Gerardo D]

Hello Maciek,

Thank you for the response and help on updating the Python Notebooks. This will be very helpful for my research. I'll go ahead an update the ODDT and let you know how it worked.  

Thanks,

Gerardo Muela

---

From: Maciek Wójcikowski <mac...@wojcikowski.pl>
Sent: Tuesday, August 8, 2017 11:07:10 AM
To: Muela, Gerardo D
Cc: od...@googlegroups.com
Subject: Re: Issue with oddt.toolkit

 

[Maciek Wójcikowski]

Hi Gerardo,

The snippets at https://github.com/oddt/jcheminf were updated. Also there is now ODDT 0.4.1 installable via pip and conda with introduced fixes.

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

[Muela, Gerardo D]

Hi Maciek,

Thank you for updating the snippets. I'll go ahead and update ODDT to the newest version. 

Thanks a lot,

Gerardo Muela

---

From: Maciek Wójcikowski <mac...@wojcikowski.pl>
Sent: Wednesday, August 9, 2017 6:54:43 AM