Installing RDKit

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I have installed Spyder3.2.1 in the current version of Miniconda3 on my Debian v-9.1.0 64 bit Linux platform. Spyder is performing well, but I am having difficulty installing the RDKit.

I followed the directions in the RDKit_Docs_current.pdf:

How to install RDKit with Conda

Creating a new conda environment with the RDKit installed using these packages requires one single command similar to the following:

$ conda create -c rdkit -n my-rdkit-env rdkit

Finally, the new environment must be activated, so that the corresponding python interpreter becomes available in the same shell:

$ source activate my-rdkit-env

There were no warning or error messages during the installation, but when I attempt running a simple Python script:

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 15 11:41:24 2017

@author: comp
"""

from __future__ import print_function
from rdkit import Chem

m = Chem.MolFromSmiles('Cc1ccccc1')
m

I get:

IPython 6.1.0 -- An enhanced Interactive Python.

runfile('/home/comp/Apps/Python/untitled0.py', 
wdir='/home/comp/Apps/Python')
Traceback (most recent call last):

File "<ipython-input-1-3842c59475d8>", line 1, in <module>
runfile('/home/comp/Apps/Python/untitled0.py', 
wdir='/home/comp/Apps/Python')

File "/home/comp/Apps/miniconda3/lib/python3.6/site-
packages/spyder/utils/site/sitecustomize.py", line 688, in runfile
execfile(filename, namespace)

File "/home/comp/Apps/miniconda3/lib/python3.6/site-
packages/spyder/utils/site/sitecustomize.py", line 101, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)

File "/home/comp/Apps/Python/untitled0.py", line 10, in <module>
from rdkit import Chem

ModuleNotFoundError: No module named 'rdkit'

RDKit is installed in ~/miniconda3/envs/mr-rdkit-env

Unfortunately, I have no clue as to what the problem(s) may be, assistance will be much appreciated.

Thanks in advance.

2 Answers

switch your currrent python edition to python2.7,you can create a enviroment:conda create -n my_env_name python=2.7

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