Re: [Rdkit-discuss] Getting rdkit to work with Anaconda Python 3.5.x

Sun, 22 Jul 2018 13:27:01 -0700

I downgraded rdkit to 2017.09 and that resolved the problem. I had already downgraded Python to 3.5.4. You need to do both of these downgrades. First downgrade Python, then downgrade rdkit. Now everything is working. Including all the other stuff like pandas, jupyter, etc.

If I just want the latest rdkit, it works fine with the Anaconda3 Python 3.6. I have scripts that want to use both rdkit and tensorflow, however.

Jon T. Swanson, Ph.D.

ChemModeling, LLC
Suite 101, 500 Huber Park Ct.
Weldon Spring, MO 63304

(636) 329-0300


-------- Original Message --------
Subject: [Rdkit-discuss] Getting rdkit to work with Anaconda Python
3.5.x
From: <[email protected]>
Date: Sun, July 22, 2018 2:08 pm
To: "RDKit Discuss" <[email protected]>

Hi,

Does anyone have a magic recipe for getting rdkit to work with python 3.5 in Anaconda3?

I am trying to create a conda environment that will allow me to run rdkit and tensorflow.

I have Anaconda3 installed (Windows 10). That installs Python 3.6 by default.

So I created an environment for Python 3.5 (which is what tensorflow wants)

conda create -n py35 python=3.5
activate py35
conda install -c anaconda tensorflow
conda install -c rdkit rdkit

both install.

Tensorflow works, but

from rdkit import Chem

gives

Fatal Python error: PyThreadState_Get: no current thread

I read some old posts on this and downgraded Python to 3.5.4, then 3.5.3 and finally 3.5.0. I've tried removing and recreating the environment. Same error. I've tried just installing rdkit. Same error.

I've spent all day on this, I'm hoping someone has tried this and has a solution!

Is there a specific rdkit version I should try? People must have run rdkit in Anaconda with Python 3.5 in the past.

Jon T. Swanson, Ph.D.

ChemModeling, LLC
Suite 101, 500 Huber Park Ct.
Weldon Spring, MO 63304

(636) 329-0300
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