Hi Jon,
I can reproduce this problem locally, which is a bit strange since the
tests passed before I uploaded the 2018.03.1 build. I will take a look and
see if I can figure out what's going on.
In the meantime, it may work to try installing the rdkit from the
conda-forge channel:
"conda install -c conda-forge rdkit"
The conda-forge builds are quite useful, but they do introduce a different
set of dependencies and may not work for you.
-greg
On Sun, Jul 22, 2018 at 10:26 PM <[email protected]> wrote:
> 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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